Starting phenix.real_space_refine on Thu Jun 4 10:54:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10oz_75366/06_2026/10oz_75366.cif Found real_map, /net/cci-nas-00/data/ceres_data/10oz_75366/06_2026/10oz_75366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/10oz_75366/06_2026/10oz_75366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10oz_75366/06_2026/10oz_75366.map" model { file = "/net/cci-nas-00/data/ceres_data/10oz_75366/06_2026/10oz_75366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10oz_75366/06_2026/10oz_75366.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.034 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 2 5.49 5 Mg 2 5.21 5 S 72 5.16 5 C 7762 2.51 5 N 2055 2.21 5 O 2252 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12147 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5805 Classifications: {'peptide': 720} Link IDs: {'PTRANS': 26, 'TRANS': 693} Chain breaks: 1 Chain: "B" Number of atoms: 5836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 724, 5836 Classifications: {'peptide': 724} Link IDs: {'PTRANS': 26, 'TRANS': 697} Chain breaks: 1 Chain: "C" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 193 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 3, 'TRANS': 20} Chain breaks: 1 Chain: "D" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 197 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 3, 'TRANS': 21} Chain breaks: 1 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 58 Unusual residues: {' MG': 1, ' ZN': 1, 'PCG': 1, 'VIA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 58 Unusual residues: {' MG': 1, ' ZN': 1, 'PCG': 1, 'VIA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 3.31, per 1000 atoms: 0.27 Number of scatterers: 12147 At special positions: 0 Unit cell: (113.258, 93.4171, 144.673, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 72 16.00 P 2 15.00 Mg 2 11.99 O 2252 8.00 N 2055 7.00 C 7762 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: 1.15 Conformation dependent library (CDL) restraints added in 670.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 904 " pdb="ZN ZN A 904 " - pdb=" NE2 HIS A 542 " pdb="ZN ZN A 904 " - pdb=" NE2 HIS A 578 " pdb=" ZN B 904 " pdb="ZN ZN B 904 " - pdb=" NE2 HIS B 542 " pdb="ZN ZN B 904 " - pdb=" NE2 HIS B 578 " 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2870 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 4 sheets defined 59.4% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 49 through 66 Processing helix chain 'A' and resid 70 through 87 Processing helix chain 'A' and resid 117 through 122 removed outlier: 3.557A pdb=" N ASN A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 128 removed outlier: 3.518A pdb=" N GLU A 128 " --> pdb=" O PRO A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 145 removed outlier: 3.527A pdb=" N GLY A 139 " --> pdb=" O VAL A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 168 Processing helix chain 'A' and resid 201 through 246 removed outlier: 3.841A pdb=" N ILE A 217 " --> pdb=" O SER A 213 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE A 218 " --> pdb=" O PHE A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 263 removed outlier: 3.598A pdb=" N THR A 262 " --> pdb=" O LYS A 258 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 351 Processing helix chain 'A' and resid 410 through 427 Processing helix chain 'A' and resid 427 through 455 removed outlier: 4.010A pdb=" N THR A 431 " --> pdb=" O SER A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 470 Processing helix chain 'A' and resid 492 through 507 Processing helix chain 'A' and resid 508 through 513 Processing helix chain 'A' and resid 516 through 531 removed outlier: 3.629A pdb=" N TYR A 531 " --> pdb=" O VAL A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 556 removed outlier: 3.736A pdb=" N ALA A 543 " --> pdb=" O ASN A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 563 removed outlier: 3.708A pdb=" N LYS A 561 " --> pdb=" O LYS A 558 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A 563 " --> pdb=" O GLN A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 577 Processing helix chain 'A' and resid 586 through 593 Processing helix chain 'A' and resid 595 through 600 Processing helix chain 'A' and resid 604 through 620 Processing helix chain 'A' and resid 630 through 647 Processing helix chain 'A' and resid 649 through 666 removed outlier: 4.546A pdb=" N GLY A 658 " --> pdb=" O ILE A 654 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLU A 659 " --> pdb=" O LYS A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 690 Processing helix chain 'A' and resid 691 through 694 Processing helix chain 'A' and resid 696 through 723 Processing helix chain 'A' and resid 731 through 736 removed outlier: 3.788A pdb=" N LYS A 735 " --> pdb=" O ARG A 732 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ASN A 736 " --> pdb=" O GLU A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 749 removed outlier: 3.636A pdb=" N ILE A 746 " --> pdb=" O GLN A 742 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP A 747 " --> pdb=" O VAL A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 761 removed outlier: 3.905A pdb=" N LEU A 753 " --> pdb=" O ILE A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 783 removed outlier: 3.772A pdb=" N LEU A 768 " --> pdb=" O CYS A 764 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG A 775 " --> pdb=" O CYS A 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 66 removed outlier: 3.823A pdb=" N ALA B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 87 removed outlier: 3.635A pdb=" N ALA B 74 " --> pdb=" O SER B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 122 Processing helix chain 'B' and resid 124 through 128 removed outlier: 3.720A pdb=" N GLU B 128 " --> pdb=" O PRO B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 145 removed outlier: 3.605A pdb=" N GLY B 139 " --> pdb=" O VAL B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 168 Processing helix chain 'B' and resid 201 through 246 removed outlier: 3.825A pdb=" N ILE B 217 " --> pdb=" O SER B 213 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE B 218 " --> pdb=" O PHE B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 262 removed outlier: 3.687A pdb=" N THR B 262 " --> pdb=" O LYS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 268 removed outlier: 4.020A pdb=" N ASN B 268 " --> pdb=" O ARG B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 351 Processing helix chain 'B' and resid 359 through 362 Processing helix chain 'B' and resid 410 through 455 removed outlier: 4.796A pdb=" N LEU B 429 " --> pdb=" O GLY B 425 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ASN B 430 " --> pdb=" O TRP B 426 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 470 Processing helix chain 'B' and resid 492 through 507 removed outlier: 3.829A pdb=" N LEU B 507 " --> pdb=" O MET B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 513 removed outlier: 3.571A pdb=" N PHE B 513 " --> pdb=" O LEU B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 531 removed outlier: 3.625A pdb=" N TYR B 531 " --> pdb=" O VAL B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 556 Processing helix chain 'B' and resid 559 through 563 Processing helix chain 'B' and resid 564 through 577 Processing helix chain 'B' and resid 586 through 593 Processing helix chain 'B' and resid 595 through 601 removed outlier: 3.549A pdb=" N GLN B 599 " --> pdb=" O HIS B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 619 Processing helix chain 'B' and resid 630 through 647 Processing helix chain 'B' and resid 649 through 666 removed outlier: 4.701A pdb=" N GLY B 658 " --> pdb=" O ILE B 654 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N GLU B 659 " --> pdb=" O LYS B 655 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE B 660 " --> pdb=" O ARG B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 690 Processing helix chain 'B' and resid 691 through 694 Processing helix chain 'B' and resid 696 through 721 removed outlier: 4.072A pdb=" N ARG B 702 " --> pdb=" O PRO B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 736 No H-bonds generated for 'chain 'B' and resid 734 through 736' Processing helix chain 'B' and resid 737 through 749 removed outlier: 3.666A pdb=" N GLY B 744 " --> pdb=" O SER B 740 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE B 745 " --> pdb=" O MET B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 761 removed outlier: 4.026A pdb=" N LEU B 753 " --> pdb=" O ILE B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 783 removed outlier: 3.819A pdb=" N LEU B 768 " --> pdb=" O CYS B 764 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ARG B 775 " --> pdb=" O CYS B 771 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B 777 " --> pdb=" O LYS B 773 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 38 Processing sheet with id=AA1, first strand: chain 'A' and resid 130 through 132 removed outlier: 3.674A pdb=" N ARG A 99 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N MET A 93 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ALA A 88 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LYS A 194 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LEU A 186 " --> pdb=" O CYS A 96 " (cutoff:3.500A) removed outlier: 11.185A pdb=" N ALA A 98 " --> pdb=" O GLU A 184 " (cutoff:3.500A) removed outlier: 12.407A pdb=" N GLU A 184 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N VAL A 185 " --> pdb=" O MET A 181 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N MET A 181 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA A 187 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 325 through 330 removed outlier: 3.821A pdb=" N LYS A 314 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N CYS A 269 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ARG A 403 " --> pdb=" O CYS A 269 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY A 396 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASN A 381 " --> pdb=" O ASN A 402 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 130 through 132 removed outlier: 3.601A pdb=" N ARG B 99 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N MET B 93 " --> pdb=" O LYS B 108 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA B 88 " --> pdb=" O LYS B 194 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LYS B 194 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LEU B 186 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 11.244A pdb=" N ALA B 98 " --> pdb=" O GLU B 184 " (cutoff:3.500A) removed outlier: 12.589A pdb=" N GLU B 184 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE B 179 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N VAL B 188 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR B 177 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N MET B 190 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU B 175 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 325 through 330 removed outlier: 3.693A pdb=" N LYS B 314 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N CYS B 269 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ARG B 403 " --> pdb=" O CYS B 269 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG B 271 " --> pdb=" O TYR B 401 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL B 395 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY B 396 " --> pdb=" O ILE B 387 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ASN B 381 " --> pdb=" O ASN B 402 " (cutoff:3.500A) 704 hydrogen bonds defined for protein. 2034 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.19 Time building geometry restraints manager: 1.44 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: 2769 1.33 - 1.45: 2520 1.45 - 1.57: 6992 1.57 - 1.69: 12 1.69 - 1.81: 114 Bond restraints: 12407 Sorted by residual: bond pdb=" C7 VIA B 902 " pdb=" S10 VIA B 902 " ideal model delta sigma weight residual 1.765 1.662 0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" C7 VIA A 901 " pdb=" S10 VIA A 901 " ideal model delta sigma weight residual 1.765 1.664 0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" C8 PCG A 902 " pdb=" N9 PCG A 902 " ideal model delta sigma weight residual 1.375 1.431 -0.056 2.00e-02 2.50e+03 7.79e+00 bond pdb=" C8 PCG B 901 " pdb=" N9 PCG B 901 " ideal model delta sigma weight residual 1.375 1.430 -0.055 2.00e-02 2.50e+03 7.66e+00 bond pdb=" C30 VIA B 902 " pdb=" N29 VIA B 902 " ideal model delta sigma weight residual 1.321 1.374 -0.053 2.00e-02 2.50e+03 7.03e+00 ... (remaining 12402 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 16608 2.26 - 4.51: 141 4.51 - 6.77: 36 6.77 - 9.03: 7 9.03 - 11.28: 4 Bond angle restraints: 16796 Sorted by residual: angle pdb=" C3' PCG A 902 " pdb=" O3' PCG A 902 " pdb=" PA PCG A 902 " ideal model delta sigma weight residual 112.82 123.48 -10.66 3.00e+00 1.11e-01 1.26e+01 angle pdb=" C3' PCG B 901 " pdb=" O3' PCG B 901 " pdb=" PA PCG B 901 " ideal model delta sigma weight residual 112.82 123.37 -10.55 3.00e+00 1.11e-01 1.24e+01 angle pdb=" CA LEU B 498 " pdb=" CB LEU B 498 " pdb=" CG LEU B 498 " ideal model delta sigma weight residual 116.30 127.58 -11.28 3.50e+00 8.16e-02 1.04e+01 angle pdb=" C16 VIA A 901 " pdb=" N17 VIA A 901 " pdb=" C18 VIA A 901 " ideal model delta sigma weight residual 110.29 119.07 -8.78 3.00e+00 1.11e-01 8.56e+00 angle pdb=" C16 VIA B 902 " pdb=" N17 VIA B 902 " pdb=" C18 VIA B 902 " ideal model delta sigma weight residual 110.29 118.81 -8.52 3.00e+00 1.11e-01 8.07e+00 ... (remaining 16791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.80: 6761 23.80 - 47.59: 631 47.59 - 71.39: 113 71.39 - 95.19: 47 95.19 - 118.99: 5 Dihedral angle restraints: 7557 sinusoidal: 3156 harmonic: 4401 Sorted by residual: dihedral pdb=" CA TYR B 401 " pdb=" C TYR B 401 " pdb=" N ASN B 402 " pdb=" CA ASN B 402 " ideal model delta harmonic sigma weight residual 180.00 159.62 20.38 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" C15 VIA B 902 " pdb=" C19 VIA B 902 " pdb=" N14 VIA B 902 " pdb=" C18 VIA B 902 " ideal model delta sinusoidal sigma weight residual 57.20 -61.79 118.99 1 3.00e+01 1.11e-03 1.58e+01 dihedral pdb=" C15 VIA A 901 " pdb=" C19 VIA A 901 " pdb=" N14 VIA A 901 " pdb=" C18 VIA A 901 " ideal model delta sinusoidal sigma weight residual 57.20 -60.44 117.64 1 3.00e+01 1.11e-03 1.56e+01 ... (remaining 7554 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1551 0.050 - 0.101: 280 0.101 - 0.151: 40 0.151 - 0.201: 2 0.201 - 0.252: 4 Chirality restraints: 1877 Sorted by residual: chirality pdb=" C4' PCG B 901 " pdb=" C3' PCG B 901 " pdb=" C5' PCG B 901 " pdb=" O4' PCG B 901 " both_signs ideal model delta sigma weight residual False -2.50 -2.25 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" C1' PCG B 901 " pdb=" C2' PCG B 901 " pdb=" N9 PCG B 901 " pdb=" O4' PCG B 901 " both_signs ideal model delta sigma weight residual False 2.45 2.69 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" C1' PCG A 902 " pdb=" C2' PCG A 902 " pdb=" N9 PCG A 902 " pdb=" O4' PCG A 902 " both_signs ideal model delta sigma weight residual False 2.45 2.69 -0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 1874 not shown) Planarity restraints: 2130 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 208 " -0.015 2.00e-02 2.50e+03 1.09e-02 2.08e+00 pdb=" CG PHE A 208 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE A 208 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 208 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 208 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 208 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 208 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 304 " -0.024 5.00e-02 4.00e+02 3.58e-02 2.05e+00 pdb=" N PRO A 305 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 305 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 305 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 770 " 0.007 2.00e-02 2.50e+03 1.41e-02 1.99e+00 pdb=" C GLY A 770 " -0.024 2.00e-02 2.50e+03 pdb=" O GLY A 770 " 0.009 2.00e-02 2.50e+03 pdb=" N CYS A 771 " 0.008 2.00e-02 2.50e+03 ... (remaining 2127 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 176 2.67 - 3.23: 11373 3.23 - 3.79: 19342 3.79 - 4.34: 25624 4.34 - 4.90: 43117 Nonbonded interactions: 99632 Sorted by model distance: nonbonded pdb=" OD1 ASP B 689 " pdb="ZN ZN B 904 " model vdw 2.118 2.230 nonbonded pdb=" OD1 ASP A 689 " pdb="ZN ZN A 904 " model vdw 2.133 2.230 nonbonded pdb=" OD1 ASP B 579 " pdb="MG MG B 903 " model vdw 2.153 2.170 nonbonded pdb=" OD1 ASP A 579 " pdb="MG MG A 903 " model vdw 2.227 2.170 nonbonded pdb=" O SER B 213 " pdb=" OG SER B 216 " model vdw 2.227 3.040 ... (remaining 99627 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 44 through 784 or resid 903 through 904)) selection = (chain 'B' and (resid 44 through 280 or resid 302 through 784 or resid 903 throu \ gh 904)) } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 26 through 40 or resid 52 through 60)) } 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: 2.160 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.790 Find NCS groups from input model: 0.240 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 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 : 0.004 0.103 12411 Z= 0.189 Angle : 0.574 11.283 16796 Z= 0.265 Chirality : 0.040 0.252 1877 Planarity : 0.003 0.036 2130 Dihedral : 19.592 118.986 4687 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.34 % Allowed : 22.98 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.23), residues: 1477 helix: 2.12 (0.19), residues: 805 sheet: 0.71 (0.44), residues: 130 loop : 0.83 (0.29), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 172 TYR 0.017 0.001 TYR A 272 PHE 0.024 0.001 PHE A 208 TRP 0.010 0.001 TRP A 426 HIS 0.002 0.001 HIS B 578 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.19 (12407) covalent geometry : angle 0.57395 / 0.27 (16796) hydrogen bonds : bond 0.12000 / 7.59 ( 704) hydrogen bonds : angle 5.16854 / 3.67 ( 2034) metal coordination : bond 0.00167 / 0.08 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: A 309 GLU cc_start: 0.6315 (mm-30) cc_final: 0.5379 (mt-10) REVERT: A 475 SER cc_start: 0.5828 (OUTLIER) cc_final: 0.5595 (p) REVERT: A 489 PHE cc_start: 0.7667 (t80) cc_final: 0.7357 (m-80) REVERT: A 509 LEU cc_start: 0.7763 (mt) cc_final: 0.7559 (mt) REVERT: A 558 LYS cc_start: 0.7872 (mttt) cc_final: 0.7492 (mmtt) REVERT: A 603 HIS cc_start: 0.7665 (m90) cc_final: 0.7187 (m90) REVERT: B 93 MET cc_start: 0.8585 (ttt) cc_final: 0.8101 (ttt) REVERT: B 161 ASP cc_start: 0.8177 (t0) cc_final: 0.7021 (p0) REVERT: B 163 MET cc_start: 0.8369 (mmm) cc_final: 0.7640 (mmm) REVERT: B 279 MET cc_start: 0.7611 (mmm) cc_final: 0.7320 (mmt) REVERT: B 340 ILE cc_start: 0.8531 (mm) cc_final: 0.8180 (mt) REVERT: B 511 GLN cc_start: 0.7710 (mm-40) cc_final: 0.7279 (pt0) REVERT: B 751 LEU cc_start: 0.6604 (mm) cc_final: 0.6404 (mm) REVERT: B 757 LEU cc_start: 0.6758 (OUTLIER) cc_final: 0.6389 (mp) REVERT: D 60 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7122 (pp) outliers start: 31 outliers final: 25 residues processed: 181 average time/residue: 0.1131 time to fit residues: 29.9620 Evaluate side-chains 182 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 763 ASP Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 586 ASN Chi-restraints excluded: chain B residue 606 MET Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 763 ASP Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain D residue 60 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 0.2980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 742 GLN B 193 ASN B 243 ASN ** B 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 742 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.185609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.126272 restraints weight = 13897.293| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.53 r_work: 0.3280 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.0655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12411 Z= 0.115 Angle : 0.516 8.585 16796 Z= 0.255 Chirality : 0.039 0.129 1877 Planarity : 0.004 0.039 2130 Dihedral : 9.854 111.073 1746 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.72 % Allowed : 20.94 % Favored : 76.34 % 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: 2.41 (0.22), residues: 1477 helix: 2.27 (0.18), residues: 812 sheet: 1.11 (0.44), residues: 121 loop : 0.80 (0.29), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 254 TYR 0.014 0.001 TYR A 272 PHE 0.029 0.001 PHE A 208 TRP 0.006 0.001 TRP B 140 HIS 0.002 0.001 HIS A 578 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (12407) covalent geometry : angle 0.51639 / 0.26 (16796) hydrogen bonds : bond 0.03992 / 2.65 ( 704) hydrogen bonds : angle 4.09828 / 2.92 ( 2034) metal coordination : bond 0.00264 / 0.13 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: A 156 ASN cc_start: 0.8166 (t0) cc_final: 0.7944 (t0) REVERT: A 190 MET cc_start: 0.7679 (mtt) cc_final: 0.7356 (mtp) REVERT: A 309 GLU cc_start: 0.6353 (mm-30) cc_final: 0.5342 (mt-10) REVERT: A 489 PHE cc_start: 0.7700 (t80) cc_final: 0.7366 (m-80) REVERT: A 558 LYS cc_start: 0.7836 (mttt) cc_final: 0.7455 (mmtt) REVERT: A 603 HIS cc_start: 0.7595 (m90) cc_final: 0.7127 (m90) REVERT: A 732 ARG cc_start: 0.5543 (mmt180) cc_final: 0.5299 (mmt180) REVERT: A 763 ASP cc_start: 0.4890 (p0) cc_final: 0.4526 (p0) REVERT: A 765 PHE cc_start: 0.7447 (t80) cc_final: 0.7103 (t80) REVERT: B 161 ASP cc_start: 0.7757 (t0) cc_final: 0.6620 (p0) REVERT: B 166 GLN cc_start: 0.7752 (tm-30) cc_final: 0.7539 (tt0) REVERT: B 279 MET cc_start: 0.7558 (mmm) cc_final: 0.7280 (mmt) REVERT: B 340 ILE cc_start: 0.8515 (mm) cc_final: 0.8156 (mt) REVERT: B 511 GLN cc_start: 0.7835 (mm-40) cc_final: 0.7468 (pt0) REVERT: B 751 LEU cc_start: 0.6668 (mm) cc_final: 0.6434 (mm) REVERT: D 60 LEU cc_start: 0.6496 (OUTLIER) cc_final: 0.6146 (pp) outliers start: 36 outliers final: 18 residues processed: 195 average time/residue: 0.1042 time to fit residues: 30.2103 Evaluate side-chains 181 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain D residue 60 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 147 optimal weight: 0.0980 chunk 89 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 146 optimal weight: 4.9990 chunk 145 optimal weight: 0.3980 chunk 9 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 700 GLN ** 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 = 0.4114 r_free = 0.4114 target = 0.185961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.126738 restraints weight = 14049.623| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.55 r_work: 0.3303 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12411 Z= 0.105 Angle : 0.474 9.544 16796 Z= 0.240 Chirality : 0.038 0.130 1877 Planarity : 0.003 0.040 2130 Dihedral : 8.229 92.232 1709 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.33 % Allowed : 20.03 % Favored : 76.64 % 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: 2.40 (0.23), residues: 1477 helix: 2.28 (0.18), residues: 825 sheet: 0.94 (0.45), residues: 125 loop : 0.77 (0.30), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 172 TYR 0.015 0.001 TYR A 272 PHE 0.027 0.001 PHE A 208 TRP 0.005 0.001 TRP B 240 HIS 0.002 0.000 HIS B 578 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (12407) covalent geometry : angle 0.47422 / 0.24 (16796) hydrogen bonds : bond 0.03707 / 2.47 ( 704) hydrogen bonds : angle 3.91458 / 2.79 ( 2034) metal coordination : bond 0.00185 / 0.10 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 166 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: A 121 ASN cc_start: 0.8139 (m110) cc_final: 0.7852 (m-40) REVERT: A 190 MET cc_start: 0.7746 (mtt) cc_final: 0.7477 (mtp) REVERT: A 468 LEU cc_start: 0.7688 (tt) cc_final: 0.7401 (mm) REVERT: A 489 PHE cc_start: 0.7681 (t80) cc_final: 0.7381 (m-80) REVERT: A 558 LYS cc_start: 0.7789 (mttt) cc_final: 0.7473 (mmtt) REVERT: A 603 HIS cc_start: 0.7613 (m90) cc_final: 0.7170 (m90) REVERT: A 710 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7352 (tp30) REVERT: A 732 ARG cc_start: 0.5567 (mmt180) cc_final: 0.5216 (mmt180) REVERT: A 763 ASP cc_start: 0.4908 (p0) cc_final: 0.4578 (p0) REVERT: A 765 PHE cc_start: 0.7483 (t80) cc_final: 0.7095 (t80) REVERT: B 161 ASP cc_start: 0.7816 (t0) cc_final: 0.6608 (p0) REVERT: B 163 MET cc_start: 0.8355 (mmm) cc_final: 0.7542 (mmm) REVERT: B 166 GLN cc_start: 0.7797 (tm-30) cc_final: 0.7590 (tt0) REVERT: B 190 MET cc_start: 0.7833 (mtt) cc_final: 0.7460 (mtp) REVERT: B 279 MET cc_start: 0.7778 (mmm) cc_final: 0.7475 (mmt) REVERT: B 340 ILE cc_start: 0.8567 (mm) cc_final: 0.8202 (mt) REVERT: B 511 GLN cc_start: 0.7808 (mm-40) cc_final: 0.7482 (pt0) REVERT: B 751 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6413 (mm) REVERT: C 38 PHE cc_start: 0.5836 (OUTLIER) cc_final: 0.5355 (t80) outliers start: 44 outliers final: 19 residues processed: 201 average time/residue: 0.1069 time to fit residues: 32.1301 Evaluate side-chains 180 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 493 ASP Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain C residue 38 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 73 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 86 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 116 optimal weight: 7.9990 chunk 142 optimal weight: 9.9990 chunk 42 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 776 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.180225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.121186 restraints weight = 13946.517| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.59 r_work: 0.3229 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12411 Z= 0.219 Angle : 0.571 8.987 16796 Z= 0.290 Chirality : 0.042 0.149 1877 Planarity : 0.004 0.042 2130 Dihedral : 8.178 101.879 1705 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.25 % Favored : 96.68 % Rotamer: Outliers : 4.38 % Allowed : 19.43 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.22), residues: 1477 helix: 1.94 (0.18), residues: 814 sheet: 0.59 (0.44), residues: 131 loop : 0.69 (0.29), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 172 TYR 0.022 0.002 TYR A 272 PHE 0.030 0.002 PHE A 208 TRP 0.015 0.001 TRP A 426 HIS 0.005 0.001 HIS A 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.22 (12407) covalent geometry : angle 0.57119 / 0.29 (16796) hydrogen bonds : bond 0.04645 / 3.10 ( 704) hydrogen bonds : angle 4.20546 / 3.01 ( 2034) metal coordination : bond 0.00636 / 0.33 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 161 time to evaluate : 0.652 Fit side-chains revert: symmetry clash REVERT: A 121 ASN cc_start: 0.8386 (m110) cc_final: 0.8175 (m-40) REVERT: A 391 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.7730 (mptt) REVERT: A 481 ILE cc_start: 0.8076 (tp) cc_final: 0.7799 (tp) REVERT: A 489 PHE cc_start: 0.7670 (t80) cc_final: 0.7351 (m-80) REVERT: A 558 LYS cc_start: 0.7784 (mttt) cc_final: 0.7540 (mmtt) REVERT: A 603 HIS cc_start: 0.7759 (m90) cc_final: 0.7338 (m90) REVERT: A 662 GLU cc_start: 0.4454 (OUTLIER) cc_final: 0.3876 (tt0) REVERT: A 710 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7697 (tp30) REVERT: A 732 ARG cc_start: 0.5815 (mmt180) cc_final: 0.5467 (mmt180) REVERT: B 81 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7657 (tpm170) REVERT: B 161 ASP cc_start: 0.8178 (t0) cc_final: 0.6839 (p0) REVERT: B 340 ILE cc_start: 0.8734 (mm) cc_final: 0.8476 (mt) REVERT: B 511 GLN cc_start: 0.7853 (mm-40) cc_final: 0.7517 (pt0) REVERT: B 533 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8486 (mttp) REVERT: B 691 SER cc_start: 0.8186 (t) cc_final: 0.7976 (m) REVERT: B 751 LEU cc_start: 0.6870 (OUTLIER) cc_final: 0.6630 (mm) REVERT: C 57 MET cc_start: 0.7578 (mmm) cc_final: 0.7349 (tpp) REVERT: D 60 LEU cc_start: 0.6914 (OUTLIER) cc_final: 0.6505 (pp) outliers start: 58 outliers final: 25 residues processed: 202 average time/residue: 0.1133 time to fit residues: 33.3794 Evaluate side-chains 191 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 159 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 81 ARG Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 493 ASP Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain B residue 533 LYS Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain B residue 606 MET Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain D residue 60 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 29 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 11 optimal weight: 0.2980 chunk 32 optimal weight: 0.8980 chunk 133 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 73 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 67 optimal weight: 30.0000 chunk 84 optimal weight: 10.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 700 GLN ** 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 = 0.4096 r_free = 0.4096 target = 0.184075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.124653 restraints weight = 14028.431| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.53 r_work: 0.3261 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12411 Z= 0.115 Angle : 0.493 10.385 16796 Z= 0.248 Chirality : 0.039 0.131 1877 Planarity : 0.004 0.042 2130 Dihedral : 7.174 73.679 1699 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.80 % Allowed : 21.01 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.22), residues: 1477 helix: 2.09 (0.18), residues: 828 sheet: 0.85 (0.45), residues: 125 loop : 0.67 (0.30), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 172 TYR 0.016 0.001 TYR A 272 PHE 0.027 0.001 PHE A 208 TRP 0.006 0.001 TRP B 240 HIS 0.003 0.000 HIS B 578 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (12407) covalent geometry : angle 0.49337 / 0.25 (16796) hydrogen bonds : bond 0.03788 / 2.53 ( 704) hydrogen bonds : angle 3.91971 / 2.80 ( 2034) metal coordination : bond 0.00248 / 0.13 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 161 time to evaluate : 0.531 Fit side-chains revert: symmetry clash REVERT: A 121 ASN cc_start: 0.8145 (m110) cc_final: 0.7859 (m-40) REVERT: A 489 PHE cc_start: 0.7697 (t80) cc_final: 0.7376 (m-80) REVERT: A 558 LYS cc_start: 0.7796 (mttt) cc_final: 0.7461 (mmtt) REVERT: A 603 HIS cc_start: 0.7598 (m90) cc_final: 0.7144 (m90) REVERT: A 710 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7389 (tp30) REVERT: A 763 ASP cc_start: 0.5110 (p0) cc_final: 0.4678 (p0) REVERT: A 765 PHE cc_start: 0.7530 (t80) cc_final: 0.6882 (t80) REVERT: B 161 ASP cc_start: 0.8025 (t0) cc_final: 0.6659 (p0) REVERT: B 163 MET cc_start: 0.8347 (mmm) cc_final: 0.7562 (mmm) REVERT: B 166 GLN cc_start: 0.7785 (tm-30) cc_final: 0.7564 (tt0) REVERT: B 190 MET cc_start: 0.7670 (mtt) cc_final: 0.7439 (mtp) REVERT: B 340 ILE cc_start: 0.8572 (mm) cc_final: 0.8241 (mt) REVERT: B 511 GLN cc_start: 0.7864 (mm-40) cc_final: 0.7492 (pt0) REVERT: B 751 LEU cc_start: 0.6739 (OUTLIER) cc_final: 0.6457 (mm) REVERT: B 765 PHE cc_start: 0.7804 (t80) cc_final: 0.7405 (t80) REVERT: C 57 MET cc_start: 0.7314 (mmm) cc_final: 0.7066 (tpp) REVERT: D 60 LEU cc_start: 0.6371 (OUTLIER) cc_final: 0.5986 (pp) outliers start: 37 outliers final: 27 residues processed: 191 average time/residue: 0.1110 time to fit residues: 31.3328 Evaluate side-chains 183 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 493 ASP Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain B residue 606 MET Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain D residue 60 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 80 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 103 optimal weight: 0.0670 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 132 optimal weight: 0.3980 chunk 56 optimal weight: 0.9980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 700 GLN ** 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 = 0.4109 r_free = 0.4109 target = 0.185366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.125963 restraints weight = 13853.472| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.53 r_work: 0.3275 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12411 Z= 0.106 Angle : 0.492 10.587 16796 Z= 0.247 Chirality : 0.039 0.131 1877 Planarity : 0.003 0.043 2130 Dihedral : 6.756 73.764 1699 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.10 % Allowed : 20.63 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.34 (0.23), residues: 1477 helix: 2.23 (0.18), residues: 829 sheet: 0.97 (0.45), residues: 124 loop : 0.72 (0.30), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 172 TYR 0.014 0.001 TYR A 272 PHE 0.026 0.001 PHE A 208 TRP 0.006 0.001 TRP B 240 HIS 0.002 0.001 HIS A 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (12407) covalent geometry : angle 0.49235 / 0.25 (16796) hydrogen bonds : bond 0.03612 / 2.42 ( 704) hydrogen bonds : angle 3.81831 / 2.73 ( 2034) metal coordination : bond 0.00182 / 0.09 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 158 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.8135 (m110) cc_final: 0.7862 (m-40) REVERT: A 489 PHE cc_start: 0.7692 (t80) cc_final: 0.7402 (m-80) REVERT: A 558 LYS cc_start: 0.7842 (mttt) cc_final: 0.7481 (mmtt) REVERT: A 603 HIS cc_start: 0.7579 (m90) cc_final: 0.7131 (m90) REVERT: A 710 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7388 (tp30) REVERT: A 763 ASP cc_start: 0.5129 (p0) cc_final: 0.4711 (p0) REVERT: A 765 PHE cc_start: 0.7507 (t80) cc_final: 0.6850 (t80) REVERT: B 81 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7751 (tpp-160) REVERT: B 161 ASP cc_start: 0.7972 (t0) cc_final: 0.6552 (p0) REVERT: B 163 MET cc_start: 0.8274 (mmm) cc_final: 0.7555 (mmm) REVERT: B 340 ILE cc_start: 0.8553 (mm) cc_final: 0.8214 (mt) REVERT: B 511 GLN cc_start: 0.7838 (mm-40) cc_final: 0.7468 (pt0) REVERT: B 751 LEU cc_start: 0.6743 (OUTLIER) cc_final: 0.6484 (mm) REVERT: B 765 PHE cc_start: 0.7810 (t80) cc_final: 0.7374 (t80) REVERT: C 57 MET cc_start: 0.7289 (OUTLIER) cc_final: 0.7033 (tpp) REVERT: D 60 LEU cc_start: 0.6412 (OUTLIER) cc_final: 0.6011 (pp) outliers start: 41 outliers final: 29 residues processed: 190 average time/residue: 0.1090 time to fit residues: 30.4836 Evaluate side-chains 183 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 149 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 81 ARG Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 493 ASP Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain B residue 606 MET Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain D residue 60 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 18 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 76 optimal weight: 8.9990 chunk 147 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 96 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 700 GLN ** 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 = 0.4107 r_free = 0.4107 target = 0.185253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.125742 restraints weight = 13980.967| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.54 r_work: 0.3271 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12411 Z= 0.109 Angle : 0.487 10.794 16796 Z= 0.244 Chirality : 0.039 0.171 1877 Planarity : 0.003 0.043 2130 Dihedral : 6.605 73.442 1699 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.80 % Allowed : 21.32 % Favored : 75.89 % 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: 2.37 (0.22), residues: 1477 helix: 2.27 (0.18), residues: 828 sheet: 0.94 (0.45), residues: 125 loop : 0.72 (0.30), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 172 TYR 0.015 0.001 TYR A 272 PHE 0.026 0.001 PHE A 208 TRP 0.006 0.001 TRP B 240 HIS 0.002 0.001 HIS B 578 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (12407) covalent geometry : angle 0.48719 / 0.24 (16796) hydrogen bonds : bond 0.03608 / 2.42 ( 704) hydrogen bonds : angle 3.78204 / 2.71 ( 2034) metal coordination : bond 0.00218 / 0.11 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 152 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 489 PHE cc_start: 0.7685 (t80) cc_final: 0.7418 (m-80) REVERT: A 558 LYS cc_start: 0.7837 (mttt) cc_final: 0.7473 (mmtt) REVERT: A 603 HIS cc_start: 0.7585 (m90) cc_final: 0.7140 (m90) REVERT: A 710 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7372 (tp30) REVERT: A 763 ASP cc_start: 0.5303 (p0) cc_final: 0.4887 (p0) REVERT: A 765 PHE cc_start: 0.7568 (t80) cc_final: 0.6956 (t80) REVERT: B 81 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7591 (tpm170) REVERT: B 161 ASP cc_start: 0.7963 (t0) cc_final: 0.6568 (p0) REVERT: B 163 MET cc_start: 0.8185 (mmm) cc_final: 0.7512 (mmm) REVERT: B 309 GLU cc_start: 0.6191 (mm-30) cc_final: 0.5225 (mt-10) REVERT: B 340 ILE cc_start: 0.8575 (mm) cc_final: 0.8226 (mt) REVERT: B 511 GLN cc_start: 0.7805 (mm-40) cc_final: 0.7454 (pt0) REVERT: B 765 PHE cc_start: 0.7828 (t80) cc_final: 0.7369 (t80) REVERT: C 57 MET cc_start: 0.7290 (OUTLIER) cc_final: 0.7044 (tpp) REVERT: D 60 LEU cc_start: 0.6470 (OUTLIER) cc_final: 0.6084 (pp) outliers start: 37 outliers final: 28 residues processed: 180 average time/residue: 0.1140 time to fit residues: 30.2023 Evaluate side-chains 182 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 81 ARG Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 493 ASP Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain B residue 606 MET Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain D residue 60 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 105 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 511 GLN ** B 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.181702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.121626 restraints weight = 14038.821| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.65 r_work: 0.3236 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12411 Z= 0.201 Angle : 0.566 11.845 16796 Z= 0.282 Chirality : 0.042 0.279 1877 Planarity : 0.004 0.042 2130 Dihedral : 6.817 73.240 1699 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.05 % Favored : 96.89 % Rotamer: Outliers : 3.33 % Allowed : 20.71 % Favored : 75.96 % 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: 2.01 (0.22), residues: 1477 helix: 1.98 (0.18), residues: 824 sheet: 0.80 (0.45), residues: 123 loop : 0.58 (0.29), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 172 TYR 0.021 0.002 TYR A 272 PHE 0.028 0.002 PHE A 208 TRP 0.007 0.001 TRP B 140 HIS 0.003 0.001 HIS B 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.20 (12407) covalent geometry : angle 0.56587 / 0.28 (16796) hydrogen bonds : bond 0.04341 / 2.91 ( 704) hydrogen bonds : angle 4.04993 / 2.90 ( 2034) metal coordination : bond 0.00602 / 0.31 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 157 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: A 121 ASN cc_start: 0.8384 (m110) cc_final: 0.8148 (m-40) REVERT: A 309 GLU cc_start: 0.6377 (mm-30) cc_final: 0.5375 (mt-10) REVERT: A 391 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7685 (mptt) REVERT: A 489 PHE cc_start: 0.7660 (t80) cc_final: 0.7385 (m-80) REVERT: A 558 LYS cc_start: 0.7763 (mttt) cc_final: 0.7508 (mmtt) REVERT: A 603 HIS cc_start: 0.7762 (m90) cc_final: 0.7340 (m90) REVERT: A 710 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7576 (tp30) REVERT: A 763 ASP cc_start: 0.5381 (p0) cc_final: 0.4998 (p0) REVERT: A 765 PHE cc_start: 0.7710 (t80) cc_final: 0.7014 (t80) REVERT: B 161 ASP cc_start: 0.8147 (t0) cc_final: 0.6823 (p0) REVERT: B 162 PHE cc_start: 0.7617 (t80) cc_final: 0.7090 (t80) REVERT: B 163 MET cc_start: 0.8469 (mmm) cc_final: 0.7773 (mmm) REVERT: B 309 GLU cc_start: 0.6396 (mm-30) cc_final: 0.5416 (mt-10) REVERT: B 340 ILE cc_start: 0.8757 (mm) cc_final: 0.8456 (mt) REVERT: B 511 GLN cc_start: 0.7860 (mm-40) cc_final: 0.7520 (pt0) REVERT: B 533 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8474 (mttp) REVERT: B 765 PHE cc_start: 0.8023 (t80) cc_final: 0.7582 (t80) REVERT: B 779 GLN cc_start: 0.6171 (mt0) cc_final: 0.5885 (mt0) REVERT: C 34 GLN cc_start: 0.7926 (tm-30) cc_final: 0.7707 (tm-30) REVERT: D 60 LEU cc_start: 0.6768 (OUTLIER) cc_final: 0.6375 (pp) outliers start: 44 outliers final: 32 residues processed: 186 average time/residue: 0.1158 time to fit residues: 31.3956 Evaluate side-chains 191 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 155 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 493 ASP Chi-restraints excluded: chain B residue 533 LYS Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain B residue 606 MET Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain D residue 60 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 31 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 69 optimal weight: 8.9990 chunk 97 optimal weight: 0.9980 chunk 147 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 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 511 GLN ** B 700 GLN ** 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 = 0.4112 r_free = 0.4112 target = 0.184009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.124362 restraints weight = 13938.377| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.65 r_work: 0.3270 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12411 Z= 0.122 Angle : 0.514 12.913 16796 Z= 0.256 Chirality : 0.040 0.307 1877 Planarity : 0.003 0.044 2130 Dihedral : 6.653 73.178 1699 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.80 % Allowed : 21.16 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.23 (0.22), residues: 1477 helix: 2.16 (0.18), residues: 829 sheet: 0.88 (0.45), residues: 123 loop : 0.65 (0.29), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 172 TYR 0.016 0.001 TYR A 272 PHE 0.027 0.001 PHE A 208 TRP 0.006 0.001 TRP B 240 HIS 0.002 0.001 HIS A 578 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (12407) covalent geometry : angle 0.51428 / 0.26 (16796) hydrogen bonds : bond 0.03777 / 2.53 ( 704) hydrogen bonds : angle 3.87618 / 2.77 ( 2034) metal coordination : bond 0.00266 / 0.14 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 155 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 ASN cc_start: 0.8155 (t0) cc_final: 0.7945 (t0) REVERT: A 309 GLU cc_start: 0.6530 (mm-30) cc_final: 0.5436 (mt-10) REVERT: A 489 PHE cc_start: 0.7632 (t80) cc_final: 0.7383 (m-80) REVERT: A 603 HIS cc_start: 0.7666 (m90) cc_final: 0.7264 (m90) REVERT: A 710 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7487 (tp30) REVERT: A 763 ASP cc_start: 0.5277 (p0) cc_final: 0.4495 (p0) REVERT: A 765 PHE cc_start: 0.7668 (t80) cc_final: 0.6998 (t80) REVERT: B 81 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7796 (tpm170) REVERT: B 161 ASP cc_start: 0.8085 (t0) cc_final: 0.6745 (p0) REVERT: B 163 MET cc_start: 0.8423 (mmm) cc_final: 0.7812 (mmm) REVERT: B 190 MET cc_start: 0.7874 (mtt) cc_final: 0.7522 (mtp) REVERT: B 309 GLU cc_start: 0.6413 (mm-30) cc_final: 0.5419 (mt-10) REVERT: B 340 ILE cc_start: 0.8737 (mm) cc_final: 0.8436 (mt) REVERT: B 511 GLN cc_start: 0.7927 (mm-40) cc_final: 0.7577 (pt0) REVERT: B 765 PHE cc_start: 0.7852 (t80) cc_final: 0.7359 (t80) REVERT: D 60 LEU cc_start: 0.6649 (OUTLIER) cc_final: 0.6308 (pp) outliers start: 37 outliers final: 28 residues processed: 182 average time/residue: 0.1137 time to fit residues: 30.3142 Evaluate side-chains 182 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 81 ARG Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 493 ASP Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain B residue 606 MET Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain D residue 60 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 69 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 135 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 27 optimal weight: 0.0370 chunk 129 optimal weight: 0.7980 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.184076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.124284 restraints weight = 14011.575| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.66 r_work: 0.3270 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12411 Z= 0.125 Angle : 0.525 13.011 16796 Z= 0.260 Chirality : 0.040 0.308 1877 Planarity : 0.004 0.043 2130 Dihedral : 6.606 73.133 1699 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.87 % Allowed : 20.79 % Favored : 76.34 % 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: 2.25 (0.22), residues: 1477 helix: 2.18 (0.18), residues: 829 sheet: 0.83 (0.46), residues: 125 loop : 0.65 (0.30), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 172 TYR 0.017 0.001 TYR A 272 PHE 0.027 0.001 PHE A 208 TRP 0.006 0.001 TRP B 240 HIS 0.003 0.001 HIS B 578 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 (12407) covalent geometry : angle 0.52463 / 0.26 (16796) hydrogen bonds : bond 0.03762 / 2.52 ( 704) hydrogen bonds : angle 3.85024 / 2.75 ( 2034) metal coordination : bond 0.00286 / 0.15 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 153 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 156 ASN cc_start: 0.8138 (t0) cc_final: 0.7937 (t0) REVERT: A 309 GLU cc_start: 0.6544 (mm-30) cc_final: 0.5452 (mt-10) REVERT: A 489 PHE cc_start: 0.7621 (t80) cc_final: 0.7388 (m-80) REVERT: A 603 HIS cc_start: 0.7663 (m90) cc_final: 0.7268 (m90) REVERT: A 710 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7490 (tp30) REVERT: A 765 PHE cc_start: 0.7694 (t80) cc_final: 0.7013 (t80) REVERT: B 81 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7846 (tpm170) REVERT: B 161 ASP cc_start: 0.8028 (t0) cc_final: 0.6693 (p0) REVERT: B 162 PHE cc_start: 0.7574 (t80) cc_final: 0.7053 (t80) REVERT: B 163 MET cc_start: 0.8383 (mmm) cc_final: 0.7775 (mmm) REVERT: B 190 MET cc_start: 0.7883 (mtt) cc_final: 0.7538 (mtp) REVERT: B 309 GLU cc_start: 0.6420 (mm-30) cc_final: 0.5467 (mt-10) REVERT: B 340 ILE cc_start: 0.8735 (mm) cc_final: 0.8431 (mt) REVERT: B 511 GLN cc_start: 0.7925 (mm-40) cc_final: 0.7596 (pt0) REVERT: B 533 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8465 (mttp) REVERT: B 765 PHE cc_start: 0.7891 (t80) cc_final: 0.7359 (t80) REVERT: D 60 LEU cc_start: 0.6764 (OUTLIER) cc_final: 0.6345 (pp) outliers start: 38 outliers final: 33 residues processed: 180 average time/residue: 0.1138 time to fit residues: 29.6577 Evaluate side-chains 187 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 150 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 81 ARG Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 493 ASP Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain B residue 533 LYS Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain B residue 606 MET Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain D residue 60 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 90 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 84 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 700 GLN ** 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 = 0.4107 r_free = 0.4107 target = 0.183623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.123799 restraints weight = 14026.413| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.66 r_work: 0.3263 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12411 Z= 0.140 Angle : 0.535 12.859 16796 Z= 0.266 Chirality : 0.040 0.310 1877 Planarity : 0.004 0.043 2130 Dihedral : 6.623 73.107 1699 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.80 % Allowed : 21.01 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.22), residues: 1477 helix: 2.12 (0.18), residues: 830 sheet: 0.81 (0.45), residues: 125 loop : 0.63 (0.30), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 172 TYR 0.017 0.001 TYR A 272 PHE 0.027 0.001 PHE A 208 TRP 0.006 0.001 TRP B 140 HIS 0.003 0.001 HIS A 578 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (12407) covalent geometry : angle 0.53465 / 0.27 (16796) hydrogen bonds : bond 0.03844 / 2.58 ( 704) hydrogen bonds : angle 3.87124 / 2.76 ( 2034) metal coordination : bond 0.00357 / 0.18 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3387.15 seconds wall clock time: 58 minutes 51.49 seconds (3531.49 seconds total)