Starting phenix.real_space_refine on Thu Jul 2 14:37:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y9m_39083/07_2026/8y9m_39083.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y9m_39083/07_2026/8y9m_39083.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8y9m_39083/07_2026/8y9m_39083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y9m_39083/07_2026/8y9m_39083.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y9m_39083/07_2026/8y9m_39083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y9m_39083/07_2026/8y9m_39083.map" } resolution = 2.76 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= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 107 5.49 5 S 27 5.16 5 C 5430 2.51 5 N 1614 2.21 5 O 1960 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9138 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 853, 6897 Classifications: {'peptide': 853} Link IDs: {'PTRANS': 33, 'TRANS': 819} Chain breaks: 2 Chain: "B" Number of atoms: 1203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1203 Classifications: {'RNA': 56} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pur': 29, 'rna3p_pyr': 22} Link IDs: {'rna2p': 4, 'rna3p': 51} Chain: "C" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 587 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "D" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 451 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Time building chain proxies: 1.91, per 1000 atoms: 0.21 Number of scatterers: 9138 At special positions: 0 Unit cell: (92.34, 104.31, 119.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 107 15.00 O 1960 8.00 N 1614 7.00 C 5430 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: 0.68 Conformation dependent library (CDL) restraints added in 196.4 milliseconds 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1600 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 7 sheets defined 47.5% alpha, 11.7% beta 34 base pairs and 69 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 21 through 41 removed outlier: 4.085A pdb=" N SER A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 72 removed outlier: 3.721A pdb=" N ALA A 63 " --> pdb=" O SER A 59 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A 64 " --> pdb=" O PRO A 60 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 88 Processing helix chain 'A' and resid 89 through 99 removed outlier: 4.386A pdb=" N SER A 94 " --> pdb=" O PRO A 91 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N CYS A 95 " --> pdb=" O SER A 92 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N TYR A 96 " --> pdb=" O SER A 93 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER A 97 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 98 " --> pdb=" O CYS A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 121 removed outlier: 4.402A pdb=" N GLY A 121 " --> pdb=" O GLU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 Processing helix chain 'A' and resid 139 through 143 removed outlier: 3.538A pdb=" N LYS A 142 " --> pdb=" O GLN A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 154 Processing helix chain 'A' and resid 156 through 165 removed outlier: 3.590A pdb=" N GLN A 163 " --> pdb=" O GLU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 173 removed outlier: 3.962A pdb=" N ARG A 173 " --> pdb=" O ASN A 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 170 through 173' Processing helix chain 'A' and resid 174 through 184 removed outlier: 3.517A pdb=" N ARG A 180 " --> pdb=" O GLY A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 231 removed outlier: 3.607A pdb=" N ARG A 205 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS A 210 " --> pdb=" O GLN A 206 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU A 212 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR A 213 " --> pdb=" O SER A 209 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N HIS A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU A 223 " --> pdb=" O ASN A 219 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N MET A 224 " --> pdb=" O GLN A 220 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LYS A 225 " --> pdb=" O THR A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 249 Processing helix chain 'A' and resid 256 through 267 removed outlier: 4.261A pdb=" N VAL A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 284 removed outlier: 3.858A pdb=" N GLN A 284 " --> pdb=" O ASP A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 293 removed outlier: 4.488A pdb=" N GLY A 289 " --> pdb=" O LYS A 286 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU A 290 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 291 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR A 292 " --> pdb=" O GLY A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 312 removed outlier: 3.507A pdb=" N GLU A 312 " --> pdb=" O LYS A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 441 removed outlier: 3.602A pdb=" N GLN A 436 " --> pdb=" O ILE A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 453 Processing helix chain 'A' and resid 508 through 511 Processing helix chain 'A' and resid 512 through 534 removed outlier: 4.015A pdb=" N SER A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 517 " --> pdb=" O GLU A 513 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS A 518 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG A 519 " --> pdb=" O ILE A 515 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A 521 " --> pdb=" O LEU A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 551 removed outlier: 3.951A pdb=" N GLU A 551 " --> pdb=" O THR A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 575 removed outlier: 3.533A pdb=" N GLN A 564 " --> pdb=" O ARG A 560 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A 568 " --> pdb=" O GLN A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 583 removed outlier: 3.830A pdb=" N TYR A 579 " --> pdb=" O ASN A 575 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N MET A 581 " --> pdb=" O PHE A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 610 removed outlier: 4.113A pdb=" N ARG A 594 " --> pdb=" O ALA A 590 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU A 596 " --> pdb=" O ALA A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 649 removed outlier: 3.791A pdb=" N LEU A 637 " --> pdb=" O PHE A 633 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG A 639 " --> pdb=" O ASP A 635 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA A 642 " --> pdb=" O ARG A 638 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR A 648 " --> pdb=" O THR A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 678 removed outlier: 3.577A pdb=" N VAL A 674 " --> pdb=" O ASN A 670 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU A 676 " --> pdb=" O ALA A 672 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 692 removed outlier: 3.660A pdb=" N LEU A 684 " --> pdb=" O ARG A 680 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A 687 " --> pdb=" O LEU A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 753 Processing helix chain 'A' and resid 782 through 790 Processing helix chain 'A' and resid 830 through 846 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8 removed outlier: 4.331A pdb=" N SER A 429 " --> pdb=" O GLU A 404 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N GLU A 404 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N HIS A 379 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA A 371 " --> pdb=" O HIS A 379 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LYS A 381 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU A 369 " --> pdb=" O LYS A 381 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 329 through 331 removed outlier: 5.409A pdb=" N PHE A 420 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE A 359 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N TYR A 17 " --> pdb=" O LYS A 357 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N LYS A 357 " --> pdb=" O TYR A 17 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 349 " --> pdb=" O GLU A 342 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 48 Processing sheet with id=AA4, first strand: chain 'A' and resid 487 through 489 removed outlier: 4.549A pdb=" N TYR A 494 " --> pdb=" O GLY A 480 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY A 480 " --> pdb=" O TYR A 494 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A 498 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LYS A 476 " --> pdb=" O ILE A 498 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL A 461 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLY A 462 " --> pdb=" O PHE A 656 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N GLU A 658 " --> pdb=" O GLY A 462 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL A 655 " --> pdb=" O VAL A 698 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N VAL A 700 " --> pdb=" O VAL A 655 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N PHE A 657 " --> pdb=" O VAL A 700 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 717 through 718 removed outlier: 4.011A pdb=" N ILE A 726 " --> pdb=" O MET A 737 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG A 852 " --> pdb=" O LEU A 734 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 760 through 762 Processing sheet with id=AA7, first strand: chain 'A' and resid 796 through 800 removed outlier: 3.740A pdb=" N LEU A 798 " --> pdb=" O THR A 806 " (cutoff:3.500A) 297 hydrogen bonds defined for protein. 810 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 84 hydrogen bonds 160 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 69 stacking parallelities Total time for adding SS restraints: 1.60 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1806 1.33 - 1.45: 2706 1.45 - 1.57: 4785 1.57 - 1.69: 210 1.69 - 1.81: 43 Bond restraints: 9550 Sorted by residual: bond pdb=" O3' DG D 11 " pdb=" P DT D 12 " ideal model delta sigma weight residual 1.607 1.510 0.097 1.50e-02 4.44e+03 4.14e+01 bond pdb=" C1' DC D 10 " pdb=" N1 DC D 10 " ideal model delta sigma weight residual 1.468 1.550 -0.082 1.40e-02 5.10e+03 3.46e+01 bond pdb=" C1' DC D 9 " pdb=" N1 DC D 9 " ideal model delta sigma weight residual 1.468 1.548 -0.080 1.40e-02 5.10e+03 3.24e+01 bond pdb=" C3' DA C -7 " pdb=" C2' DA C -7 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DA C 5 " pdb=" C2' DA C 5 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.69e+00 ... (remaining 9545 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 13128 2.46 - 4.93: 223 4.93 - 7.39: 15 7.39 - 9.85: 3 9.85 - 12.32: 1 Bond angle restraints: 13370 Sorted by residual: angle pdb=" N ILE A 432 " pdb=" CA ILE A 432 " pdb=" C ILE A 432 " ideal model delta sigma weight residual 111.91 105.97 5.94 8.90e-01 1.26e+00 4.46e+01 angle pdb=" O2' A B 19 " pdb=" C2' A B 19 " pdb=" C1' A B 19 " ideal model delta sigma weight residual 108.40 100.58 7.82 1.50e+00 4.44e-01 2.72e+01 angle pdb=" O5' DA C -18 " pdb=" C5' DA C -18 " pdb=" C4' DA C -18 " ideal model delta sigma weight residual 109.40 113.55 -4.15 8.00e-01 1.56e+00 2.69e+01 angle pdb=" O3' DT C -19 " pdb=" C3' DT C -19 " pdb=" C2' DT C -19 " ideal model delta sigma weight residual 109.40 97.08 12.32 2.50e+00 1.60e-01 2.43e+01 angle pdb=" C3' DT C -19 " pdb=" C2' DT C -19 " pdb=" C1' DT C -19 " ideal model delta sigma weight residual 102.50 108.32 -5.82 1.20e+00 6.94e-01 2.36e+01 ... (remaining 13365 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.04: 5273 32.04 - 64.08: 407 64.08 - 96.11: 35 96.11 - 128.15: 2 128.15 - 160.19: 1 Dihedral angle restraints: 5718 sinusoidal: 3231 harmonic: 2487 Sorted by residual: dihedral pdb=" O4' U B -18 " pdb=" C1' U B -18 " pdb=" N1 U B -18 " pdb=" C2 U B -18 " ideal model delta sinusoidal sigma weight residual 200.00 39.81 160.19 1 1.50e+01 4.44e-03 8.28e+01 dihedral pdb=" C5' G B 20 " pdb=" C4' G B 20 " pdb=" C3' G B 20 " pdb=" O3' G B 20 " ideal model delta sinusoidal sigma weight residual 147.00 111.27 35.73 1 8.00e+00 1.56e-02 2.82e+01 dihedral pdb=" O4' G B 20 " pdb=" C4' G B 20 " pdb=" C3' G B 20 " pdb=" C2' G B 20 " ideal model delta sinusoidal sigma weight residual 24.00 -10.06 34.06 1 8.00e+00 1.56e-02 2.57e+01 ... (remaining 5715 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1406 0.087 - 0.175: 94 0.175 - 0.262: 1 0.262 - 0.350: 1 0.350 - 0.437: 1 Chirality restraints: 1503 Sorted by residual: chirality pdb=" C2' G B 20 " pdb=" C3' G B 20 " pdb=" O2' G B 20 " pdb=" C1' G B 20 " both_signs ideal model delta sigma weight residual False -2.52 -2.08 -0.44 2.00e-01 2.50e+01 4.78e+00 chirality pdb=" CA VAL A 762 " pdb=" N VAL A 762 " pdb=" C VAL A 762 " pdb=" CB VAL A 762 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CB VAL A 762 " pdb=" CA VAL A 762 " pdb=" CG1 VAL A 762 " pdb=" CG2 VAL A 762 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 1500 not shown) Planarity restraints: 1325 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT C -19 " 0.043 2.00e-02 2.50e+03 2.58e-02 1.66e+01 pdb=" N1 DT C -19 " -0.068 2.00e-02 2.50e+03 pdb=" C2 DT C -19 " 0.003 2.00e-02 2.50e+03 pdb=" O2 DT C -19 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DT C -19 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DT C -19 " 0.002 2.00e-02 2.50e+03 pdb=" O4 DT C -19 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DT C -19 " 0.004 2.00e-02 2.50e+03 pdb=" C7 DT C -19 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DT C -19 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 20 " -0.053 2.00e-02 2.50e+03 2.30e-02 1.58e+01 pdb=" N9 G B 20 " 0.052 2.00e-02 2.50e+03 pdb=" C8 G B 20 " 0.007 2.00e-02 2.50e+03 pdb=" N7 G B 20 " -0.003 2.00e-02 2.50e+03 pdb=" C5 G B 20 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G B 20 " -0.022 2.00e-02 2.50e+03 pdb=" O6 G B 20 " -0.003 2.00e-02 2.50e+03 pdb=" N1 G B 20 " -0.007 2.00e-02 2.50e+03 pdb=" C2 G B 20 " 0.004 2.00e-02 2.50e+03 pdb=" N2 G B 20 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G B 20 " 0.010 2.00e-02 2.50e+03 pdb=" C4 G B 20 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 19 " -0.029 2.00e-02 2.50e+03 1.40e-02 5.42e+00 pdb=" N9 A B 19 " 0.032 2.00e-02 2.50e+03 pdb=" C8 A B 19 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A B 19 " -0.010 2.00e-02 2.50e+03 pdb=" C5 A B 19 " 0.005 2.00e-02 2.50e+03 pdb=" C6 A B 19 " -0.005 2.00e-02 2.50e+03 pdb=" N6 A B 19 " -0.002 2.00e-02 2.50e+03 pdb=" N1 A B 19 " -0.007 2.00e-02 2.50e+03 pdb=" C2 A B 19 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A B 19 " 0.006 2.00e-02 2.50e+03 pdb=" C4 A B 19 " 0.009 2.00e-02 2.50e+03 ... (remaining 1322 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 499 2.71 - 3.26: 8391 3.26 - 3.81: 14785 3.81 - 4.35: 18699 4.35 - 4.90: 29600 Nonbonded interactions: 71974 Sorted by model distance: nonbonded pdb=" O ALA A 445 " pdb=" NH1 ARG A 784 " model vdw 2.167 3.120 nonbonded pdb=" OH TYR A 365 " pdb=" OH TYR A 426 " model vdw 2.188 3.040 nonbonded pdb=" O2' C B -19 " pdb=" OP2 A B -17 " model vdw 2.189 3.040 nonbonded pdb=" NH2 ARG A 634 " pdb=" O LEU A 676 " model vdw 2.192 3.120 nonbonded pdb=" O TYR A 586 " pdb=" NH2 ARG A 640 " model vdw 2.193 3.120 ... (remaining 71969 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.920 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 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 0.097 9550 Z= 0.368 Angle : 0.783 12.318 13370 Z= 0.572 Chirality : 0.047 0.437 1503 Planarity : 0.005 0.051 1325 Dihedral : 19.546 160.188 4118 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.40 % Allowed : 0.81 % Favored : 98.79 % 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: -1.32 (0.28), residues: 847 helix: -0.41 (0.27), residues: 361 sheet: -0.47 (0.47), residues: 119 loop : -1.40 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 440 TYR 0.025 0.002 TYR A 778 PHE 0.014 0.002 PHE A 242 TRP 0.021 0.002 TRP A 259 HIS 0.007 0.001 HIS A 824 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.37 ( 9550) covalent geometry : angle 0.78321 / 0.57 (13370) hydrogen bonds : bond 0.20685 / 14.68 ( 381) hydrogen bonds : angle 6.76614 / 4.76 ( 970) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 110 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 112 average time/residue: 0.6324 time to fit residues: 74.8997 Evaluate side-chains 75 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 777 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.0870 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 231 ASN A 834 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.182234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.137127 restraints weight = 11959.373| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.65 r_work: 0.3641 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9550 Z= 0.154 Angle : 0.611 7.546 13370 Z= 0.349 Chirality : 0.042 0.235 1503 Planarity : 0.005 0.049 1325 Dihedral : 21.376 159.533 2384 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.29 % Allowed : 11.74 % Favored : 85.96 % 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: -0.75 (0.28), residues: 847 helix: 0.14 (0.28), residues: 372 sheet: -0.31 (0.45), residues: 133 loop : -1.18 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 68 TYR 0.013 0.001 TYR A 822 PHE 0.011 0.001 PHE A 531 TRP 0.013 0.002 TRP A 259 HIS 0.007 0.001 HIS A 824 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.15 ( 9550) covalent geometry : angle 0.61113 / 0.35 (13370) hydrogen bonds : bond 0.06076 / 4.09 ( 381) hydrogen bonds : angle 4.72023 / 3.27 ( 970) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.305 Fit side-chains REVERT: A 11 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.7992 (mt) REVERT: A 404 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8318 (mt-10) REVERT: A 581 MET cc_start: 0.6803 (tmt) cc_final: 0.6586 (tmt) REVERT: A 697 MET cc_start: 0.8675 (ttp) cc_final: 0.8424 (ttp) REVERT: A 738 ASP cc_start: 0.7958 (t0) cc_final: 0.7685 (t0) REVERT: A 787 LYS cc_start: 0.6202 (mttp) cc_final: 0.5750 (mmtm) REVERT: A 848 GLU cc_start: 0.8503 (mp0) cc_final: 0.8082 (mp0) outliers start: 17 outliers final: 10 residues processed: 85 average time/residue: 0.5950 time to fit residues: 54.0414 Evaluate side-chains 76 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 822 TYR Chi-restraints excluded: chain A residue 850 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 14 optimal weight: 20.0000 chunk 0 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 67 optimal weight: 0.0070 chunk 5 optimal weight: 6.9990 chunk 34 optimal weight: 0.0000 chunk 77 optimal weight: 5.9990 overall best weight: 1.8008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.180152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.134716 restraints weight = 11874.286| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.65 r_work: 0.3610 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9550 Z= 0.178 Angle : 0.596 6.873 13370 Z= 0.341 Chirality : 0.041 0.198 1503 Planarity : 0.004 0.042 1325 Dihedral : 21.348 159.671 2384 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.24 % Allowed : 12.69 % Favored : 84.08 % 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: -0.77 (0.28), residues: 847 helix: 0.15 (0.28), residues: 370 sheet: -0.15 (0.45), residues: 131 loop : -1.30 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 750 TYR 0.018 0.002 TYR A 217 PHE 0.016 0.001 PHE A 531 TRP 0.016 0.002 TRP A 255 HIS 0.009 0.001 HIS A 824 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.18 ( 9550) covalent geometry : angle 0.59568 / 0.34 (13370) hydrogen bonds : bond 0.05894 / 3.95 ( 381) hydrogen bonds : angle 4.43140 / 3.08 ( 970) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 291 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7402 (mm) REVERT: A 404 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8360 (mt-10) REVERT: A 498 ILE cc_start: 0.7758 (OUTLIER) cc_final: 0.7259 (pt) REVERT: A 562 MET cc_start: 0.5280 (mtt) cc_final: 0.4994 (mtp) REVERT: A 581 MET cc_start: 0.6835 (OUTLIER) cc_final: 0.6590 (tmt) REVERT: A 697 MET cc_start: 0.8718 (ttp) cc_final: 0.8493 (ttp) REVERT: A 787 LYS cc_start: 0.6166 (mttp) cc_final: 0.5657 (mmtm) REVERT: A 848 GLU cc_start: 0.8526 (mp0) cc_final: 0.8135 (mp0) outliers start: 24 outliers final: 14 residues processed: 82 average time/residue: 0.6066 time to fit residues: 53.0347 Evaluate side-chains 82 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 534 CYS Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 822 TYR Chi-restraints excluded: chain A residue 846 GLU Chi-restraints excluded: chain A residue 850 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 5 optimal weight: 5.9990 chunk 80 optimal weight: 0.0050 chunk 4 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 93 optimal weight: 20.0000 chunk 61 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 79 optimal weight: 10.0000 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.182958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.137490 restraints weight = 12034.413| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.69 r_work: 0.3637 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9550 Z= 0.128 Angle : 0.529 6.019 13370 Z= 0.310 Chirality : 0.039 0.201 1503 Planarity : 0.004 0.035 1325 Dihedral : 21.303 157.871 2384 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.32 % Allowed : 14.44 % Favored : 81.24 % 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: -0.51 (0.29), residues: 847 helix: 0.39 (0.28), residues: 374 sheet: -0.02 (0.46), residues: 129 loop : -1.19 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 67 TYR 0.013 0.001 TYR A 822 PHE 0.010 0.001 PHE A 531 TRP 0.011 0.001 TRP A 255 HIS 0.004 0.001 HIS A 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.13 ( 9550) covalent geometry : angle 0.52865 / 0.31 (13370) hydrogen bonds : bond 0.04763 / 3.19 ( 381) hydrogen bonds : angle 4.09453 / 2.86 ( 970) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 67 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 291 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7388 (mm) REVERT: A 404 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8295 (mt-10) REVERT: A 498 ILE cc_start: 0.7632 (pt) cc_final: 0.7194 (pt) REVERT: A 562 MET cc_start: 0.5248 (mtt) cc_final: 0.5032 (mtp) REVERT: A 697 MET cc_start: 0.8682 (ttp) cc_final: 0.8452 (ttp) REVERT: A 787 LYS cc_start: 0.6122 (mttp) cc_final: 0.5679 (mmtm) REVERT: A 848 GLU cc_start: 0.8557 (mp0) cc_final: 0.8136 (mp0) outliers start: 32 outliers final: 14 residues processed: 87 average time/residue: 0.5450 time to fit residues: 50.7937 Evaluate side-chains 79 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 534 CYS Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 846 GLU Chi-restraints excluded: chain A residue 850 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 55 optimal weight: 0.0170 chunk 70 optimal weight: 0.0370 chunk 0 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 overall best weight: 1.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 564 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.180660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.135048 restraints weight = 12042.653| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.69 r_work: 0.3619 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9550 Z= 0.161 Angle : 0.553 6.963 13370 Z= 0.318 Chirality : 0.040 0.183 1503 Planarity : 0.004 0.038 1325 Dihedral : 21.277 158.223 2382 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.51 % Allowed : 15.92 % Favored : 80.57 % 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: -0.46 (0.29), residues: 847 helix: 0.44 (0.28), residues: 376 sheet: -0.03 (0.45), residues: 131 loop : -1.19 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 68 TYR 0.016 0.001 TYR A 217 PHE 0.014 0.001 PHE A 531 TRP 0.011 0.001 TRP A 24 HIS 0.004 0.001 HIS A 824 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 ( 9550) covalent geometry : angle 0.55342 / 0.32 (13370) hydrogen bonds : bond 0.05204 / 3.49 ( 381) hydrogen bonds : angle 4.03984 / 2.82 ( 970) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 65 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: A 291 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7445 (mm) REVERT: A 404 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8326 (mt-10) REVERT: A 498 ILE cc_start: 0.7751 (OUTLIER) cc_final: 0.7240 (pt) REVERT: A 562 MET cc_start: 0.5238 (mtt) cc_final: 0.5016 (mtp) REVERT: A 697 MET cc_start: 0.8722 (ttp) cc_final: 0.8501 (ttp) REVERT: A 787 LYS cc_start: 0.6183 (mttp) cc_final: 0.5760 (mmtp) REVERT: A 846 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7684 (mp0) REVERT: A 848 GLU cc_start: 0.8579 (mp0) cc_final: 0.8168 (mp0) outliers start: 26 outliers final: 14 residues processed: 78 average time/residue: 0.5424 time to fit residues: 45.0268 Evaluate side-chains 78 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 534 CYS Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 846 GLU Chi-restraints excluded: chain A residue 850 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 61 optimal weight: 0.0170 overall best weight: 1.0820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.181621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.136646 restraints weight = 12211.465| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.70 r_work: 0.3615 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9550 Z= 0.134 Angle : 0.532 7.799 13370 Z= 0.308 Chirality : 0.039 0.186 1503 Planarity : 0.004 0.036 1325 Dihedral : 21.241 157.470 2382 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.64 % Allowed : 16.46 % Favored : 79.89 % 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: -0.33 (0.29), residues: 847 helix: 0.55 (0.28), residues: 376 sheet: 0.06 (0.46), residues: 129 loop : -1.14 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 68 TYR 0.014 0.001 TYR A 822 PHE 0.011 0.001 PHE A 442 TRP 0.010 0.001 TRP A 24 HIS 0.004 0.001 HIS A 824 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 ( 9550) covalent geometry : angle 0.53191 / 0.31 (13370) hydrogen bonds : bond 0.04708 / 3.16 ( 381) hydrogen bonds : angle 3.95409 / 2.75 ( 970) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 66 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 291 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7459 (mm) REVERT: A 399 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8590 (mm) REVERT: A 404 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8305 (mt-10) REVERT: A 498 ILE cc_start: 0.7685 (OUTLIER) cc_final: 0.7253 (pt) REVERT: A 562 MET cc_start: 0.5241 (mtt) cc_final: 0.5032 (mtp) REVERT: A 581 MET cc_start: 0.6393 (OUTLIER) cc_final: 0.5986 (tmt) REVERT: A 697 MET cc_start: 0.8732 (ttp) cc_final: 0.8531 (ttp) REVERT: A 787 LYS cc_start: 0.6170 (mttp) cc_final: 0.5746 (mmtm) REVERT: A 848 GLU cc_start: 0.8587 (mp0) cc_final: 0.8269 (mp0) outliers start: 27 outliers final: 13 residues processed: 82 average time/residue: 0.5052 time to fit residues: 44.6348 Evaluate side-chains 81 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 822 TYR Chi-restraints excluded: chain A residue 846 GLU Chi-restraints excluded: chain A residue 850 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 15 optimal weight: 30.0000 chunk 18 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 10 optimal weight: 0.0970 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.181219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.136160 restraints weight = 12161.267| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.69 r_work: 0.3610 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9550 Z= 0.139 Angle : 0.539 8.275 13370 Z= 0.312 Chirality : 0.039 0.188 1503 Planarity : 0.004 0.038 1325 Dihedral : 21.209 157.288 2382 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.70 % Allowed : 18.22 % Favored : 79.08 % 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: -0.27 (0.29), residues: 847 helix: 0.61 (0.28), residues: 376 sheet: 0.10 (0.46), residues: 129 loop : -1.12 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 116 TYR 0.013 0.001 TYR A 217 PHE 0.012 0.001 PHE A 531 TRP 0.010 0.001 TRP A 24 HIS 0.004 0.001 HIS A 824 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 ( 9550) covalent geometry : angle 0.53851 / 0.31 (13370) hydrogen bonds : bond 0.04744 / 3.17 ( 381) hydrogen bonds : angle 3.93770 / 2.73 ( 970) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.244 Fit side-chains REVERT: A 125 MET cc_start: 0.2472 (OUTLIER) cc_final: 0.1453 (tmm) REVERT: A 399 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8624 (mm) REVERT: A 404 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8300 (mt-10) REVERT: A 498 ILE cc_start: 0.7704 (OUTLIER) cc_final: 0.7260 (pt) REVERT: A 562 MET cc_start: 0.5292 (mtt) cc_final: 0.5084 (mtp) REVERT: A 581 MET cc_start: 0.6440 (OUTLIER) cc_final: 0.6033 (tmt) REVERT: A 697 MET cc_start: 0.8739 (ttp) cc_final: 0.8530 (ttp) REVERT: A 787 LYS cc_start: 0.6162 (mttp) cc_final: 0.5738 (mmtm) REVERT: A 846 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7702 (mp0) REVERT: A 848 GLU cc_start: 0.8602 (mp0) cc_final: 0.8240 (mp0) REVERT: A 861 ILE cc_start: 0.7372 (OUTLIER) cc_final: 0.7140 (mt) outliers start: 20 outliers final: 10 residues processed: 74 average time/residue: 0.5255 time to fit residues: 41.7181 Evaluate side-chains 77 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 846 GLU Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 861 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 90 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.175611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.130218 restraints weight = 12157.391| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.67 r_work: 0.3539 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 9550 Z= 0.275 Angle : 0.683 8.746 13370 Z= 0.382 Chirality : 0.046 0.190 1503 Planarity : 0.005 0.055 1325 Dihedral : 21.323 160.752 2382 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.37 % Allowed : 18.22 % Favored : 78.41 % 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: -0.77 (0.28), residues: 847 helix: 0.09 (0.27), residues: 380 sheet: -0.00 (0.47), residues: 126 loop : -1.31 (0.31), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 611 TYR 0.031 0.002 TYR A 217 PHE 0.025 0.002 PHE A 531 TRP 0.015 0.002 TRP A 323 HIS 0.008 0.002 HIS A 824 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.27 ( 9550) covalent geometry : angle 0.68341 / 0.38 (13370) hydrogen bonds : bond 0.06915 / 4.55 ( 381) hydrogen bonds : angle 4.34024 / 3.01 ( 970) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 65 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.2450 (OUTLIER) cc_final: 0.1609 (tmm) REVERT: A 399 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8659 (mm) REVERT: A 404 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8366 (mt-10) REVERT: A 562 MET cc_start: 0.5341 (mtt) cc_final: 0.5110 (mtp) REVERT: A 581 MET cc_start: 0.6802 (OUTLIER) cc_final: 0.6346 (tmt) REVERT: A 848 GLU cc_start: 0.8569 (mp0) cc_final: 0.8097 (mp0) outliers start: 25 outliers final: 12 residues processed: 80 average time/residue: 0.5310 time to fit residues: 45.6024 Evaluate side-chains 74 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 846 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 34 optimal weight: 0.3980 chunk 27 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 231 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.181030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.136064 restraints weight = 12173.034| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.69 r_work: 0.3598 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9550 Z= 0.131 Angle : 0.559 9.473 13370 Z= 0.321 Chirality : 0.039 0.212 1503 Planarity : 0.004 0.035 1325 Dihedral : 21.259 158.431 2382 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.43 % Allowed : 19.43 % Favored : 78.14 % 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: -0.34 (0.29), residues: 847 helix: 0.52 (0.28), residues: 376 sheet: 0.08 (0.46), residues: 129 loop : -1.12 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 68 TYR 0.016 0.001 TYR A 822 PHE 0.011 0.001 PHE A 442 TRP 0.013 0.001 TRP A 323 HIS 0.005 0.001 HIS A 824 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 ( 9550) covalent geometry : angle 0.55905 / 0.32 (13370) hydrogen bonds : bond 0.04701 / 3.13 ( 381) hydrogen bonds : angle 3.98088 / 2.76 ( 970) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 125 MET cc_start: 0.2376 (OUTLIER) cc_final: 0.1358 (tmm) REVERT: A 399 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8604 (mm) REVERT: A 404 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8252 (mt-10) REVERT: A 498 ILE cc_start: 0.7658 (pt) cc_final: 0.7246 (pt) REVERT: A 562 MET cc_start: 0.5365 (mtt) cc_final: 0.5157 (mtp) REVERT: A 737 MET cc_start: 0.8012 (mmt) cc_final: 0.7778 (mtp) REVERT: A 738 ASP cc_start: 0.8053 (t0) cc_final: 0.7418 (t0) REVERT: A 787 LYS cc_start: 0.6199 (mttp) cc_final: 0.5754 (mmtp) REVERT: A 848 GLU cc_start: 0.8572 (mp0) cc_final: 0.8180 (mp0) REVERT: A 861 ILE cc_start: 0.7313 (OUTLIER) cc_final: 0.7099 (mt) outliers start: 18 outliers final: 10 residues processed: 71 average time/residue: 0.5358 time to fit residues: 40.7785 Evaluate side-chains 74 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 846 GLU Chi-restraints excluded: chain A residue 861 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 86 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.176178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.130813 restraints weight = 12279.586| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.69 r_work: 0.3541 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 9550 Z= 0.260 Angle : 0.662 9.421 13370 Z= 0.371 Chirality : 0.045 0.197 1503 Planarity : 0.005 0.045 1325 Dihedral : 21.319 160.799 2382 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.56 % Allowed : 19.03 % Favored : 78.41 % 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: -0.68 (0.28), residues: 847 helix: 0.16 (0.27), residues: 378 sheet: 0.06 (0.47), residues: 124 loop : -1.25 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 68 TYR 0.027 0.002 TYR A 217 PHE 0.024 0.002 PHE A 531 TRP 0.013 0.002 TRP A 323 HIS 0.007 0.001 HIS A 824 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.26 ( 9550) covalent geometry : angle 0.66245 / 0.37 (13370) hydrogen bonds : bond 0.06481 / 4.26 ( 381) hydrogen bonds : angle 4.29249 / 2.98 ( 970) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 125 MET cc_start: 0.2096 (OUTLIER) cc_final: 0.1088 (tmm) REVERT: A 399 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8619 (mm) REVERT: A 404 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8325 (mt-10) REVERT: A 498 ILE cc_start: 0.7789 (pt) cc_final: 0.7356 (pt) REVERT: A 562 MET cc_start: 0.5358 (mtt) cc_final: 0.5141 (mtp) REVERT: A 581 MET cc_start: 0.6894 (OUTLIER) cc_final: 0.6666 (tmt) REVERT: A 787 LYS cc_start: 0.6398 (mttp) cc_final: 0.5849 (mmtm) REVERT: A 848 GLU cc_start: 0.8567 (mp0) cc_final: 0.8043 (mp0) REVERT: A 861 ILE cc_start: 0.7454 (OUTLIER) cc_final: 0.7165 (mt) outliers start: 19 outliers final: 10 residues processed: 69 average time/residue: 0.5486 time to fit residues: 40.6737 Evaluate side-chains 72 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 846 GLU Chi-restraints excluded: chain A residue 861 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 19 optimal weight: 0.8980 chunk 13 optimal weight: 20.0000 chunk 44 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 231 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.180910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.135844 restraints weight = 12067.181| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.67 r_work: 0.3615 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9550 Z= 0.131 Angle : 0.556 9.845 13370 Z= 0.319 Chirality : 0.039 0.204 1503 Planarity : 0.004 0.035 1325 Dihedral : 21.269 158.439 2382 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.70 % Allowed : 19.16 % Favored : 78.14 % 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: -0.31 (0.29), residues: 847 helix: 0.55 (0.28), residues: 374 sheet: 0.07 (0.46), residues: 129 loop : -1.08 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 68 TYR 0.011 0.001 TYR A 217 PHE 0.010 0.001 PHE A 442 TRP 0.014 0.001 TRP A 548 HIS 0.004 0.001 HIS A 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 ( 9550) covalent geometry : angle 0.55645 / 0.32 (13370) hydrogen bonds : bond 0.04646 / 3.09 ( 381) hydrogen bonds : angle 3.98106 / 2.76 ( 970) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2800.76 seconds wall clock time: 48 minutes 27.25 seconds (2907.25 seconds total)