Starting phenix.real_space_refine on Thu Mar 13 16:07:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y9m_39083/03_2025/8y9m_39083.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y9m_39083/03_2025/8y9m_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8y9m_39083/03_2025/8y9m_39083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y9m_39083/03_2025/8y9m_39083.map" model { file = "/net/cci-nas-00/data/ceres_data/8y9m_39083/03_2025/8y9m_39083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y9m_39083/03_2025/8y9m_39083.cif" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 6.02, per 1000 atoms: 0.66 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: 2.22 Conformation dependent library (CDL) restraints added in 757.3 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: 3.20 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: 4.03 Time building geometry restraints manager: 2.65 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=" O3' DC C -20 " pdb=" P DT C -19 " ideal model delta sigma weight residual 1.607 1.570 0.037 1.50e-02 4.44e+03 5.95e+00 bond pdb=" N THR A 763 " pdb=" CA THR A 763 " ideal model delta sigma weight residual 1.456 1.487 -0.030 1.28e-02 6.10e+03 5.55e+00 bond pdb=" C VAL A 762 " pdb=" O VAL A 762 " ideal model delta sigma weight residual 1.238 1.214 0.024 1.10e-02 8.26e+03 4.68e+00 bond pdb=" O3' DT C -19 " pdb=" P DA C -18 " ideal model delta sigma weight residual 1.607 1.637 -0.030 1.50e-02 4.44e+03 4.07e+00 ... (remaining 9545 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 13220 2.88 - 5.77: 138 5.77 - 8.65: 11 8.65 - 11.53: 0 11.53 - 14.42: 1 Bond angle restraints: 13370 Sorted by residual: angle pdb=" O3' DT C -19 " pdb=" C3' DT C -19 " pdb=" C2' DT C -19 " ideal model delta sigma weight residual 111.50 97.08 14.42 1.50e+00 4.44e-01 9.24e+01 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=" O2' G B 20 " pdb=" C2' G B 20 " pdb=" C1' G B 20 " ideal model delta sigma weight residual 111.80 118.88 -7.08 1.50e+00 4.44e-01 2.23e+01 angle pdb=" C3' DT C -19 " pdb=" C2' DT C -19 " pdb=" C1' DT C -19 " ideal model delta sigma weight residual 101.60 108.32 -6.72 1.50e+00 4.44e-01 2.01e+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: 1422 0.087 - 0.175: 78 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: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.600 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 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= 0.284 Angle : 0.754 14.418 13370 Z= 0.453 Chirality : 0.045 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (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 TRP 0.021 0.002 TRP A 259 HIS 0.007 0.001 HIS A 824 PHE 0.014 0.002 PHE A 242 TYR 0.025 0.002 TYR A 778 ARG 0.007 0.001 ARG A 440 *********************** 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 : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 112 average time/residue: 1.4252 time to fit residues: 169.2836 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 : 0.848 ------------------------------------------------------------------------------- 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 79 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 39 optimal weight: 0.4980 chunk 24 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 28 optimal weight: 0.0770 chunk 44 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 chunk 85 optimal weight: 7.9990 overall best weight: 1.5142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN ** A 834 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 = 0.4158 r_free = 0.4158 target = 0.181086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.136146 restraints weight = 11890.821| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.64 r_work: 0.3627 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9550 Z= 0.235 Angle : 0.620 7.866 13370 Z= 0.331 Chirality : 0.040 0.211 1503 Planarity : 0.005 0.041 1325 Dihedral : 21.181 162.498 2384 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.56 % Allowed : 10.39 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.28), residues: 847 helix: 0.06 (0.27), residues: 375 sheet: -0.23 (0.46), residues: 131 loop : -1.29 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 548 HIS 0.009 0.001 HIS A 824 PHE 0.015 0.002 PHE A 531 TYR 0.016 0.001 TYR A 217 ARG 0.004 0.000 ARG A 67 *********************** 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 100 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.864 Fit side-chains REVERT: A 291 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7447 (mm) REVERT: A 404 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8356 (mt-10) REVERT: A 498 ILE cc_start: 0.7741 (OUTLIER) cc_final: 0.7245 (pt) REVERT: A 572 ARG cc_start: 0.7180 (mtm110) cc_final: 0.6833 (ttm170) REVERT: A 697 MET cc_start: 0.8704 (ttp) cc_final: 0.8429 (ttp) REVERT: A 738 ASP cc_start: 0.7983 (t0) cc_final: 0.7654 (t0) REVERT: A 753 ASN cc_start: 0.8333 (t0) cc_final: 0.8122 (t0) REVERT: A 787 LYS cc_start: 0.6180 (mttp) cc_final: 0.5758 (mmtm) REVERT: A 848 GLU cc_start: 0.8558 (mp0) cc_final: 0.8150 (mp0) outliers start: 19 outliers final: 9 residues processed: 91 average time/residue: 1.2852 time to fit residues: 125.2747 Evaluate side-chains 79 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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 291 LEU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 805 VAL 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 68 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 61 optimal weight: 0.3980 chunk 16 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 9 optimal weight: 0.4980 chunk 74 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.182540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.137271 restraints weight = 12343.248| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.74 r_work: 0.3620 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9550 Z= 0.170 Angle : 0.542 5.932 13370 Z= 0.294 Chirality : 0.037 0.168 1503 Planarity : 0.004 0.034 1325 Dihedral : 21.003 160.150 2382 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.45 % Allowed : 13.36 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.29), residues: 847 helix: 0.39 (0.28), residues: 374 sheet: 0.01 (0.46), residues: 131 loop : -1.16 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 24 HIS 0.007 0.001 HIS A 824 PHE 0.014 0.001 PHE A 242 TYR 0.013 0.001 TYR A 822 ARG 0.002 0.000 ARG A 67 *********************** 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 104 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 71 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 291 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7404 (mm) REVERT: A 404 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8271 (mt-10) REVERT: A 498 ILE cc_start: 0.7640 (OUTLIER) cc_final: 0.7152 (pt) REVERT: A 572 ARG cc_start: 0.7226 (mtm110) cc_final: 0.6948 (ttm170) REVERT: A 581 MET cc_start: 0.6479 (OUTLIER) cc_final: 0.6250 (tmt) REVERT: A 697 MET cc_start: 0.8660 (ttp) cc_final: 0.8405 (ttp) REVERT: A 753 ASN cc_start: 0.8317 (t0) cc_final: 0.7972 (t0) REVERT: A 787 LYS cc_start: 0.6122 (mttp) cc_final: 0.5682 (mmtm) REVERT: A 848 GLU cc_start: 0.8563 (mp0) cc_final: 0.8255 (mp0) outliers start: 33 outliers final: 12 residues processed: 88 average time/residue: 1.2914 time to fit residues: 121.3312 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 : 0.783 ------------------------------------------------------------------------------- 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 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 581 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 14 optimal weight: 20.0000 chunk 60 optimal weight: 2.9990 chunk 13 optimal weight: 20.0000 chunk 85 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 50 optimal weight: 7.9990 chunk 34 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN A 834 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.179514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.133475 restraints weight = 12246.327| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.75 r_work: 0.3591 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 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 : 0.004 0.030 9550 Z= 0.242 Angle : 0.581 7.497 13370 Z= 0.310 Chirality : 0.039 0.173 1503 Planarity : 0.004 0.039 1325 Dihedral : 20.999 161.433 2382 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.37 % Allowed : 16.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.29), residues: 847 helix: 0.32 (0.28), residues: 379 sheet: -0.05 (0.46), residues: 129 loop : -1.22 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 24 HIS 0.006 0.001 HIS A 824 PHE 0.029 0.002 PHE A 242 TYR 0.018 0.001 TYR A 217 ARG 0.003 0.000 ARG A 836 *********************** 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 96 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 291 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7472 (mm) REVERT: A 404 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8288 (mt-10) REVERT: A 436 GLN cc_start: 0.6888 (mm110) cc_final: 0.6518 (mm-40) REVERT: A 572 ARG cc_start: 0.7177 (mtm110) cc_final: 0.6764 (ttm110) REVERT: A 581 MET cc_start: 0.6501 (OUTLIER) cc_final: 0.6077 (tmt) REVERT: A 753 ASN cc_start: 0.8399 (t0) cc_final: 0.7893 (t0) REVERT: A 787 LYS cc_start: 0.6174 (mttp) cc_final: 0.5736 (mmtp) REVERT: A 848 GLU cc_start: 0.8591 (mp0) cc_final: 0.8248 (mp0) outliers start: 25 outliers final: 13 residues processed: 84 average time/residue: 1.4030 time to fit residues: 125.5454 Evaluate side-chains 78 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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 245 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 299 LYS 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 54 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.175988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.130863 restraints weight = 12297.680| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.68 r_work: 0.3541 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 9550 Z= 0.360 Angle : 0.666 7.050 13370 Z= 0.353 Chirality : 0.043 0.190 1503 Planarity : 0.005 0.049 1325 Dihedral : 21.128 166.175 2382 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.18 % Allowed : 16.33 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.28), residues: 847 helix: -0.03 (0.27), residues: 379 sheet: 0.01 (0.47), residues: 124 loop : -1.25 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 323 HIS 0.010 0.002 HIS A 824 PHE 0.025 0.002 PHE A 242 TYR 0.025 0.002 TYR A 217 ARG 0.004 0.001 ARG A 836 *********************** 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 97 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 66 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 404 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8313 (mt-10) REVERT: A 572 ARG cc_start: 0.7169 (mtm110) cc_final: 0.6672 (ttm110) REVERT: A 753 ASN cc_start: 0.8475 (t0) cc_final: 0.7795 (t0) REVERT: A 787 LYS cc_start: 0.6459 (mttp) cc_final: 0.5993 (mmtm) REVERT: A 848 GLU cc_start: 0.8580 (mp0) cc_final: 0.8204 (mp0) outliers start: 31 outliers final: 14 residues processed: 84 average time/residue: 1.4588 time to fit residues: 131.2262 Evaluate side-chains 74 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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 77 VAL 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 245 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 540 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 34 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.181389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.136672 restraints weight = 12181.576| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.68 r_work: 0.3613 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9550 Z= 0.171 Angle : 0.547 8.110 13370 Z= 0.294 Chirality : 0.037 0.182 1503 Planarity : 0.004 0.036 1325 Dihedral : 20.928 163.638 2382 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.05 % Allowed : 17.68 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.29), residues: 847 helix: 0.54 (0.28), residues: 375 sheet: 0.02 (0.46), residues: 129 loop : -1.09 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 24 HIS 0.006 0.001 HIS A 824 PHE 0.019 0.001 PHE A 242 TYR 0.011 0.001 TYR A 217 ARG 0.006 0.000 ARG A 836 *********************** 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 101 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 71 time to evaluate : 0.846 Fit side-chains revert: symmetry clash REVERT: A 404 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8302 (mt-10) REVERT: A 436 GLN cc_start: 0.6865 (mm110) cc_final: 0.6440 (mm-40) REVERT: A 442 PHE cc_start: 0.7787 (OUTLIER) cc_final: 0.6994 (m-10) REVERT: A 572 ARG cc_start: 0.7260 (mtm110) cc_final: 0.6898 (ttm170) REVERT: A 753 ASN cc_start: 0.8356 (t0) cc_final: 0.7797 (t0) REVERT: A 787 LYS cc_start: 0.6155 (mttp) cc_final: 0.5745 (mmtm) REVERT: A 845 VAL cc_start: 0.8341 (OUTLIER) cc_final: 0.7781 (p) REVERT: A 846 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7648 (mp0) REVERT: A 848 GLU cc_start: 0.8618 (mp0) cc_final: 0.8300 (mp0) outliers start: 30 outliers final: 14 residues processed: 92 average time/residue: 1.3421 time to fit residues: 133.2876 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 : 0.935 ------------------------------------------------------------------------------- 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 245 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 846 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 50 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 67 optimal weight: 0.0010 chunk 39 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.178135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.132899 restraints weight = 12319.016| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.70 r_work: 0.3573 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9550 Z= 0.271 Angle : 0.601 8.463 13370 Z= 0.320 Chirality : 0.040 0.195 1503 Planarity : 0.004 0.040 1325 Dihedral : 20.991 163.882 2382 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.32 % Allowed : 18.35 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.29), residues: 847 helix: 0.37 (0.27), residues: 379 sheet: 0.00 (0.46), residues: 129 loop : -1.15 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 323 HIS 0.008 0.001 HIS A 824 PHE 0.021 0.002 PHE A 242 TYR 0.019 0.002 TYR A 217 ARG 0.004 0.000 ARG A 566 *********************** 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 93 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 61 time to evaluate : 0.897 Fit side-chains REVERT: A 125 MET cc_start: 0.2524 (OUTLIER) cc_final: 0.1363 (tmm) REVERT: A 291 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7533 (mm) REVERT: A 394 ARG cc_start: 0.8142 (mtt180) cc_final: 0.7859 (mtt180) REVERT: A 399 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8659 (mm) REVERT: A 404 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8320 (mt-10) REVERT: A 442 PHE cc_start: 0.7821 (OUTLIER) cc_final: 0.7155 (m-10) REVERT: A 551 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6877 (pt0) REVERT: A 572 ARG cc_start: 0.7244 (mtm110) cc_final: 0.6846 (ttm110) REVERT: A 753 ASN cc_start: 0.8410 (t0) cc_final: 0.7775 (t0) REVERT: A 787 LYS cc_start: 0.6400 (mttp) cc_final: 0.5878 (mmtm) REVERT: A 845 VAL cc_start: 0.8339 (OUTLIER) cc_final: 0.7790 (p) REVERT: A 846 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7649 (mp0) REVERT: A 848 GLU cc_start: 0.8619 (mp0) cc_final: 0.8293 (mp0) REVERT: A 861 ILE cc_start: 0.7408 (OUTLIER) cc_final: 0.7189 (mt) outliers start: 32 outliers final: 12 residues processed: 81 average time/residue: 1.2661 time to fit residues: 109.9878 Evaluate side-chains 79 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 130 ILE 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 291 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 551 GLU Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 846 GLU 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 65 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 90 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 7 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 72 optimal weight: 0.0570 chunk 44 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.183779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.138996 restraints weight = 12457.016| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.72 r_work: 0.3645 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9550 Z= 0.149 Angle : 0.542 8.133 13370 Z= 0.291 Chirality : 0.036 0.183 1503 Planarity : 0.003 0.036 1325 Dihedral : 20.857 160.877 2382 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.37 % Allowed : 18.76 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.29), residues: 847 helix: 0.74 (0.28), residues: 374 sheet: 0.15 (0.46), residues: 129 loop : -1.01 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 548 HIS 0.006 0.001 HIS A 824 PHE 0.021 0.001 PHE A 242 TYR 0.010 0.001 TYR A 729 ARG 0.003 0.000 ARG A 68 *********************** 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 97 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.885 Fit side-chains REVERT: A 105 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.7195 (tt) REVERT: A 125 MET cc_start: 0.2436 (OUTLIER) cc_final: 0.1316 (tmm) REVERT: A 291 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7451 (mm) REVERT: A 391 ARG cc_start: 0.8244 (mmp-170) cc_final: 0.7857 (tpp-160) REVERT: A 394 ARG cc_start: 0.8068 (mtt180) cc_final: 0.7758 (mtt180) REVERT: A 404 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8236 (mt-10) REVERT: A 436 GLN cc_start: 0.6803 (mm110) cc_final: 0.6403 (mm-40) REVERT: A 442 PHE cc_start: 0.7540 (OUTLIER) cc_final: 0.6955 (m-10) REVERT: A 498 ILE cc_start: 0.7664 (pt) cc_final: 0.7235 (pt) REVERT: A 551 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6506 (pm20) REVERT: A 572 ARG cc_start: 0.7171 (mtm110) cc_final: 0.6843 (ttm170) REVERT: A 669 ARG cc_start: 0.8483 (mtt180) cc_final: 0.8177 (mtt180) REVERT: A 753 ASN cc_start: 0.8320 (t0) cc_final: 0.7774 (t0) REVERT: A 787 LYS cc_start: 0.6170 (mttp) cc_final: 0.5722 (mmtp) REVERT: A 845 VAL cc_start: 0.8328 (OUTLIER) cc_final: 0.7867 (p) REVERT: A 846 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7622 (mp0) REVERT: A 848 GLU cc_start: 0.8643 (mp0) cc_final: 0.8274 (mp0) outliers start: 25 outliers final: 10 residues processed: 89 average time/residue: 1.1744 time to fit residues: 112.3772 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 : 0.813 ------------------------------------------------------------------------------- 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 105 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 291 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 551 GLU Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 845 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 67 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 41 optimal weight: 0.3980 chunk 27 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 35 optimal weight: 0.9980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 707 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.177565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.132295 restraints weight = 12220.819| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.72 r_work: 0.3567 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9550 Z= 0.303 Angle : 0.640 9.347 13370 Z= 0.337 Chirality : 0.041 0.173 1503 Planarity : 0.004 0.039 1325 Dihedral : 20.962 162.514 2382 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.78 % Allowed : 19.30 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.29), residues: 847 helix: 0.43 (0.28), residues: 377 sheet: 0.07 (0.46), residues: 129 loop : -1.11 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 323 HIS 0.004 0.001 HIS A 384 PHE 0.027 0.002 PHE A 242 TYR 0.021 0.002 TYR A 217 ARG 0.003 0.000 ARG A 394 *********************** 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 88 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 60 time to evaluate : 0.863 Fit side-chains REVERT: A 105 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7044 (tt) REVERT: A 125 MET cc_start: 0.2315 (OUTLIER) cc_final: 0.1243 (tmm) REVERT: A 291 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7532 (mm) REVERT: A 391 ARG cc_start: 0.8309 (mmp-170) cc_final: 0.7950 (tpp-160) REVERT: A 394 ARG cc_start: 0.8155 (mtt180) cc_final: 0.7837 (mtt180) REVERT: A 404 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8337 (mt-10) REVERT: A 442 PHE cc_start: 0.7712 (OUTLIER) cc_final: 0.7179 (m-10) REVERT: A 498 ILE cc_start: 0.7823 (pt) cc_final: 0.7368 (pt) REVERT: A 551 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6781 (pt0) REVERT: A 572 ARG cc_start: 0.7296 (mtm110) cc_final: 0.6887 (ttm110) REVERT: A 738 ASP cc_start: 0.8163 (t0) cc_final: 0.7534 (t0) REVERT: A 753 ASN cc_start: 0.8428 (t0) cc_final: 0.7754 (t0) REVERT: A 787 LYS cc_start: 0.6392 (mttp) cc_final: 0.5847 (mmtm) REVERT: A 845 VAL cc_start: 0.8318 (OUTLIER) cc_final: 0.7839 (p) REVERT: A 846 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7586 (mp0) REVERT: A 848 GLU cc_start: 0.8652 (mp0) cc_final: 0.8311 (mp0) outliers start: 28 outliers final: 11 residues processed: 79 average time/residue: 1.2051 time to fit residues: 102.3926 Evaluate side-chains 76 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.823 ------------------------------------------------------------------------------- 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 105 LEU Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 130 ILE 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 291 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 551 GLU Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 846 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 80 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 82 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN A 824 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.181636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.136719 restraints weight = 12264.421| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.72 r_work: 0.3624 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.2272 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= 0.181 Angle : 0.572 9.206 13370 Z= 0.304 Chirality : 0.037 0.179 1503 Planarity : 0.004 0.038 1325 Dihedral : 20.835 160.864 2382 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.97 % Allowed : 20.24 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.29), residues: 847 helix: 0.73 (0.28), residues: 373 sheet: 0.13 (0.46), residues: 129 loop : -1.07 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 548 HIS 0.005 0.001 HIS A 643 PHE 0.022 0.001 PHE A 242 TYR 0.014 0.001 TYR A 729 ARG 0.003 0.000 ARG A 789 ********************** 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 85 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 0.824 Fit side-chains REVERT: A 105 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7305 (tt) REVERT: A 291 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7519 (mm) REVERT: A 391 ARG cc_start: 0.8255 (mmp-170) cc_final: 0.7887 (tpp-160) REVERT: A 394 ARG cc_start: 0.8108 (mtt180) cc_final: 0.7842 (mtt180) REVERT: A 404 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8291 (mt-10) REVERT: A 436 GLN cc_start: 0.6870 (mm110) cc_final: 0.6461 (mm-40) REVERT: A 442 PHE cc_start: 0.7571 (OUTLIER) cc_final: 0.6991 (m-10) REVERT: A 498 ILE cc_start: 0.7741 (pt) cc_final: 0.7305 (pt) REVERT: A 551 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6853 (pt0) REVERT: A 572 ARG cc_start: 0.7196 (mtm110) cc_final: 0.6857 (ttm170) REVERT: A 738 ASP cc_start: 0.8017 (t0) cc_final: 0.7421 (t0) REVERT: A 753 ASN cc_start: 0.8332 (t0) cc_final: 0.7763 (t0) REVERT: A 787 LYS cc_start: 0.6235 (mttp) cc_final: 0.5767 (mmtp) REVERT: A 845 VAL cc_start: 0.8306 (OUTLIER) cc_final: 0.7871 (p) REVERT: A 846 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7659 (mp0) REVERT: A 848 GLU cc_start: 0.8641 (mp0) cc_final: 0.8296 (mp0) outliers start: 22 outliers final: 12 residues processed: 79 average time/residue: 1.3011 time to fit residues: 110.4775 Evaluate side-chains 81 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.815 ------------------------------------------------------------------------------- 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 105 LEU Chi-restraints excluded: chain A residue 130 ILE 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 291 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 551 GLU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 846 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 55 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 15 optimal weight: 20.0000 chunk 82 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.179167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.134129 restraints weight = 12261.407| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.72 r_work: 0.3588 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9550 Z= 0.245 Angle : 0.604 9.629 13370 Z= 0.319 Chirality : 0.039 0.177 1503 Planarity : 0.004 0.038 1325 Dihedral : 20.894 161.104 2382 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.37 % Allowed : 19.84 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.29), residues: 847 helix: 0.56 (0.27), residues: 376 sheet: 0.09 (0.46), residues: 129 loop : -1.10 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 323 HIS 0.003 0.001 HIS A 643 PHE 0.021 0.002 PHE A 242 TYR 0.017 0.001 TYR A 217 ARG 0.002 0.000 ARG A 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6375.15 seconds wall clock time: 111 minutes 40.97 seconds (6700.97 seconds total)