Starting phenix.real_space_refine on Fri Sep 11 13:49:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8g6r_29779/09_2026/8g6r_29779.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g6r_29779/09_2026/8g6r_29779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g6r_29779/09_2026/8g6r_29779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g6r_29779/09_2026/8g6r_29779.map" model { file = "/net/cci-nas-00/data/ceres_data/8g6r_29779/09_2026/8g6r_29779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g6r_29779/09_2026/8g6r_29779.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8g6r_29779/09_2026/8g6r_29779.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8g6r_29779/09_2026/8g6r_29779.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 40 5.49 5 S 71 5.16 5 C 5846 2.51 5 N 1565 2.21 5 O 1882 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9406 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7198 Classifications: {'peptide': 899} Link IDs: {'PTRANS': 25, 'TRANS': 873} Chain breaks: 2 Chain: "B" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 878 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "C" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 477 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 1, 'TRANS': 60} Chain: "I" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 428 Classifications: {'RNAv2': 20} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 12, 'rna3p_pyr': 7} Link IDs: {'rna3p': 19} Chain: "J" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 423 Classifications: {'RNAv2': 20} Modifications used: {'rna3p_pur': 9, 'rna3p_pyr': 11} Link IDs: {'rna3p': 19} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2370 SG CYS A 296 27.578 61.099 83.170 1.00104.05 S ATOM 2408 SG CYS A 301 28.842 64.368 84.713 1.00 97.50 S ATOM 2439 SG CYS A 305 30.494 60.986 85.568 1.00 91.72 S ATOM 3802 SG CYS A 482 18.288 63.589 63.785 1.00111.18 S ATOM 5042 SG CYS A 640 18.703 66.880 65.627 1.00110.13 S ATOM 5048 SG CYS A 641 17.625 63.682 67.468 1.00111.44 S Time building chain proxies: 2.07, per 1000 atoms: 0.22 Number of scatterers: 9406 At special positions: 0 Unit cell: (91.74, 97.578, 124.266, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 71 16.00 P 40 15.00 O 1882 8.00 N 1565 7.00 C 5846 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: 0.95 Conformation dependent library (CDL) restraints added in 328.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 290 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 305 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 296 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 637 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 641 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 482 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 640 " Number of angles added : 6 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2030 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 11 sheets defined 54.7% alpha, 11.5% beta 14 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 3 through 15 removed outlier: 3.889A pdb=" N ARG A 9 " --> pdb=" O ALA A 5 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL A 10 " --> pdb=" O TYR A 6 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER A 13 " --> pdb=" O ARG A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'A' and resid 73 through 86 removed outlier: 4.509A pdb=" N LYS A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 126 Processing helix chain 'A' and resid 133 through 143 Processing helix chain 'A' and resid 147 through 153 removed outlier: 3.812A pdb=" N ASN A 153 " --> pdb=" O TYR A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 194 removed outlier: 4.097A pdb=" N ARG A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU A 172 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 228 through 242 removed outlier: 3.760A pdb=" N MET A 235 " --> pdb=" O TYR A 231 " (cutoff:3.500A) Proline residue: A 237 - end of helix Processing helix chain 'A' and resid 245 through 249 Processing helix chain 'A' and resid 262 through 267 Processing helix chain 'A' and resid 270 through 282 Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 298 through 314 removed outlier: 4.074A pdb=" N THR A 314 " --> pdb=" O THR A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 372 removed outlier: 4.707A pdb=" N GLN A 368 " --> pdb=" O ASN A 364 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N CYS A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 379 removed outlier: 4.342A pdb=" N LEU A 376 " --> pdb=" O ASP A 372 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER A 379 " --> pdb=" O LEU A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 422 Processing helix chain 'A' and resid 442 through 449 removed outlier: 3.721A pdb=" N LYS A 446 " --> pdb=" O ASP A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 454 Processing helix chain 'A' and resid 460 through 474 removed outlier: 4.170A pdb=" N VAL A 466 " --> pdb=" O CYS A 462 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL A 467 " --> pdb=" O GLN A 463 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR A 474 " --> pdb=" O ILE A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 488 Processing helix chain 'A' and resid 498 through 503 removed outlier: 4.529A pdb=" N LYS A 503 " --> pdb=" O TYR A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 514 removed outlier: 3.996A pdb=" N TYR A 510 " --> pdb=" O LYS A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 527 Processing helix chain 'A' and resid 556 through 577 removed outlier: 3.684A pdb=" N THR A 560 " --> pdb=" O SER A 556 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LYS A 569 " --> pdb=" O GLN A 565 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N HIS A 570 " --> pdb=" O TYR A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 616 through 621 Processing helix chain 'A' and resid 624 through 635 Processing helix chain 'A' and resid 642 through 658 Processing helix chain 'A' and resid 681 through 704 removed outlier: 3.621A pdb=" N ASN A 698 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER A 704 " --> pdb=" O ASN A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 710 removed outlier: 5.805A pdb=" N ASN A 708 " --> pdb=" O VAL A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 727 Processing helix chain 'A' and resid 733 through 747 Processing helix chain 'A' and resid 763 through 768 Processing helix chain 'A' and resid 773 through 784 Processing helix chain 'A' and resid 799 through 803 Processing helix chain 'A' and resid 828 through 837 Processing helix chain 'A' and resid 847 through 862 Processing helix chain 'A' and resid 863 through 867 Processing helix chain 'A' and resid 869 through 890 removed outlier: 3.578A pdb=" N VAL A 875 " --> pdb=" O GLU A 871 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE A 876 " --> pdb=" O TYR A 872 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR A 877 " --> pdb=" O LYS A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 912 Processing helix chain 'A' and resid 912 through 920 removed outlier: 4.280A pdb=" N TYR A 916 " --> pdb=" O ASP A 912 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET A 919 " --> pdb=" O PHE A 915 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR A 920 " --> pdb=" O TYR A 916 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 97 Processing helix chain 'B' and resid 99 through 108 removed outlier: 3.610A pdb=" N VAL B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 112 removed outlier: 5.825A pdb=" N ASP B 112 " --> pdb=" O LEU B 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 109 through 112' Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 134 through 142 Processing helix chain 'B' and resid 168 through 174 removed outlier: 3.697A pdb=" N VAL B 172 " --> pdb=" O HIS B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 180 Processing helix chain 'C' and resid 3 through 20 removed outlier: 4.052A pdb=" N VAL C 11 " --> pdb=" O LYS C 7 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL C 12 " --> pdb=" O CYS C 8 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C 13 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET C 20 " --> pdb=" O CYS C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 24 Processing helix chain 'C' and resid 25 through 42 removed outlier: 3.553A pdb=" N TRP C 29 " --> pdb=" O ASN C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 63 removed outlier: 3.597A pdb=" N ALA C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS C 62 " --> pdb=" O PHE C 58 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 20 removed outlier: 4.838A pdb=" N PHE A 63 " --> pdb=" O ASP A 112 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 32 removed outlier: 4.647A pdb=" N VAL A 29 " --> pdb=" O LYS A 48 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS A 48 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA4, first strand: chain 'A' and resid 197 through 198 removed outlier: 6.757A pdb=" N GLY A 197 " --> pdb=" O ILE A 227 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 347 through 350 removed outlier: 6.762A pdb=" N LEU A 324 " --> pdb=" O ALA A 339 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N TYR A 341 " --> pdb=" O GLY A 322 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLY A 322 " --> pdb=" O TYR A 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 382 through 385 removed outlier: 6.205A pdb=" N ALA A 382 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N VAL B 131 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL A 384 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ILE B 156 " --> pdb=" O GLU B 189 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 392 through 395 removed outlier: 6.200A pdb=" N SER A 392 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU A 670 " --> pdb=" O SER A 392 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ALA A 394 " --> pdb=" O PHE A 668 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 409 through 410 Processing sheet with id=AA9, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AB1, first strand: chain 'A' and resid 748 through 753 removed outlier: 3.628A pdb=" N SER A 749 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TRP A 795 " --> pdb=" O GLY A 611 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 811 through 817 removed outlier: 3.674A pdb=" N HIS A 811 " --> pdb=" O TYR A 826 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR A 826 " --> pdb=" O HIS A 811 " (cutoff:3.500A) 413 hydrogen bonds defined for protein. 1131 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 64 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 2.09 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2799 1.33 - 1.45: 1852 1.45 - 1.57: 4865 1.57 - 1.69: 78 1.69 - 1.81: 100 Bond restraints: 9694 Sorted by residual: bond pdb=" N ASP A 3 " pdb=" CA ASP A 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N LYS C 2 " pdb=" CA LYS C 2 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.81e+00 bond pdb=" N ARG B 79 " pdb=" CA ARG B 79 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.78e+00 bond pdb=" CB CYS A 651 " pdb=" SG CYS A 651 " ideal model delta sigma weight residual 1.808 1.771 0.037 3.30e-02 9.18e+02 1.28e+00 bond pdb=" CB ASN A 698 " pdb=" CG ASN A 698 " ideal model delta sigma weight residual 1.516 1.488 0.028 2.50e-02 1.60e+03 1.22e+00 ... (remaining 9689 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 12772 1.23 - 2.45: 397 2.45 - 3.68: 130 3.68 - 4.91: 17 4.91 - 6.14: 3 Bond angle restraints: 13319 Sorted by residual: angle pdb=" C TYR A 782 " pdb=" N TYR A 783 " pdb=" CA TYR A 783 " ideal model delta sigma weight residual 122.38 117.34 5.04 1.81e+00 3.05e-01 7.75e+00 angle pdb=" C3' A I 33 " pdb=" C2' A I 33 " pdb=" O2' A I 33 " ideal model delta sigma weight residual 109.80 114.50 -4.70 2.00e+00 2.50e-01 5.52e+00 angle pdb=" O3' A I 33 " pdb=" C3' A I 33 " pdb=" C2' A I 33 " ideal model delta sigma weight residual 113.80 109.89 3.91 2.00e+00 2.50e-01 3.81e+00 angle pdb=" O2' A I 33 " pdb=" C2' A I 33 " pdb=" C1' A I 33 " ideal model delta sigma weight residual 108.20 111.99 -3.79 2.00e+00 2.50e-01 3.60e+00 angle pdb=" C GLU C 50 " pdb=" N MET C 51 " pdb=" CA MET C 51 " ideal model delta sigma weight residual 120.28 117.75 2.53 1.34e+00 5.57e-01 3.57e+00 ... (remaining 13314 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 5171 17.55 - 35.11: 371 35.11 - 52.66: 88 52.66 - 70.21: 20 70.21 - 87.77: 10 Dihedral angle restraints: 5660 sinusoidal: 2497 harmonic: 3163 Sorted by residual: dihedral pdb=" C4' A I 33 " pdb=" C3' A I 33 " pdb=" C2' A I 33 " pdb=" C1' A I 33 " ideal model delta sinusoidal sigma weight residual 36.35 -36.27 72.61 1 3.10e+00 1.04e-01 7.00e+02 dihedral pdb=" O4' A I 33 " pdb=" C4' A I 33 " pdb=" C3' A I 33 " pdb=" C2' A I 33 " ideal model delta sinusoidal sigma weight residual -35.15 25.07 -60.22 1 4.00e+00 6.25e-02 3.02e+02 dihedral pdb=" O4' A I 33 " pdb=" C2' A I 33 " pdb=" C1' A I 33 " pdb=" C3' A I 33 " ideal model delta sinusoidal sigma weight residual -94.41 -35.85 -58.56 3 3.80e+00 6.93e-02 1.48e+02 ... (remaining 5657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1272 0.056 - 0.113: 193 0.113 - 0.169: 9 0.169 - 0.226: 13 0.226 - 0.282: 29 Chirality restraints: 1516 Sorted by residual: chirality pdb=" C2' A I 33 " pdb=" C3' A I 33 " pdb=" O2' A I 33 " pdb=" C1' A I 33 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" P U J 27 " pdb=" OP1 U J 27 " pdb=" OP2 U J 27 " pdb=" O5' U J 27 " both_signs ideal model delta sigma weight residual True 2.17 -2.42 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" P G J 28 " pdb=" OP1 G J 28 " pdb=" OP2 G J 28 " pdb=" O5' G J 28 " both_signs ideal model delta sigma weight residual True 2.17 -2.42 -0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 1513 not shown) Planarity restraints: 1545 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 531 " -0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO A 532 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 532 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 532 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 380 " -0.025 5.00e-02 4.00e+02 3.73e-02 2.22e+00 pdb=" N PRO A 381 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 381 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 381 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 158 " 0.024 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO A 159 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 159 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 159 " 0.020 5.00e-02 4.00e+02 ... (remaining 1542 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 102 2.51 - 3.11: 8157 3.11 - 3.71: 14949 3.71 - 4.30: 21408 4.30 - 4.90: 33968 Nonbonded interactions: 78584 Sorted by model distance: nonbonded pdb=" OG SER A 809 " pdb=" OP1 A I 33 " model vdw 1.919 3.040 nonbonded pdb=" OG1 THR A 533 " pdb=" OE1 GLN A 656 " model vdw 1.967 3.040 nonbonded pdb=" OD1 ASP A 618 " pdb=" OG1 THR A 675 " model vdw 1.981 3.040 nonbonded pdb=" O LEU A 509 " pdb=" OG SER A 513 " model vdw 1.984 3.040 nonbonded pdb=" OH TYR A 289 " pdb=" OD1 ASN A 309 " model vdw 2.052 3.040 ... (remaining 78579 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.830 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 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 : 0.005 0.042 9702 Z= 0.229 Angle : 0.571 6.136 13325 Z= 0.301 Chirality : 0.054 0.282 1516 Planarity : 0.003 0.041 1545 Dihedral : 13.500 87.768 3630 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.26), residues: 1065 helix: 0.50 (0.24), residues: 478 sheet: -1.14 (0.46), residues: 116 loop : -0.45 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 548 TYR 0.016 0.002 TYR A 234 PHE 0.013 0.001 PHE A 648 TRP 0.018 0.001 TRP A 911 HIS 0.010 0.001 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.23 ( 9694) covalent geometry : angle 0.56915 / 0.30 (13319) hydrogen bonds : bond 0.21461 / 14.82 ( 445) hydrogen bonds : angle 8.31244 / 5.87 ( 1195) metal coordination : bond 0.01920 / 0.89 ( 8) metal coordination : angle 2.00026 / 1.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 GLU cc_start: 0.7563 (mp0) cc_final: 0.7355 (mp0) REVERT: A 547 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7725 (mp0) REVERT: A 660 GLU cc_start: 0.7104 (pm20) cc_final: 0.6883 (pm20) REVERT: A 698 ASN cc_start: 0.8392 (m110) cc_final: 0.8160 (m110) REVERT: B 137 SER cc_start: 0.9516 (m) cc_final: 0.8964 (p) REVERT: B 159 ILE cc_start: 0.9303 (mp) cc_final: 0.9056 (mt) REVERT: B 160 LYS cc_start: 0.8629 (mmmt) cc_final: 0.8334 (mmmt) REVERT: C 8 CYS cc_start: 0.8537 (p) cc_final: 0.8191 (p) REVERT: C 37 ASN cc_start: 0.9373 (m-40) cc_final: 0.8932 (m-40) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.0842 time to fit residues: 21.3930 Evaluate side-chains 147 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 chunk 106 optimal weight: 20.0000 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 345 GLN A 403 GLN A 421 GLN A 454 ASN A 568 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.106758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.071632 restraints weight = 23160.556| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 3.53 r_work: 0.3044 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 9702 Z= 0.268 Angle : 0.703 10.753 13325 Z= 0.352 Chirality : 0.047 0.201 1516 Planarity : 0.004 0.040 1545 Dihedral : 9.203 69.171 1645 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.64 % Allowed : 9.18 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.26), residues: 1065 helix: 0.66 (0.23), residues: 499 sheet: -0.94 (0.50), residues: 110 loop : -0.06 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 167 TYR 0.029 0.002 TYR A 783 PHE 0.013 0.002 PHE A 736 TRP 0.019 0.002 TRP B 154 HIS 0.005 0.001 HIS A 811 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.27 ( 9694) covalent geometry : angle 0.70195 / 0.35 (13319) hydrogen bonds : bond 0.04892 / 3.40 ( 445) hydrogen bonds : angle 5.39963 / 3.78 ( 1195) metal coordination : bond 0.03082 / 1.37 ( 8) metal coordination : angle 1.82279 / 1.43 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 TRP cc_start: 0.6811 (t-100) cc_final: 0.6579 (t-100) REVERT: A 248 GLU cc_start: 0.9177 (mm-30) cc_final: 0.8733 (mp0) REVERT: A 403 GLN cc_start: 0.8666 (tt0) cc_final: 0.7963 (pm20) REVERT: A 419 LEU cc_start: 0.9286 (mm) cc_final: 0.8965 (mt) REVERT: A 534 MET cc_start: 0.8909 (mpp) cc_final: 0.8641 (mpp) REVERT: A 614 TYR cc_start: 0.9134 (m-10) cc_final: 0.8775 (m-10) REVERT: A 660 GLU cc_start: 0.8010 (pm20) cc_final: 0.7647 (pm20) REVERT: A 887 TYR cc_start: 0.9245 (t80) cc_final: 0.8618 (t80) REVERT: A 912 ASP cc_start: 0.8836 (t0) cc_final: 0.8322 (p0) REVERT: B 137 SER cc_start: 0.9685 (m) cc_final: 0.9317 (p) REVERT: B 159 ILE cc_start: 0.9252 (mp) cc_final: 0.8842 (mp) REVERT: B 160 LYS cc_start: 0.8920 (mmmt) cc_final: 0.8587 (mmmt) REVERT: B 189 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8442 (tm-30) REVERT: C 8 CYS cc_start: 0.8871 (p) cc_final: 0.8532 (p) REVERT: C 20 MET cc_start: 0.8430 (mtm) cc_final: 0.8208 (ptt) REVERT: C 35 LEU cc_start: 0.9208 (tp) cc_final: 0.8961 (tp) REVERT: C 38 LYS cc_start: 0.8679 (ptmm) cc_final: 0.8289 (ptmm) REVERT: C 51 MET cc_start: 0.9496 (mpp) cc_final: 0.9087 (mpp) outliers start: 25 outliers final: 15 residues processed: 172 average time/residue: 0.0794 time to fit residues: 19.8836 Evaluate side-chains 164 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 26 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 106 optimal weight: 20.0000 chunk 25 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 99 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 345 GLN A 364 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.109497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.074702 restraints weight = 22885.510| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 3.56 r_work: 0.3078 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9702 Z= 0.162 Angle : 0.624 9.536 13325 Z= 0.306 Chirality : 0.045 0.207 1516 Planarity : 0.004 0.037 1545 Dihedral : 8.959 69.269 1645 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.85 % Allowed : 12.55 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.26), residues: 1065 helix: 0.89 (0.24), residues: 495 sheet: -0.76 (0.52), residues: 108 loop : 0.02 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 548 TYR 0.025 0.002 TYR A 211 PHE 0.015 0.001 PHE C 58 TRP 0.023 0.002 TRP B 182 HIS 0.004 0.001 HIS B 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 9694) covalent geometry : angle 0.62300 / 0.31 (13319) hydrogen bonds : bond 0.04093 / 2.83 ( 445) hydrogen bonds : angle 4.81647 / 3.38 ( 1195) metal coordination : bond 0.01818 / 0.82 ( 8) metal coordination : angle 1.53000 / 1.15 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 TRP cc_start: 0.7035 (t-100) cc_final: 0.6782 (t-100) REVERT: A 119 MET cc_start: 0.9124 (OUTLIER) cc_final: 0.8882 (tpt) REVERT: A 223 MET cc_start: 0.9184 (mmm) cc_final: 0.8772 (ptp) REVERT: A 248 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8696 (mp0) REVERT: A 267 GLU cc_start: 0.8294 (mp0) cc_final: 0.8090 (mp0) REVERT: A 415 TYR cc_start: 0.8413 (t80) cc_final: 0.8170 (t80) REVERT: A 419 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8947 (mm) REVERT: A 614 TYR cc_start: 0.9060 (m-10) cc_final: 0.8805 (m-10) REVERT: A 627 MET cc_start: 0.9010 (ttp) cc_final: 0.8778 (ttp) REVERT: A 660 GLU cc_start: 0.8062 (pm20) cc_final: 0.7646 (pm20) REVERT: A 887 TYR cc_start: 0.9360 (t80) cc_final: 0.9151 (t80) REVERT: A 919 MET cc_start: 0.9060 (mmt) cc_final: 0.8688 (mmt) REVERT: B 91 LEU cc_start: 0.7279 (OUTLIER) cc_final: 0.7038 (tt) REVERT: B 140 ARG cc_start: 0.9036 (mtm-85) cc_final: 0.8716 (mtm-85) REVERT: B 158 ASP cc_start: 0.9022 (t0) cc_final: 0.8767 (t0) REVERT: B 159 ILE cc_start: 0.9255 (mp) cc_final: 0.8816 (mp) REVERT: B 160 LYS cc_start: 0.8977 (mmmt) cc_final: 0.8664 (mmmt) REVERT: B 165 LYS cc_start: 0.9405 (ptmm) cc_final: 0.8982 (ptmm) REVERT: B 170 LYS cc_start: 0.9318 (pptt) cc_final: 0.9112 (pptt) REVERT: C 20 MET cc_start: 0.8475 (mtm) cc_final: 0.8079 (ptt) REVERT: C 35 LEU cc_start: 0.9247 (tp) cc_final: 0.9006 (tp) REVERT: C 38 LYS cc_start: 0.8729 (ptmm) cc_final: 0.8379 (ptmm) REVERT: C 46 GLU cc_start: 0.9178 (pm20) cc_final: 0.8972 (pm20) REVERT: C 51 MET cc_start: 0.9511 (mpp) cc_final: 0.9180 (mpp) outliers start: 27 outliers final: 20 residues processed: 172 average time/residue: 0.0873 time to fit residues: 21.8785 Evaluate side-chains 173 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 777 PHE Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 26 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 79 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 106 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 345 GLN ** B 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.106923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.072681 restraints weight = 22600.353| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 3.54 r_work: 0.2997 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 9702 Z= 0.206 Angle : 0.656 14.146 13325 Z= 0.315 Chirality : 0.045 0.235 1516 Planarity : 0.004 0.039 1545 Dihedral : 8.897 68.291 1645 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.69 % Allowed : 13.40 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.26), residues: 1065 helix: 0.88 (0.24), residues: 496 sheet: -0.61 (0.54), residues: 98 loop : -0.01 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 548 TYR 0.026 0.002 TYR A 211 PHE 0.013 0.001 PHE A 736 TRP 0.028 0.002 TRP B 182 HIS 0.004 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.21 ( 9694) covalent geometry : angle 0.65553 / 0.31 (13319) hydrogen bonds : bond 0.04017 / 2.78 ( 445) hydrogen bonds : angle 4.78678 / 3.36 ( 1195) metal coordination : bond 0.02309 / 1.01 ( 8) metal coordination : angle 1.55852 / 1.22 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 155 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 GLU cc_start: 0.9123 (mm-30) cc_final: 0.8689 (mp0) REVERT: A 267 GLU cc_start: 0.8314 (mp0) cc_final: 0.8033 (mp0) REVERT: A 403 GLN cc_start: 0.8741 (tt0) cc_final: 0.7954 (pm20) REVERT: A 415 TYR cc_start: 0.8566 (t80) cc_final: 0.8366 (t80) REVERT: A 419 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8930 (mm) REVERT: A 534 MET cc_start: 0.8808 (mpp) cc_final: 0.8504 (mpp) REVERT: A 614 TYR cc_start: 0.9084 (m-10) cc_final: 0.8846 (m-10) REVERT: A 660 GLU cc_start: 0.8052 (pm20) cc_final: 0.7611 (pm20) REVERT: A 887 TYR cc_start: 0.9398 (t80) cc_final: 0.9055 (t80) REVERT: A 919 MET cc_start: 0.8985 (mmt) cc_final: 0.8642 (mmt) REVERT: B 140 ARG cc_start: 0.9036 (mtm-85) cc_final: 0.8673 (mtm-85) REVERT: B 158 ASP cc_start: 0.9004 (t0) cc_final: 0.8485 (t0) REVERT: B 159 ILE cc_start: 0.9212 (mp) cc_final: 0.8575 (mp) REVERT: B 160 LYS cc_start: 0.8951 (mmmt) cc_final: 0.8583 (mmmt) REVERT: B 165 LYS cc_start: 0.9398 (ptmm) cc_final: 0.9029 (ptmm) REVERT: B 170 LYS cc_start: 0.9343 (pptt) cc_final: 0.9137 (pptt) REVERT: C 8 CYS cc_start: 0.8837 (p) cc_final: 0.8541 (p) REVERT: C 35 LEU cc_start: 0.9289 (tp) cc_final: 0.9031 (tp) REVERT: C 38 LYS cc_start: 0.8666 (ptmm) cc_final: 0.8318 (ptmm) REVERT: C 51 MET cc_start: 0.9544 (OUTLIER) cc_final: 0.9182 (mpp) outliers start: 35 outliers final: 26 residues processed: 171 average time/residue: 0.0815 time to fit residues: 20.1530 Evaluate side-chains 176 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 777 PHE Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain A residue 911 TRP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain C residue 2 LYS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 51 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 38 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 109 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 148 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.108333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.074475 restraints weight = 22522.541| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 3.54 r_work: 0.3027 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9702 Z= 0.155 Angle : 0.641 14.967 13325 Z= 0.302 Chirality : 0.044 0.236 1516 Planarity : 0.004 0.039 1545 Dihedral : 8.783 66.925 1645 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.59 % Allowed : 14.98 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.27), residues: 1065 helix: 0.90 (0.24), residues: 503 sheet: -0.62 (0.53), residues: 106 loop : 0.09 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 548 TYR 0.026 0.001 TYR A 211 PHE 0.012 0.001 PHE A 736 TRP 0.031 0.002 TRP B 182 HIS 0.003 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 9694) covalent geometry : angle 0.64066 / 0.30 (13319) hydrogen bonds : bond 0.03642 / 2.51 ( 445) hydrogen bonds : angle 4.56685 / 3.23 ( 1195) metal coordination : bond 0.01697 / 0.74 ( 8) metal coordination : angle 1.49141 / 1.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 162 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.9181 (mmm) cc_final: 0.8944 (mmp) REVERT: A 248 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8681 (mp0) REVERT: A 267 GLU cc_start: 0.8350 (mp0) cc_final: 0.8002 (mp0) REVERT: A 403 GLN cc_start: 0.8678 (tt0) cc_final: 0.7933 (pm20) REVERT: A 415 TYR cc_start: 0.8439 (t80) cc_final: 0.8237 (t80) REVERT: A 419 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8937 (mm) REVERT: A 660 GLU cc_start: 0.8049 (pm20) cc_final: 0.7641 (pm20) REVERT: A 887 TYR cc_start: 0.9370 (t80) cc_final: 0.8973 (t80) REVERT: A 919 MET cc_start: 0.8932 (mmt) cc_final: 0.8589 (mmt) REVERT: B 158 ASP cc_start: 0.9018 (t0) cc_final: 0.8577 (t0) REVERT: B 159 ILE cc_start: 0.9173 (mp) cc_final: 0.8533 (mp) REVERT: B 160 LYS cc_start: 0.8950 (mmmt) cc_final: 0.8558 (mmmt) REVERT: B 165 LYS cc_start: 0.9396 (ptmm) cc_final: 0.9035 (ptmm) REVERT: C 8 CYS cc_start: 0.8821 (p) cc_final: 0.8486 (p) REVERT: C 35 LEU cc_start: 0.9294 (tp) cc_final: 0.9030 (tp) REVERT: C 38 LYS cc_start: 0.8639 (ptmm) cc_final: 0.8293 (ptmm) REVERT: C 51 MET cc_start: 0.9553 (OUTLIER) cc_final: 0.9224 (mpp) outliers start: 34 outliers final: 25 residues processed: 179 average time/residue: 0.0763 time to fit residues: 20.1926 Evaluate side-chains 179 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 777 PHE Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain A residue 911 TRP Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 51 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 67 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 chunk 32 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 7.9990 chunk 23 optimal weight: 0.6980 chunk 1 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 168 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.110149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.076247 restraints weight = 22484.208| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.59 r_work: 0.3072 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9702 Z= 0.113 Angle : 0.617 12.677 13325 Z= 0.290 Chirality : 0.043 0.227 1516 Planarity : 0.003 0.034 1545 Dihedral : 8.678 65.132 1645 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.74 % Allowed : 16.24 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.27), residues: 1065 helix: 0.97 (0.24), residues: 508 sheet: -0.59 (0.55), residues: 94 loop : 0.11 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 548 TYR 0.023 0.001 TYR A 211 PHE 0.014 0.001 PHE A 689 TRP 0.034 0.002 TRP B 182 HIS 0.002 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 9694) covalent geometry : angle 0.61644 / 0.29 (13319) hydrogen bonds : bond 0.03300 / 2.25 ( 445) hydrogen bonds : angle 4.34708 / 3.09 ( 1195) metal coordination : bond 0.00951 / 0.42 ( 8) metal coordination : angle 1.39774 / 0.93 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.8956 (tpt) cc_final: 0.8243 (tpp) REVERT: A 223 MET cc_start: 0.9119 (mmp) cc_final: 0.8897 (mpp) REVERT: A 248 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8636 (mp0) REVERT: A 263 TYR cc_start: 0.7800 (p90) cc_final: 0.7568 (p90) REVERT: A 267 GLU cc_start: 0.8383 (mp0) cc_final: 0.8015 (mp0) REVERT: A 419 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.8968 (mt) REVERT: A 450 TYR cc_start: 0.8904 (m-80) cc_final: 0.8559 (m-80) REVERT: A 660 GLU cc_start: 0.8032 (pm20) cc_final: 0.7664 (pm20) REVERT: A 887 TYR cc_start: 0.9336 (t80) cc_final: 0.8960 (t80) REVERT: A 888 LYS cc_start: 0.9431 (mttt) cc_final: 0.9228 (mtpp) REVERT: A 912 ASP cc_start: 0.8746 (t0) cc_final: 0.8395 (p0) REVERT: A 919 MET cc_start: 0.8842 (mmt) cc_final: 0.8547 (mmt) REVERT: B 140 ARG cc_start: 0.9138 (mtm-85) cc_final: 0.8896 (mtm-85) REVERT: B 158 ASP cc_start: 0.9024 (t0) cc_final: 0.8632 (t0) REVERT: B 159 ILE cc_start: 0.9137 (mp) cc_final: 0.8630 (mp) REVERT: B 160 LYS cc_start: 0.8989 (mmmt) cc_final: 0.8589 (mmmt) REVERT: B 165 LYS cc_start: 0.9446 (ptmm) cc_final: 0.9138 (ptmm) REVERT: B 171 GLU cc_start: 0.8959 (mp0) cc_final: 0.8634 (pm20) REVERT: C 8 CYS cc_start: 0.8744 (p) cc_final: 0.8386 (p) REVERT: C 35 LEU cc_start: 0.9295 (tp) cc_final: 0.9074 (tp) REVERT: C 38 LYS cc_start: 0.8636 (ptmm) cc_final: 0.8337 (ptmm) REVERT: C 51 MET cc_start: 0.9541 (OUTLIER) cc_final: 0.9285 (mpp) outliers start: 26 outliers final: 18 residues processed: 180 average time/residue: 0.0824 time to fit residues: 21.5536 Evaluate side-chains 172 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 777 PHE Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 911 TRP Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 51 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 105 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 65 optimal weight: 0.0570 chunk 49 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 overall best weight: 1.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 148 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.110529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.075489 restraints weight = 23140.777| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 3.59 r_work: 0.3106 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9702 Z= 0.170 Angle : 0.664 17.147 13325 Z= 0.312 Chirality : 0.044 0.267 1516 Planarity : 0.004 0.037 1545 Dihedral : 8.700 64.309 1645 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.38 % Allowed : 17.09 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.27), residues: 1065 helix: 0.98 (0.24), residues: 508 sheet: -0.56 (0.53), residues: 106 loop : 0.17 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 548 TYR 0.031 0.002 TYR A 415 PHE 0.012 0.001 PHE A 748 TRP 0.040 0.002 TRP B 182 HIS 0.003 0.001 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 ( 9694) covalent geometry : angle 0.66310 / 0.31 (13319) hydrogen bonds : bond 0.03573 / 2.45 ( 445) hydrogen bonds : angle 4.50525 / 3.22 ( 1195) metal coordination : bond 0.01815 / 0.78 ( 8) metal coordination : angle 1.55633 / 1.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.9139 (mmm) cc_final: 0.8931 (mmm) REVERT: A 115 GLU cc_start: 0.9066 (tt0) cc_final: 0.8741 (tp30) REVERT: A 248 GLU cc_start: 0.9090 (mm-30) cc_final: 0.8764 (mp0) REVERT: A 263 TYR cc_start: 0.7875 (p90) cc_final: 0.7637 (p90) REVERT: A 267 GLU cc_start: 0.8414 (mp0) cc_final: 0.8049 (mp0) REVERT: A 415 TYR cc_start: 0.8644 (t80) cc_final: 0.8434 (t80) REVERT: A 419 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9047 (mm) REVERT: A 660 GLU cc_start: 0.8011 (pm20) cc_final: 0.7681 (pm20) REVERT: A 887 TYR cc_start: 0.9298 (t80) cc_final: 0.8177 (t80) REVERT: A 888 LYS cc_start: 0.9413 (mttt) cc_final: 0.9165 (mtmm) REVERT: A 911 TRP cc_start: 0.7813 (OUTLIER) cc_final: 0.7478 (m-90) REVERT: A 912 ASP cc_start: 0.8733 (t0) cc_final: 0.8445 (p0) REVERT: A 919 MET cc_start: 0.9008 (mmt) cc_final: 0.8675 (mmt) REVERT: B 131 VAL cc_start: 0.9623 (t) cc_final: 0.9384 (p) REVERT: B 158 ASP cc_start: 0.9022 (t0) cc_final: 0.8541 (t0) REVERT: B 159 ILE cc_start: 0.9162 (mp) cc_final: 0.8532 (mp) REVERT: B 160 LYS cc_start: 0.9060 (mmmt) cc_final: 0.8658 (mmmt) REVERT: B 165 LYS cc_start: 0.9432 (ptmm) cc_final: 0.9149 (ptmm) REVERT: B 171 GLU cc_start: 0.9032 (mp0) cc_final: 0.8754 (pm20) REVERT: C 8 CYS cc_start: 0.8885 (p) cc_final: 0.8486 (p) REVERT: C 35 LEU cc_start: 0.9301 (tp) cc_final: 0.9006 (tp) REVERT: C 38 LYS cc_start: 0.8683 (ptmm) cc_final: 0.8318 (ptmm) REVERT: C 46 GLU cc_start: 0.9126 (pm20) cc_final: 0.8749 (pm20) REVERT: C 51 MET cc_start: 0.9531 (OUTLIER) cc_final: 0.9199 (mpp) outliers start: 32 outliers final: 25 residues processed: 168 average time/residue: 0.0836 time to fit residues: 20.5103 Evaluate side-chains 178 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 911 TRP Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 51 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 42 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 chunk 108 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 148 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.110552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.075342 restraints weight = 22992.185| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 3.59 r_work: 0.3098 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9702 Z= 0.166 Angle : 0.672 16.839 13325 Z= 0.312 Chirality : 0.044 0.311 1516 Planarity : 0.004 0.034 1545 Dihedral : 8.721 64.425 1645 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.48 % Allowed : 17.51 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.27), residues: 1065 helix: 0.97 (0.24), residues: 513 sheet: -0.50 (0.53), residues: 106 loop : 0.12 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 548 TYR 0.029 0.001 TYR A 415 PHE 0.012 0.001 PHE A 748 TRP 0.042 0.002 TRP B 182 HIS 0.003 0.001 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 ( 9694) covalent geometry : angle 0.67101 / 0.31 (13319) hydrogen bonds : bond 0.03553 / 2.44 ( 445) hydrogen bonds : angle 4.50913 / 3.22 ( 1195) metal coordination : bond 0.01799 / 0.77 ( 8) metal coordination : angle 1.47888 / 1.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.9190 (mmm) cc_final: 0.8968 (mmm) REVERT: A 115 GLU cc_start: 0.9142 (tt0) cc_final: 0.8665 (tp30) REVERT: A 248 GLU cc_start: 0.9082 (mm-30) cc_final: 0.8741 (mp0) REVERT: A 263 TYR cc_start: 0.7866 (p90) cc_final: 0.7618 (p90) REVERT: A 267 GLU cc_start: 0.8436 (mp0) cc_final: 0.8058 (mp0) REVERT: A 415 TYR cc_start: 0.8633 (t80) cc_final: 0.8371 (t80) REVERT: A 419 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9040 (mm) REVERT: A 660 GLU cc_start: 0.7999 (pm20) cc_final: 0.7672 (pm20) REVERT: A 887 TYR cc_start: 0.9312 (t80) cc_final: 0.8219 (t80) REVERT: A 888 LYS cc_start: 0.9420 (mttt) cc_final: 0.9168 (mtmm) REVERT: A 911 TRP cc_start: 0.7832 (OUTLIER) cc_final: 0.7495 (m-90) REVERT: A 912 ASP cc_start: 0.8714 (t0) cc_final: 0.8458 (p0) REVERT: A 919 MET cc_start: 0.9000 (mmt) cc_final: 0.8650 (mmt) REVERT: B 131 VAL cc_start: 0.9625 (t) cc_final: 0.9360 (p) REVERT: B 158 ASP cc_start: 0.9045 (t0) cc_final: 0.8468 (t0) REVERT: B 159 ILE cc_start: 0.9159 (mp) cc_final: 0.8938 (mp) REVERT: B 160 LYS cc_start: 0.9078 (mmmt) cc_final: 0.8640 (mmmt) REVERT: B 165 LYS cc_start: 0.9416 (ptmm) cc_final: 0.9176 (ptmm) REVERT: B 171 GLU cc_start: 0.9038 (mp0) cc_final: 0.8774 (pm20) REVERT: C 8 CYS cc_start: 0.8885 (p) cc_final: 0.8461 (p) REVERT: C 35 LEU cc_start: 0.9307 (tp) cc_final: 0.9025 (tp) REVERT: C 38 LYS cc_start: 0.8645 (ptmm) cc_final: 0.8271 (ptmm) REVERT: C 51 MET cc_start: 0.9528 (OUTLIER) cc_final: 0.9212 (mpp) outliers start: 33 outliers final: 28 residues processed: 168 average time/residue: 0.0835 time to fit residues: 20.0050 Evaluate side-chains 182 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 911 TRP Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 51 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 6 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 87 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 106 optimal weight: 20.0000 chunk 82 optimal weight: 0.3980 chunk 49 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 148 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.107346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.072033 restraints weight = 23067.285| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 3.57 r_work: 0.3043 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 9702 Z= 0.265 Angle : 0.728 16.125 13325 Z= 0.345 Chirality : 0.046 0.341 1516 Planarity : 0.004 0.036 1545 Dihedral : 8.823 64.652 1645 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.48 % Allowed : 17.72 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.27), residues: 1065 helix: 0.85 (0.24), residues: 506 sheet: -0.77 (0.54), residues: 100 loop : 0.08 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 548 TYR 0.029 0.002 TYR A 415 PHE 0.013 0.002 PHE A 692 TRP 0.046 0.002 TRP B 182 HIS 0.005 0.001 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.26 ( 9694) covalent geometry : angle 0.72781 / 0.35 (13319) hydrogen bonds : bond 0.03978 / 2.75 ( 445) hydrogen bonds : angle 4.78649 / 3.42 ( 1195) metal coordination : bond 0.02913 / 1.24 ( 8) metal coordination : angle 1.61313 / 1.29 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.9162 (tt0) cc_final: 0.8693 (tp30) REVERT: A 248 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8763 (mp0) REVERT: A 263 TYR cc_start: 0.7970 (p90) cc_final: 0.7737 (p90) REVERT: A 267 GLU cc_start: 0.8478 (mp0) cc_final: 0.8107 (mp0) REVERT: A 385 ASP cc_start: 0.8200 (t0) cc_final: 0.7965 (t0) REVERT: A 403 GLN cc_start: 0.8685 (tt0) cc_final: 0.8006 (pm20) REVERT: A 419 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9013 (mm) REVERT: A 536 GLN cc_start: 0.8271 (tt0) cc_final: 0.8049 (tt0) REVERT: A 660 GLU cc_start: 0.8026 (pm20) cc_final: 0.7694 (pm20) REVERT: A 887 TYR cc_start: 0.9350 (t80) cc_final: 0.8270 (t80) REVERT: A 888 LYS cc_start: 0.9414 (mttt) cc_final: 0.9177 (mtmm) REVERT: A 911 TRP cc_start: 0.7924 (t-100) cc_final: 0.7537 (m-90) REVERT: A 912 ASP cc_start: 0.8778 (t0) cc_final: 0.8464 (p0) REVERT: A 919 MET cc_start: 0.9051 (mmt) cc_final: 0.8702 (mmt) REVERT: B 131 VAL cc_start: 0.9620 (t) cc_final: 0.9299 (p) REVERT: B 158 ASP cc_start: 0.9091 (t0) cc_final: 0.8781 (t0) REVERT: B 159 ILE cc_start: 0.9175 (mp) cc_final: 0.8739 (mp) REVERT: B 160 LYS cc_start: 0.9082 (mmmt) cc_final: 0.8646 (mmmt) REVERT: B 165 LYS cc_start: 0.9395 (ptmm) cc_final: 0.9027 (ptmm) REVERT: B 171 GLU cc_start: 0.9062 (mp0) cc_final: 0.8669 (pm20) REVERT: C 35 LEU cc_start: 0.9323 (tp) cc_final: 0.9063 (tp) REVERT: C 38 LYS cc_start: 0.8684 (ptmm) cc_final: 0.8351 (ptmm) REVERT: C 51 MET cc_start: 0.9549 (OUTLIER) cc_final: 0.9237 (mpp) outliers start: 33 outliers final: 28 residues processed: 168 average time/residue: 0.0783 time to fit residues: 19.0402 Evaluate side-chains 179 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 149 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 51 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 10 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 148 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.109142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.074131 restraints weight = 22811.515| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 3.55 r_work: 0.3087 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9702 Z= 0.176 Angle : 0.695 16.162 13325 Z= 0.324 Chirality : 0.046 0.354 1516 Planarity : 0.004 0.035 1545 Dihedral : 8.774 64.247 1645 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.27 % Allowed : 18.78 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.27), residues: 1065 helix: 0.91 (0.24), residues: 507 sheet: -0.68 (0.54), residues: 100 loop : 0.14 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 548 TYR 0.025 0.002 TYR A 211 PHE 0.011 0.001 PHE A 748 TRP 0.041 0.002 TRP B 182 HIS 0.003 0.001 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 ( 9694) covalent geometry : angle 0.69399 / 0.32 (13319) hydrogen bonds : bond 0.03627 / 2.50 ( 445) hydrogen bonds : angle 4.63252 / 3.32 ( 1195) metal coordination : bond 0.01992 / 0.86 ( 8) metal coordination : angle 1.52346 / 1.08 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.9140 (tt0) cc_final: 0.8642 (tp30) REVERT: A 248 GLU cc_start: 0.9098 (mm-30) cc_final: 0.8728 (mp0) REVERT: A 263 TYR cc_start: 0.7895 (p90) cc_final: 0.7652 (p90) REVERT: A 267 GLU cc_start: 0.8439 (mp0) cc_final: 0.8051 (mp0) REVERT: A 385 ASP cc_start: 0.8202 (t0) cc_final: 0.7970 (t0) REVERT: A 412 LYS cc_start: 0.9432 (tttp) cc_final: 0.9121 (tppt) REVERT: A 419 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9046 (mm) REVERT: A 660 GLU cc_start: 0.8009 (pm20) cc_final: 0.7720 (pm20) REVERT: A 887 TYR cc_start: 0.9330 (t80) cc_final: 0.8268 (t80) REVERT: A 888 LYS cc_start: 0.9406 (mttt) cc_final: 0.9164 (mtmm) REVERT: A 911 TRP cc_start: 0.7877 (t-100) cc_final: 0.7519 (m-90) REVERT: A 912 ASP cc_start: 0.8752 (t0) cc_final: 0.8468 (p0) REVERT: A 919 MET cc_start: 0.8991 (mmt) cc_final: 0.8657 (mmt) REVERT: B 131 VAL cc_start: 0.9631 (t) cc_final: 0.9341 (p) REVERT: B 134 ASP cc_start: 0.8608 (t0) cc_final: 0.8222 (t0) REVERT: B 158 ASP cc_start: 0.9071 (t0) cc_final: 0.8813 (t0) REVERT: B 159 ILE cc_start: 0.9185 (mp) cc_final: 0.8815 (mp) REVERT: B 160 LYS cc_start: 0.9105 (mmmt) cc_final: 0.8647 (mmmm) REVERT: B 165 LYS cc_start: 0.9405 (ptmm) cc_final: 0.9116 (ptmm) REVERT: B 171 GLU cc_start: 0.9045 (mp0) cc_final: 0.8648 (pm20) REVERT: C 35 LEU cc_start: 0.9326 (tp) cc_final: 0.9054 (tp) REVERT: C 38 LYS cc_start: 0.8658 (ptmm) cc_final: 0.8285 (ptmm) REVERT: C 51 MET cc_start: 0.9527 (OUTLIER) cc_final: 0.9224 (mpp) outliers start: 31 outliers final: 28 residues processed: 168 average time/residue: 0.0816 time to fit residues: 19.7295 Evaluate side-chains 178 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 51 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 2 optimal weight: 0.0670 chunk 90 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 13 optimal weight: 0.3980 chunk 25 optimal weight: 5.9990 chunk 31 optimal weight: 0.2980 chunk 79 optimal weight: 0.8980 chunk 98 optimal weight: 0.0980 chunk 84 optimal weight: 0.8980 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 307 ASN B 148 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.113207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.078342 restraints weight = 22524.517| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 3.63 r_work: 0.3173 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 9702 Z= 0.113 Angle : 0.685 17.016 13325 Z= 0.314 Chirality : 0.045 0.348 1516 Planarity : 0.004 0.034 1545 Dihedral : 8.622 63.977 1645 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.32 % Allowed : 19.73 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.27), residues: 1065 helix: 1.08 (0.24), residues: 504 sheet: -0.56 (0.59), residues: 83 loop : 0.24 (0.31), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 548 TYR 0.024 0.001 TYR A 415 PHE 0.015 0.001 PHE A 321 TRP 0.033 0.002 TRP B 182 HIS 0.002 0.000 HIS A 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 9694) covalent geometry : angle 0.68420 / 0.31 (13319) hydrogen bonds : bond 0.03223 / 2.17 ( 445) hydrogen bonds : angle 4.34200 / 3.12 ( 1195) metal coordination : bond 0.00662 / 0.29 ( 8) metal coordination : angle 1.37205 / 0.86 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2206.34 seconds wall clock time: 38 minutes 41.04 seconds (2321.04 seconds total)