Starting phenix.real_space_refine on Thu Jul 2 19:50:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kck_62254/07_2026/9kck_62254.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kck_62254/07_2026/9kck_62254.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kck_62254/07_2026/9kck_62254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kck_62254/07_2026/9kck_62254.map" model { file = "/net/cci-nas-00/data/ceres_data/9kck_62254/07_2026/9kck_62254.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kck_62254/07_2026/9kck_62254.cif" } resolution = 2.9 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= 0.004 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: 8 Type Number sf(0) Gaussians K 3 8.98 5 Al 1 5.89 5 Mg 1 5.21 5 S 59 5.16 5 C 6283 2.51 5 N 1624 2.21 5 O 1825 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9800 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 7627 Classifications: {'peptide': 984} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 940} Chain: "B" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2130 Classifications: {'peptide': 268} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 247} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 6 Ad-hoc single atom residues: {' K': 3} Unusual residues: {' MG': 1, 'ALF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 3 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 1.81, per 1000 atoms: 0.18 Number of scatterers: 9800 At special positions: 0 Unit cell: (121.18, 88.81, 170.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) K 3 19.00 S 59 16.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1825 8.00 N 1624 7.00 C 6283 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 144 " distance=2.03 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 170 " distance=2.03 Simple disulfide: pdb=" SG CYS B 191 " - pdb=" SG CYS B 250 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 246.1 milliseconds 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2326 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 9 sheets defined 48.6% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 87 through 96 removed outlier: 3.523A pdb=" N LYS A 91 " --> pdb=" O PRO A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 123 removed outlier: 3.569A pdb=" N LEU A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 150 Processing helix chain 'A' and resid 156 through 163 Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 261 through 264 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 282 through 313 Processing helix chain 'A' and resid 316 through 332 Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 362 through 370 removed outlier: 3.812A pdb=" N THR A 366 " --> pdb=" O GLU A 362 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLY A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 428 Processing helix chain 'A' and resid 441 through 445 removed outlier: 3.517A pdb=" N ARG A 445 " --> pdb=" O ILE A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 464 Processing helix chain 'A' and resid 466 through 474 Processing helix chain 'A' and resid 510 through 515 removed outlier: 4.023A pdb=" N LEU A 515 " --> pdb=" O PRO A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 547 Processing helix chain 'A' and resid 598 through 609 Processing helix chain 'A' and resid 620 through 632 Processing helix chain 'A' and resid 640 through 649 Processing helix chain 'A' and resid 667 through 673 removed outlier: 3.803A pdb=" N ASP A 672 " --> pdb=" O SER A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 685 Processing helix chain 'A' and resid 694 through 707 removed outlier: 3.528A pdb=" N LEU A 699 " --> pdb=" O PRO A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 720 No H-bonds generated for 'chain 'A' and resid 718 through 720' Processing helix chain 'A' and resid 721 through 728 Processing helix chain 'A' and resid 739 through 746 Processing helix chain 'A' and resid 756 through 782 removed outlier: 3.929A pdb=" N SER A 782 " --> pdb=" O TYR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 797 Proline residue: A 789 - end of helix Processing helix chain 'A' and resid 803 through 812 Processing helix chain 'A' and resid 815 through 822 removed outlier: 3.520A pdb=" N LEU A 822 " --> pdb=" O PRO A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 825 No H-bonds generated for 'chain 'A' and resid 823 through 825' Processing helix chain 'A' and resid 846 through 856 Processing helix chain 'A' and resid 856 through 876 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 907 through 938 removed outlier: 3.561A pdb=" N VAL A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA A 932 " --> pdb=" O VAL A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 971 removed outlier: 3.870A pdb=" N ILE A 955 " --> pdb=" O ASN A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 978 Processing helix chain 'A' and resid 984 through 990 removed outlier: 3.847A pdb=" N CYS A 990 " --> pdb=" O TRP A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1012 Processing helix chain 'A' and resid 1015 through 1022 Processing helix chain 'B' and resid 14 through 20 removed outlier: 4.317A pdb=" N LEU B 18 " --> pdb=" O ALA B 14 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE B 19 " --> pdb=" O GLU B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 64 removed outlier: 3.571A pdb=" N THR B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 115 Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 120 through 124 removed outlier: 4.097A pdb=" N LYS B 123 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASN B 124 " --> pdb=" O GLU B 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 120 through 124' Processing helix chain 'B' and resid 147 through 152 Processing helix chain 'B' and resid 211 through 215 removed outlier: 3.543A pdb=" N TYR B 214 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 181 removed outlier: 11.506A pdb=" N GLN A 168 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 9.544A pdb=" N LYS A 194 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU A 170 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU A 190 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N CYS A 249 " --> pdb=" O LYS A 212 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LYS A 212 " --> pdb=" O CYS A 249 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N GLU A 251 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLY A 210 " --> pdb=" O GLU A 251 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR A 253 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA A 208 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ARG A 255 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ASP A 202 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 176 through 181 removed outlier: 11.506A pdb=" N GLN A 168 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 9.544A pdb=" N LYS A 194 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU A 170 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU A 190 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N CYS A 249 " --> pdb=" O LYS A 212 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LYS A 212 " --> pdb=" O CYS A 249 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N GLU A 251 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLY A 210 " --> pdb=" O GLU A 251 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR A 253 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA A 208 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ARG A 255 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ASP A 202 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 356 through 358 removed outlier: 6.329A pdb=" N GLY A 731 " --> pdb=" O MET A 748 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N LEU A 750 " --> pdb=" O GLY A 731 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ALA A 733 " --> pdb=" O LEU A 750 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL A 712 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N VAL A 732 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL A 714 " --> pdb=" O VAL A 732 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N MET A 734 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N GLY A 716 " --> pdb=" O MET A 734 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR A 372 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N THR A 715 " --> pdb=" O THR A 372 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N CYS A 374 " --> pdb=" O THR A 715 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL A 613 " --> pdb=" O ILE A 688 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N PHE A 690 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N MET A 615 " --> pdb=" O PHE A 690 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N CYS A 663 " --> pdb=" O VAL A 689 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ALA A 691 " --> pdb=" O CYS A 663 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL A 665 " --> pdb=" O ALA A 691 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 396 through 399 removed outlier: 5.159A pdb=" N VAL A 388 " --> pdb=" O ILE A 592 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE A 592 " --> pdb=" O VAL A 388 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS A 390 " --> pdb=" O SER A 590 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N LEU A 583 " --> pdb=" O PHE A 559 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N PHE A 559 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N PHE A 585 " --> pdb=" O HIS A 557 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N HIS A 557 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LYS A 494 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N LYS A 476 " --> pdb=" O LYS A 494 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 396 through 399 removed outlier: 5.159A pdb=" N VAL A 388 " --> pdb=" O ILE A 592 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE A 592 " --> pdb=" O VAL A 388 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS A 390 " --> pdb=" O SER A 590 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N PHE A 585 " --> pdb=" O SER A 519 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE A 521 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 9.150A pdb=" N GLY A 587 " --> pdb=" O ILE A 521 " (cutoff:3.500A) removed outlier: 11.617A pdb=" N LEU A 523 " --> pdb=" O GLY A 587 " (cutoff:3.500A) removed outlier: 17.151A pdb=" N ILE A 589 " --> pdb=" O LEU A 523 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 432 through 433 Processing sheet with id=AA7, first strand: chain 'A' and resid 898 through 899 Processing sheet with id=AA8, first strand: chain 'B' and resid 81 through 84 Processing sheet with id=AA9, first strand: chain 'B' and resid 92 through 96 removed outlier: 3.638A pdb=" N PHE B 95 " --> pdb=" O THR B 276 " (cutoff:3.500A) 506 hydrogen bonds defined for protein. 1461 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.43 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3170 1.34 - 1.46: 1954 1.46 - 1.58: 4783 1.58 - 1.69: 0 1.69 - 1.81: 93 Bond restraints: 10000 Sorted by residual: bond pdb=" F2 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.685 1.800 -0.115 2.00e-02 2.50e+03 3.31e+01 bond pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.684 1.798 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" F3 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.685 1.798 -0.113 2.00e-02 2.50e+03 3.19e+01 bond pdb=" F4 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.686 1.798 -0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" CG PRO A 481 " pdb=" CD PRO A 481 " ideal model delta sigma weight residual 1.503 1.445 0.058 3.40e-02 8.65e+02 2.92e+00 ... (remaining 9995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.21: 13576 14.21 - 28.41: 4 28.41 - 42.62: 0 42.62 - 56.83: 0 56.83 - 71.04: 2 Bond angle restraints: 13582 Sorted by residual: angle pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " pdb=" F2 ALF A1101 " ideal model delta sigma weight residual 108.68 179.72 -71.04 3.00e+00 1.11e-01 5.61e+02 angle pdb=" F3 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 109.63 179.74 -70.11 3.00e+00 1.11e-01 5.46e+02 angle pdb=" F2 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 110.21 89.93 20.28 3.00e+00 1.11e-01 4.57e+01 angle pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " pdb=" F3 ALF A1101 " ideal model delta sigma weight residual 109.69 89.81 19.88 3.00e+00 1.11e-01 4.39e+01 angle pdb=" F2 ALF A1101 " pdb="AL ALF A1101 " pdb=" F3 ALF A1101 " ideal model delta sigma weight residual 109.59 90.18 19.41 3.00e+00 1.11e-01 4.19e+01 ... (remaining 13577 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.93: 5474 15.93 - 31.87: 475 31.87 - 47.80: 97 47.80 - 63.73: 17 63.73 - 79.67: 3 Dihedral angle restraints: 6066 sinusoidal: 2452 harmonic: 3614 Sorted by residual: dihedral pdb=" CA LYS A 194 " pdb=" C LYS A 194 " pdb=" N GLY A 195 " pdb=" CA GLY A 195 " ideal model delta harmonic sigma weight residual 180.00 162.06 17.94 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CG ARG B 73 " pdb=" CD ARG B 73 " pdb=" NE ARG B 73 " pdb=" CZ ARG B 73 " ideal model delta sinusoidal sigma weight residual 180.00 137.93 42.07 2 1.50e+01 4.44e-03 9.58e+00 dihedral pdb=" CA THR B 89 " pdb=" C THR B 89 " pdb=" N ALA B 90 " pdb=" CA ALA B 90 " ideal model delta harmonic sigma weight residual 180.00 164.71 15.29 0 5.00e+00 4.00e-02 9.35e+00 ... (remaining 6063 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1309 0.057 - 0.114: 222 0.114 - 0.171: 21 0.171 - 0.228: 2 0.228 - 0.286: 1 Chirality restraints: 1555 Sorted by residual: chirality pdb=" CB ILE B 76 " pdb=" CA ILE B 76 " pdb=" CG1 ILE B 76 " pdb=" CG2 ILE B 76 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C13 CLR B 301 " pdb=" C12 CLR B 301 " pdb=" C14 CLR B 301 " pdb=" C17 CLR B 301 " both_signs ideal model delta sigma weight residual False -2.93 -2.71 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" C10 CLR B 301 " pdb=" C1 CLR B 301 " pdb=" C5 CLR B 301 " pdb=" C9 CLR B 301 " both_signs ideal model delta sigma weight residual False -2.85 -2.67 -0.18 2.00e-01 2.50e+01 8.01e-01 ... (remaining 1552 not shown) Planarity restraints: 1740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 99 " -0.061 5.00e-02 4.00e+02 9.12e-02 1.33e+01 pdb=" N PRO B 100 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO B 100 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 100 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 81 " 0.052 5.00e-02 4.00e+02 7.88e-02 9.93e+00 pdb=" N PRO A 82 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 800 " 0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO A 801 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 801 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 801 " 0.025 5.00e-02 4.00e+02 ... (remaining 1737 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.53: 53 2.53 - 3.19: 8735 3.19 - 3.84: 19217 3.84 - 4.49: 26564 4.49 - 5.14: 42741 Nonbonded interactions: 97310 Sorted by model distance: nonbonded pdb=" F4 ALF A1101 " pdb="MG MG A1102 " model vdw 1.884 2.120 nonbonded pdb=" OD1 ASP A 717 " pdb="MG MG A1102 " model vdw 1.987 2.170 nonbonded pdb=" O THR A 378 " pdb="MG MG A1102 " model vdw 2.034 2.170 nonbonded pdb="MG MG A1102 " pdb=" O HOH A1203 " model vdw 2.138 2.170 nonbonded pdb=" OE1 GLU A 88 " pdb=" OH TYR A 148 " model vdw 2.165 3.040 ... (remaining 97305 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.380 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 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 0.115 10003 Z= 0.172 Angle : 1.077 71.037 13588 Z= 0.425 Chirality : 0.044 0.286 1555 Planarity : 0.005 0.091 1740 Dihedral : 12.511 79.667 3731 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 1.14 (0.24), residues: 1248 helix: 1.60 (0.23), residues: 527 sheet: -0.19 (0.40), residues: 134 loop : 0.34 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 513 TYR 0.014 0.001 TYR A 488 PHE 0.016 0.001 PHE B 273 TRP 0.011 0.001 TRP A 392 HIS 0.005 0.001 HIS B 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (10000) covalent geometry : angle 1.07741 / 0.42 (13582) SS BOND : bond 0.00101 / 0.05 ( 3) SS BOND : angle 0.45644 / 0.25 ( 6) hydrogen bonds : bond 0.13572 / 8.77 ( 483) hydrogen bonds : angle 5.63072 / 3.94 ( 1461) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.237 Fit side-chains REVERT: A 399 GLU cc_start: 0.6749 (pt0) cc_final: 0.6544 (pp20) REVERT: A 488 TYR cc_start: 0.5937 (p90) cc_final: 0.5345 (p90) REVERT: A 833 LYS cc_start: 0.7787 (mmtm) cc_final: 0.7301 (mtpp) REVERT: A 852 MET cc_start: 0.7739 (tpt) cc_final: 0.6563 (tmm) REVERT: A 900 ASP cc_start: 0.8499 (p0) cc_final: 0.8141 (p0) REVERT: A 974 MET cc_start: 0.7753 (mmt) cc_final: 0.7415 (mmt) REVERT: B 92 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6550 (mt-10) REVERT: B 188 ARG cc_start: 0.8081 (ptm-80) cc_final: 0.7700 (ptm-80) REVERT: B 259 LYS cc_start: 0.7328 (tttm) cc_final: 0.7022 (mttm) REVERT: B 272 MET cc_start: 0.8211 (ttm) cc_final: 0.7902 (ttp) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.5343 time to fit residues: 98.5508 Evaluate side-chains 128 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 123 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.153736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.115034 restraints weight = 12159.549| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.92 r_work: 0.3028 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10003 Z= 0.146 Angle : 0.798 30.375 13588 Z= 0.350 Chirality : 0.044 0.226 1555 Planarity : 0.005 0.063 1740 Dihedral : 4.586 26.094 1407 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.87 % Allowed : 10.29 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 1.17 (0.24), residues: 1248 helix: 1.69 (0.22), residues: 535 sheet: -0.21 (0.39), residues: 161 loop : 0.31 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 551 TYR 0.016 0.002 TYR B 204 PHE 0.038 0.002 PHE A 291 TRP 0.017 0.002 TRP A 89 HIS 0.005 0.001 HIS A 557 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (10000) covalent geometry : angle 0.79795 / 0.35 (13582) SS BOND : bond 0.00136 / 0.07 ( 3) SS BOND : angle 0.64546 / 0.36 ( 6) hydrogen bonds : bond 0.04724 / 3.24 ( 483) hydrogen bonds : angle 4.63648 / 3.34 ( 1461) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.362 Fit side-chains REVERT: A 94 ARG cc_start: 0.7085 (mmm-85) cc_final: 0.6495 (mmm160) REVERT: A 161 PHE cc_start: 0.7780 (m-80) cc_final: 0.7504 (m-80) REVERT: A 221 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7055 (mm-30) REVERT: A 238 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.6492 (mp0) REVERT: A 353 ARG cc_start: 0.7169 (OUTLIER) cc_final: 0.6829 (mtt180) REVERT: A 399 GLU cc_start: 0.7235 (pt0) cc_final: 0.6730 (pp20) REVERT: A 447 VAL cc_start: 0.7827 (t) cc_final: 0.7617 (p) REVERT: A 488 TYR cc_start: 0.6041 (p90) cc_final: 0.5435 (p90) REVERT: A 528 GLN cc_start: 0.5818 (pm20) cc_final: 0.5347 (pt0) REVERT: A 636 GLU cc_start: 0.6535 (pt0) cc_final: 0.6017 (pm20) REVERT: A 686 THR cc_start: 0.8068 (p) cc_final: 0.7862 (p) REVERT: A 687 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7153 (mp0) REVERT: A 708 GLN cc_start: 0.7376 (OUTLIER) cc_final: 0.7025 (mp-120) REVERT: A 833 LYS cc_start: 0.8110 (mmtm) cc_final: 0.7618 (mtpp) REVERT: A 900 ASP cc_start: 0.8734 (p0) cc_final: 0.8425 (p0) REVERT: A 974 MET cc_start: 0.8042 (mmt) cc_final: 0.7824 (mmt) REVERT: B 92 GLU cc_start: 0.7469 (mt-10) cc_final: 0.6844 (mt-10) REVERT: B 150 LEU cc_start: 0.7560 (mt) cc_final: 0.7234 (mm) REVERT: B 161 ASP cc_start: 0.5674 (m-30) cc_final: 0.5258 (m-30) REVERT: B 188 ARG cc_start: 0.8296 (ptm-80) cc_final: 0.7946 (ptm-80) REVERT: B 259 LYS cc_start: 0.7588 (tttm) cc_final: 0.6895 (mttm) REVERT: B 272 MET cc_start: 0.8879 (ttm) cc_final: 0.8470 (ttp) outliers start: 20 outliers final: 10 residues processed: 152 average time/residue: 0.5055 time to fit residues: 82.1934 Evaluate side-chains 144 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 708 GLN Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 127 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 110 optimal weight: 0.0570 chunk 84 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 113 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 528 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 = 0.3769 r_free = 0.3769 target = 0.154068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.115552 restraints weight = 12099.015| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.86 r_work: 0.3065 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10003 Z= 0.125 Angle : 0.783 29.487 13588 Z= 0.336 Chirality : 0.043 0.198 1555 Planarity : 0.004 0.050 1740 Dihedral : 4.383 25.134 1407 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.15 % Allowed : 12.54 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 1.22 (0.24), residues: 1248 helix: 1.81 (0.22), residues: 536 sheet: -0.32 (0.38), residues: 161 loop : 0.29 (0.27), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 551 TYR 0.014 0.001 TYR B 204 PHE 0.033 0.001 PHE A 291 TRP 0.014 0.001 TRP A 89 HIS 0.006 0.001 HIS A 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (10000) covalent geometry : angle 0.78332 / 0.34 (13582) SS BOND : bond 0.00111 / 0.06 ( 3) SS BOND : angle 0.50361 / 0.27 ( 6) hydrogen bonds : bond 0.04246 / 2.93 ( 483) hydrogen bonds : angle 4.40648 / 3.18 ( 1461) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.409 Fit side-chains REVERT: A 67 ARG cc_start: 0.6990 (tpp80) cc_final: 0.6711 (tpp-160) REVERT: A 95 GLN cc_start: 0.6243 (OUTLIER) cc_final: 0.5586 (mp10) REVERT: A 161 PHE cc_start: 0.7932 (m-80) cc_final: 0.7632 (m-80) REVERT: A 399 GLU cc_start: 0.7202 (pt0) cc_final: 0.6804 (pp20) REVERT: A 488 TYR cc_start: 0.6211 (p90) cc_final: 0.5543 (p90) REVERT: A 528 GLN cc_start: 0.5904 (pm20) cc_final: 0.5284 (pt0) REVERT: A 636 GLU cc_start: 0.6537 (pt0) cc_final: 0.6050 (pm20) REVERT: A 687 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7197 (mp0) REVERT: A 708 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.7078 (mp-120) REVERT: A 797 ASN cc_start: 0.8274 (m-40) cc_final: 0.7997 (m-40) REVERT: A 833 LYS cc_start: 0.8136 (mmtm) cc_final: 0.7655 (mtpp) REVERT: A 900 ASP cc_start: 0.8653 (p0) cc_final: 0.8364 (p0) REVERT: A 974 MET cc_start: 0.8276 (mmt) cc_final: 0.8071 (mmt) REVERT: A 1011 ARG cc_start: 0.6470 (mtp85) cc_final: 0.6166 (mtt90) REVERT: B 27 GLU cc_start: 0.6797 (mt-10) cc_final: 0.6464 (mt-10) REVERT: B 92 GLU cc_start: 0.7569 (mt-10) cc_final: 0.6949 (mt-10) REVERT: B 137 LYS cc_start: 0.7131 (pptt) cc_final: 0.6392 (tptp) REVERT: B 150 LEU cc_start: 0.7666 (mt) cc_final: 0.7362 (mm) REVERT: B 161 ASP cc_start: 0.5687 (m-30) cc_final: 0.5259 (m-30) REVERT: B 249 GLU cc_start: 0.7280 (tt0) cc_final: 0.6929 (tt0) REVERT: B 272 MET cc_start: 0.8871 (ttm) cc_final: 0.8521 (ttp) outliers start: 23 outliers final: 10 residues processed: 149 average time/residue: 0.4761 time to fit residues: 76.2927 Evaluate side-chains 145 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 708 GLN Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 248 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 71 optimal weight: 0.1980 chunk 66 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.154687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.116500 restraints weight = 12296.497| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.88 r_work: 0.3061 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10003 Z= 0.109 Angle : 0.762 29.503 13588 Z= 0.323 Chirality : 0.042 0.186 1555 Planarity : 0.004 0.046 1740 Dihedral : 4.187 25.640 1407 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.53 % Allowed : 14.31 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 1.37 (0.24), residues: 1248 helix: 1.94 (0.22), residues: 537 sheet: -0.34 (0.41), residues: 148 loop : 0.37 (0.27), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 551 TYR 0.012 0.001 TYR A 869 PHE 0.029 0.001 PHE A 291 TRP 0.014 0.001 TRP A 89 HIS 0.004 0.001 HIS A 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (10000) covalent geometry : angle 0.76188 / 0.32 (13582) SS BOND : bond 0.00082 / 0.04 ( 3) SS BOND : angle 0.40688 / 0.22 ( 6) hydrogen bonds : bond 0.03891 / 2.69 ( 483) hydrogen bonds : angle 4.26742 / 3.08 ( 1461) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.370 Fit side-chains REVERT: A 94 ARG cc_start: 0.7320 (mmm-85) cc_final: 0.6661 (mmm-85) REVERT: A 161 PHE cc_start: 0.7886 (m-80) cc_final: 0.7566 (m-80) REVERT: A 238 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.6595 (mp0) REVERT: A 399 GLU cc_start: 0.7223 (pt0) cc_final: 0.6758 (pp20) REVERT: A 488 TYR cc_start: 0.6139 (p90) cc_final: 0.5478 (p90) REVERT: A 591 MET cc_start: 0.7759 (mtt) cc_final: 0.7459 (mtm) REVERT: A 636 GLU cc_start: 0.6555 (pt0) cc_final: 0.6043 (pm20) REVERT: A 708 GLN cc_start: 0.7382 (OUTLIER) cc_final: 0.7017 (mp-120) REVERT: A 747 ASP cc_start: 0.8464 (m-30) cc_final: 0.8256 (m-30) REVERT: A 797 ASN cc_start: 0.8275 (m-40) cc_final: 0.7967 (m-40) REVERT: A 833 LYS cc_start: 0.8124 (mmtm) cc_final: 0.7633 (mtpp) REVERT: A 900 ASP cc_start: 0.8604 (p0) cc_final: 0.8306 (p0) REVERT: A 1011 ARG cc_start: 0.6473 (mtp85) cc_final: 0.6127 (mtt90) REVERT: B 27 GLU cc_start: 0.6734 (mt-10) cc_final: 0.6419 (mt-10) REVERT: B 92 GLU cc_start: 0.7519 (mt-10) cc_final: 0.6900 (mt-10) REVERT: B 108 GLU cc_start: 0.7388 (mm-30) cc_final: 0.6926 (mt-10) REVERT: B 137 LYS cc_start: 0.7080 (pptt) cc_final: 0.6322 (tptp) REVERT: B 150 LEU cc_start: 0.7581 (mt) cc_final: 0.7249 (mm) REVERT: B 161 ASP cc_start: 0.5763 (m-30) cc_final: 0.5402 (m-30) outliers start: 27 outliers final: 11 residues processed: 158 average time/residue: 0.4414 time to fit residues: 75.0550 Evaluate side-chains 138 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 708 GLN Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 248 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 17 optimal weight: 9.9990 chunk 33 optimal weight: 0.0980 chunk 23 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 97 optimal weight: 0.0870 chunk 24 optimal weight: 0.8980 chunk 36 optimal weight: 10.0000 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.155401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.117741 restraints weight = 12184.584| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.83 r_work: 0.3092 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10003 Z= 0.103 Angle : 0.761 29.516 13588 Z= 0.320 Chirality : 0.041 0.181 1555 Planarity : 0.004 0.045 1740 Dihedral : 4.049 27.307 1407 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.62 % Allowed : 15.15 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 1.45 (0.24), residues: 1248 helix: 2.03 (0.23), residues: 539 sheet: -0.32 (0.41), residues: 148 loop : 0.37 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 551 TYR 0.012 0.001 TYR A 869 PHE 0.027 0.001 PHE A 291 TRP 0.012 0.001 TRP A 392 HIS 0.002 0.001 HIS A 557 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (10000) covalent geometry : angle 0.76125 / 0.32 (13582) SS BOND : bond 0.00058 / 0.03 ( 3) SS BOND : angle 0.36377 / 0.19 ( 6) hydrogen bonds : bond 0.03681 / 2.55 ( 483) hydrogen bonds : angle 4.18433 / 3.02 ( 1461) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.234 Fit side-chains REVERT: A 67 ARG cc_start: 0.7109 (mmm160) cc_final: 0.6874 (tpp80) REVERT: A 94 ARG cc_start: 0.7201 (mmm-85) cc_final: 0.6692 (mmm-85) REVERT: A 161 PHE cc_start: 0.7898 (m-80) cc_final: 0.7580 (m-80) REVERT: A 248 ASN cc_start: 0.8327 (OUTLIER) cc_final: 0.7646 (p0) REVERT: A 351 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.7418 (mtm) REVERT: A 399 GLU cc_start: 0.7118 (pt0) cc_final: 0.6653 (pp20) REVERT: A 488 TYR cc_start: 0.6156 (p90) cc_final: 0.5616 (p90) REVERT: A 636 GLU cc_start: 0.6563 (pt0) cc_final: 0.6066 (pm20) REVERT: A 687 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7201 (mp0) REVERT: A 708 GLN cc_start: 0.7408 (OUTLIER) cc_final: 0.7048 (mp-120) REVERT: A 797 ASN cc_start: 0.8242 (m-40) cc_final: 0.7934 (m-40) REVERT: A 900 ASP cc_start: 0.8531 (p0) cc_final: 0.8242 (p0) REVERT: A 1011 ARG cc_start: 0.6445 (mtp85) cc_final: 0.6178 (mtt90) REVERT: B 108 GLU cc_start: 0.7411 (mm-30) cc_final: 0.6958 (mt-10) REVERT: B 150 LEU cc_start: 0.7662 (mt) cc_final: 0.7357 (mm) REVERT: B 161 ASP cc_start: 0.5779 (m-30) cc_final: 0.5425 (m-30) REVERT: B 276 THR cc_start: 0.7053 (OUTLIER) cc_final: 0.6783 (p) outliers start: 28 outliers final: 11 residues processed: 155 average time/residue: 0.3950 time to fit residues: 66.3778 Evaluate side-chains 138 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 708 GLN Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 276 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 54 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 79 optimal weight: 0.2980 chunk 61 optimal weight: 0.0980 chunk 50 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 19 optimal weight: 0.0370 chunk 103 optimal weight: 0.5980 overall best weight: 0.3458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 528 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 = 0.3803 r_free = 0.3803 target = 0.156726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.118324 restraints weight = 12165.349| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.73 r_work: 0.3120 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10003 Z= 0.096 Angle : 0.752 29.557 13588 Z= 0.315 Chirality : 0.041 0.177 1555 Planarity : 0.004 0.044 1740 Dihedral : 3.901 28.754 1407 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.25 % Allowed : 16.56 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 1.54 (0.24), residues: 1248 helix: 2.10 (0.23), residues: 546 sheet: -0.31 (0.43), residues: 137 loop : 0.40 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 551 TYR 0.012 0.001 TYR A 869 PHE 0.023 0.001 PHE A 291 TRP 0.015 0.001 TRP A 392 HIS 0.003 0.001 HIS A 557 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 (10000) covalent geometry : angle 0.75182 / 0.32 (13582) SS BOND : bond 0.00038 / 0.02 ( 3) SS BOND : angle 0.29054 / 0.15 ( 6) hydrogen bonds : bond 0.03444 / 2.38 ( 483) hydrogen bonds : angle 4.08378 / 2.94 ( 1461) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.241 Fit side-chains REVERT: A 161 PHE cc_start: 0.7917 (m-80) cc_final: 0.7594 (m-80) REVERT: A 238 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7307 (mp0) REVERT: A 248 ASN cc_start: 0.8348 (OUTLIER) cc_final: 0.7619 (p0) REVERT: A 351 MET cc_start: 0.7659 (OUTLIER) cc_final: 0.7456 (mtm) REVERT: A 399 GLU cc_start: 0.7115 (pt0) cc_final: 0.6650 (pp20) REVERT: A 488 TYR cc_start: 0.6106 (p90) cc_final: 0.5739 (p90) REVERT: A 636 GLU cc_start: 0.6528 (pt0) cc_final: 0.6020 (pm20) REVERT: A 687 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7115 (mp0) REVERT: A 797 ASN cc_start: 0.8239 (m-40) cc_final: 0.7934 (m-40) REVERT: A 833 LYS cc_start: 0.8121 (mmtm) cc_final: 0.7605 (mtpp) REVERT: A 852 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.6508 (tmm) REVERT: A 900 ASP cc_start: 0.8481 (p0) cc_final: 0.8191 (p0) REVERT: A 1011 ARG cc_start: 0.6533 (mtp85) cc_final: 0.6229 (mtt90) REVERT: B 92 GLU cc_start: 0.7601 (mt-10) cc_final: 0.6963 (mt-10) REVERT: B 108 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7023 (mt-10) REVERT: B 119 LEU cc_start: 0.7485 (tp) cc_final: 0.7036 (tm) REVERT: B 150 LEU cc_start: 0.7690 (mt) cc_final: 0.7392 (mm) REVERT: B 161 ASP cc_start: 0.5743 (m-30) cc_final: 0.5402 (m-30) REVERT: B 276 THR cc_start: 0.7018 (OUTLIER) cc_final: 0.6731 (p) outliers start: 24 outliers final: 11 residues processed: 154 average time/residue: 0.4290 time to fit residues: 71.5820 Evaluate side-chains 142 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 696 GLN Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 852 MET Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 276 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 40 optimal weight: 0.2980 chunk 94 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 495 ASN ** 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 = 0.3781 r_free = 0.3781 target = 0.154906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.116203 restraints weight = 12089.956| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.83 r_work: 0.3067 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10003 Z= 0.116 Angle : 0.770 29.510 13588 Z= 0.326 Chirality : 0.042 0.180 1555 Planarity : 0.004 0.055 1740 Dihedral : 4.009 28.017 1407 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.62 % Allowed : 16.93 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 1.41 (0.24), residues: 1248 helix: 1.99 (0.22), residues: 545 sheet: -0.39 (0.43), residues: 138 loop : 0.36 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 551 TYR 0.013 0.001 TYR A 869 PHE 0.029 0.001 PHE B 95 TRP 0.011 0.001 TRP A 392 HIS 0.003 0.001 HIS A 557 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (10000) covalent geometry : angle 0.77049 / 0.33 (13582) SS BOND : bond 0.00091 / 0.05 ( 3) SS BOND : angle 0.38743 / 0.21 ( 6) hydrogen bonds : bond 0.03841 / 2.66 ( 483) hydrogen bonds : angle 4.15551 / 3.00 ( 1461) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.304 Fit side-chains REVERT: A 161 PHE cc_start: 0.7862 (m-80) cc_final: 0.7508 (m-80) REVERT: A 238 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.6661 (mp0) REVERT: A 291 PHE cc_start: 0.7736 (OUTLIER) cc_final: 0.6861 (p90) REVERT: A 312 ILE cc_start: 0.7360 (OUTLIER) cc_final: 0.6711 (mp) REVERT: A 399 GLU cc_start: 0.7117 (pt0) cc_final: 0.6604 (pp20) REVERT: A 461 GLU cc_start: 0.6949 (mm-30) cc_final: 0.6653 (mm-30) REVERT: A 488 TYR cc_start: 0.6051 (p90) cc_final: 0.5608 (p90) REVERT: A 636 GLU cc_start: 0.6436 (pt0) cc_final: 0.5915 (pm20) REVERT: A 687 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7316 (mp0) REVERT: A 708 GLN cc_start: 0.7360 (OUTLIER) cc_final: 0.6994 (mp-120) REVERT: A 900 ASP cc_start: 0.8538 (p0) cc_final: 0.8261 (p0) REVERT: A 1011 ARG cc_start: 0.6428 (mtp85) cc_final: 0.6176 (mtt90) REVERT: B 119 LEU cc_start: 0.7492 (tp) cc_final: 0.7008 (tm) REVERT: B 150 LEU cc_start: 0.7624 (mt) cc_final: 0.7301 (mm) REVERT: B 161 ASP cc_start: 0.5750 (m-30) cc_final: 0.5407 (m-30) REVERT: B 276 THR cc_start: 0.7023 (OUTLIER) cc_final: 0.6783 (p) outliers start: 28 outliers final: 12 residues processed: 144 average time/residue: 0.4824 time to fit residues: 75.1370 Evaluate side-chains 140 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 708 GLN Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 276 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 94 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 83 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 495 ASN ** 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 = 0.3772 r_free = 0.3772 target = 0.154119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.115124 restraints weight = 12106.528| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.87 r_work: 0.3093 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 10003 Z= 0.122 Angle : 0.782 29.523 13588 Z= 0.334 Chirality : 0.042 0.179 1555 Planarity : 0.004 0.060 1740 Dihedral : 4.068 27.842 1407 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.81 % Allowed : 17.40 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 1.37 (0.24), residues: 1248 helix: 1.93 (0.22), residues: 539 sheet: -0.39 (0.43), residues: 138 loop : 0.37 (0.27), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 551 TYR 0.013 0.001 TYR B 204 PHE 0.027 0.001 PHE B 95 TRP 0.015 0.001 TRP A 392 HIS 0.004 0.001 HIS B 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (10000) covalent geometry : angle 0.78240 / 0.33 (13582) SS BOND : bond 0.00103 / 0.05 ( 3) SS BOND : angle 0.40050 / 0.22 ( 6) hydrogen bonds : bond 0.03926 / 2.71 ( 483) hydrogen bonds : angle 4.19432 / 3.02 ( 1461) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 0.251 Fit side-chains REVERT: A 161 PHE cc_start: 0.7929 (m-80) cc_final: 0.7652 (m-80) REVERT: A 238 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.6683 (mp0) REVERT: A 291 PHE cc_start: 0.7816 (OUTLIER) cc_final: 0.6930 (p90) REVERT: A 312 ILE cc_start: 0.7411 (OUTLIER) cc_final: 0.6737 (mp) REVERT: A 351 MET cc_start: 0.7715 (OUTLIER) cc_final: 0.7468 (mtm) REVERT: A 399 GLU cc_start: 0.7115 (pt0) cc_final: 0.6674 (pp20) REVERT: A 461 GLU cc_start: 0.6973 (mm-30) cc_final: 0.6673 (mm-30) REVERT: A 488 TYR cc_start: 0.6073 (p90) cc_final: 0.5653 (p90) REVERT: A 591 MET cc_start: 0.7767 (mtt) cc_final: 0.7496 (mtm) REVERT: A 636 GLU cc_start: 0.6475 (pt0) cc_final: 0.5973 (pm20) REVERT: A 687 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7375 (mp0) REVERT: A 708 GLN cc_start: 0.7425 (OUTLIER) cc_final: 0.7069 (mp-120) REVERT: A 797 ASN cc_start: 0.8267 (m-40) cc_final: 0.8002 (m-40) REVERT: A 900 ASP cc_start: 0.8551 (p0) cc_final: 0.8254 (p0) REVERT: A 1011 ARG cc_start: 0.6484 (mtp85) cc_final: 0.6267 (mtt90) REVERT: B 92 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7059 (mt-10) REVERT: B 108 GLU cc_start: 0.7382 (mt-10) cc_final: 0.6933 (mt-10) REVERT: B 111 LYS cc_start: 0.7857 (tppt) cc_final: 0.7300 (tttm) REVERT: B 119 LEU cc_start: 0.7549 (tp) cc_final: 0.7062 (tm) REVERT: B 150 LEU cc_start: 0.7723 (mt) cc_final: 0.7413 (mm) REVERT: B 161 ASP cc_start: 0.5782 (m-30) cc_final: 0.5372 (m-30) REVERT: B 211 ASP cc_start: 0.7301 (t0) cc_final: 0.7056 (t0) REVERT: B 259 LYS cc_start: 0.7707 (tttm) cc_final: 0.7351 (tptp) outliers start: 30 outliers final: 15 residues processed: 154 average time/residue: 0.4767 time to fit residues: 79.1959 Evaluate side-chains 143 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 708 GLN Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 275 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 11 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 68 optimal weight: 0.0270 chunk 101 optimal weight: 3.9990 overall best weight: 1.4042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 495 ASN ** 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 = 0.3741 r_free = 0.3741 target = 0.151678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.112654 restraints weight = 12239.683| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.90 r_work: 0.3033 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10003 Z= 0.154 Angle : 0.812 29.848 13588 Z= 0.353 Chirality : 0.044 0.236 1555 Planarity : 0.004 0.071 1740 Dihedral : 4.330 24.860 1407 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.06 % Allowed : 18.71 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 1.16 (0.24), residues: 1248 helix: 1.72 (0.22), residues: 541 sheet: -0.45 (0.41), residues: 146 loop : 0.30 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 551 TYR 0.016 0.002 TYR B 204 PHE 0.023 0.002 PHE A 793 TRP 0.012 0.002 TRP A 392 HIS 0.005 0.001 HIS B 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.15 (10000) covalent geometry : angle 0.81216 / 0.35 (13582) SS BOND : bond 0.00170 / 0.09 ( 3) SS BOND : angle 0.55947 / 0.31 ( 6) hydrogen bonds : bond 0.04501 / 3.10 ( 483) hydrogen bonds : angle 4.37852 / 3.15 ( 1461) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.289 Fit side-chains REVERT: A 161 PHE cc_start: 0.7876 (m-80) cc_final: 0.7559 (m-80) REVERT: A 238 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.6672 (mp0) REVERT: A 291 PHE cc_start: 0.7843 (OUTLIER) cc_final: 0.6909 (p90) REVERT: A 312 ILE cc_start: 0.7450 (OUTLIER) cc_final: 0.6811 (mp) REVERT: A 399 GLU cc_start: 0.7084 (pt0) cc_final: 0.6673 (pp20) REVERT: A 461 GLU cc_start: 0.6980 (mm-30) cc_final: 0.6637 (mm-30) REVERT: A 488 TYR cc_start: 0.6004 (p90) cc_final: 0.5489 (p90) REVERT: A 515 LEU cc_start: 0.6344 (OUTLIER) cc_final: 0.5878 (pt) REVERT: A 636 GLU cc_start: 0.6495 (pt0) cc_final: 0.6063 (pm20) REVERT: A 687 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7416 (mp0) REVERT: A 708 GLN cc_start: 0.7420 (OUTLIER) cc_final: 0.7068 (mp-120) REVERT: A 833 LYS cc_start: 0.8179 (mmtm) cc_final: 0.7721 (mtpp) REVERT: A 900 ASP cc_start: 0.8635 (p0) cc_final: 0.8336 (p0) REVERT: A 1020 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7880 (mm-30) REVERT: B 95 PHE cc_start: 0.7550 (p90) cc_final: 0.7317 (p90) REVERT: B 108 GLU cc_start: 0.7414 (mt-10) cc_final: 0.6940 (mt-10) REVERT: B 119 LEU cc_start: 0.7661 (tp) cc_final: 0.7154 (tm) REVERT: B 150 LEU cc_start: 0.7590 (mt) cc_final: 0.7243 (mm) REVERT: B 161 ASP cc_start: 0.5905 (m-30) cc_final: 0.5107 (m-30) REVERT: B 211 ASP cc_start: 0.7357 (t0) cc_final: 0.7155 (t0) outliers start: 22 outliers final: 13 residues processed: 146 average time/residue: 0.4603 time to fit residues: 72.5599 Evaluate side-chains 131 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 708 GLN Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 248 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 105 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 52 optimal weight: 0.0270 chunk 49 optimal weight: 5.9990 chunk 93 optimal weight: 0.0970 chunk 98 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 ASN ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.153766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.115128 restraints weight = 12228.879| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.14 r_work: 0.3068 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 10003 Z= 0.112 Angle : 0.782 29.534 13588 Z= 0.336 Chirality : 0.042 0.212 1555 Planarity : 0.004 0.061 1740 Dihedral : 4.048 27.770 1407 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.87 % Allowed : 19.55 % Favored : 78.58 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.17 % 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: 1.35 (0.24), residues: 1248 helix: 1.93 (0.22), residues: 545 sheet: -0.21 (0.44), residues: 128 loop : 0.25 (0.27), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 551 TYR 0.012 0.001 TYR A 869 PHE 0.013 0.001 PHE A 793 TRP 0.017 0.001 TRP A 392 HIS 0.003 0.001 HIS B 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (10000) covalent geometry : angle 0.78253 / 0.34 (13582) SS BOND : bond 0.00075 / 0.04 ( 3) SS BOND : angle 0.33443 / 0.18 ( 6) hydrogen bonds : bond 0.03655 / 2.53 ( 483) hydrogen bonds : angle 4.22665 / 3.04 ( 1461) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.287 Fit side-chains REVERT: A 67 ARG cc_start: 0.7067 (tpp80) cc_final: 0.6831 (tpp-160) REVERT: A 161 PHE cc_start: 0.7936 (m-80) cc_final: 0.7646 (m-80) REVERT: A 238 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7453 (mp0) REVERT: A 291 PHE cc_start: 0.7759 (OUTLIER) cc_final: 0.6777 (p90) REVERT: A 351 MET cc_start: 0.7696 (mtp) cc_final: 0.7442 (mtm) REVERT: A 399 GLU cc_start: 0.7115 (pt0) cc_final: 0.6712 (pp20) REVERT: A 461 GLU cc_start: 0.6962 (mm-30) cc_final: 0.6592 (mm-30) REVERT: A 488 TYR cc_start: 0.6056 (p90) cc_final: 0.5642 (p90) REVERT: A 515 LEU cc_start: 0.6282 (OUTLIER) cc_final: 0.5778 (pt) REVERT: A 636 GLU cc_start: 0.6465 (pt0) cc_final: 0.6045 (pm20) REVERT: A 687 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7289 (mp0) REVERT: A 797 ASN cc_start: 0.8287 (m-40) cc_final: 0.8083 (m-40) REVERT: A 900 ASP cc_start: 0.8474 (p0) cc_final: 0.8137 (p0) REVERT: A 1020 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7918 (mm-30) REVERT: B 92 GLU cc_start: 0.7582 (mt-10) cc_final: 0.6969 (mt-10) REVERT: B 95 PHE cc_start: 0.7517 (p90) cc_final: 0.7298 (p90) REVERT: B 108 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7009 (mt-10) REVERT: B 111 LYS cc_start: 0.7822 (tppt) cc_final: 0.7284 (tttm) REVERT: B 119 LEU cc_start: 0.7632 (tp) cc_final: 0.7135 (tm) REVERT: B 137 LYS cc_start: 0.6987 (pptt) cc_final: 0.6299 (tptp) REVERT: B 150 LEU cc_start: 0.7693 (mt) cc_final: 0.7398 (mm) REVERT: B 161 ASP cc_start: 0.5765 (m-30) cc_final: 0.5290 (m-30) outliers start: 20 outliers final: 15 residues processed: 138 average time/residue: 0.4542 time to fit residues: 67.6896 Evaluate side-chains 139 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 248 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 23 optimal weight: 2.9990 chunk 116 optimal weight: 0.0470 chunk 12 optimal weight: 1.9990 chunk 44 optimal weight: 20.0000 chunk 50 optimal weight: 4.9990 chunk 123 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 overall best weight: 1.3284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 495 ASN ** 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 = 0.3758 r_free = 0.3758 target = 0.153358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.116295 restraints weight = 12328.900| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.30 r_work: 0.3064 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 10003 Z= 0.156 Angle : 1.014 59.174 13588 Z= 0.527 Chirality : 0.053 1.242 1555 Planarity : 0.005 0.098 1740 Dihedral : 4.109 27.740 1407 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.87 % Allowed : 19.55 % Favored : 78.58 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.17 % 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: 1.34 (0.24), residues: 1248 helix: 1.92 (0.22), residues: 545 sheet: -0.20 (0.44), residues: 128 loop : 0.25 (0.27), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 551 TYR 0.012 0.001 TYR A 869 PHE 0.014 0.001 PHE A 793 TRP 0.015 0.002 TRP A 392 HIS 0.003 0.001 HIS B 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.16 (10000) covalent geometry : angle 1.01374 / 0.53 (13582) SS BOND : bond 0.00064 / 0.03 ( 3) SS BOND : angle 0.36574 / 0.20 ( 6) hydrogen bonds : bond 0.03711 / 2.57 ( 483) hydrogen bonds : angle 4.23085 / 3.04 ( 1461) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3272.34 seconds wall clock time: 56 minutes 21.15 seconds (3381.15 seconds total)