Starting phenix.real_space_refine on Thu Sep 18 07:34:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uie_64191/09_2025/9uie_64191.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uie_64191/09_2025/9uie_64191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uie_64191/09_2025/9uie_64191.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uie_64191/09_2025/9uie_64191.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uie_64191/09_2025/9uie_64191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uie_64191/09_2025/9uie_64191.map" } resolution = 2.88 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 31 5.49 5 S 98 5.16 5 C 9351 2.51 5 N 2551 2.21 5 O 2816 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14849 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 659 Classifications: {'RNA': 31} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 16, 'rna3p_pyr': 13} Link IDs: {'rna2p': 2, 'rna3p': 28} Chain: "B" Number of atoms: 7094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 886, 7094 Classifications: {'peptide': 886} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 844} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 7094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 886, 7094 Classifications: {'peptide': 886} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 844} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2928 SG CYS B 284 70.708 58.932 53.571 1.00 51.34 S ATOM 3202 SG CYS B 318 69.883 57.312 50.188 1.00 43.81 S ATOM 3208 SG CYS B 319 67.519 59.898 51.669 1.00 34.07 S ATOM 10022 SG CYS C 284 21.826 73.472 55.444 1.00 39.54 S ATOM 10296 SG CYS C 318 22.580 75.105 51.942 1.00 31.96 S ATOM 10302 SG CYS C 319 25.245 72.941 53.690 1.00 34.55 S Time building chain proxies: 3.66, per 1000 atoms: 0.25 Number of scatterers: 14849 At special positions: 0 Unit cell: (93.7869, 129.252, 130.829, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 98 16.00 P 31 15.00 O 2816 8.00 N 2551 7.00 C 9351 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: 1.25 Conformation dependent library (CDL) restraints added in 638.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" ND1 HIS B 282 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 318 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 284 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 319 " pdb=" ZN C1001 " pdb="ZN ZN C1001 " - pdb=" ND1 HIS C 282 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 319 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 318 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 284 " Number of angles added : 6 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3368 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 18 sheets defined 45.0% alpha, 18.7% beta 9 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'B' and resid 25 through 31 Processing helix chain 'B' and resid 34 through 54 Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 77 through 88 Processing helix chain 'B' and resid 91 through 94 removed outlier: 3.701A pdb=" N LYS B 94 " --> pdb=" O GLY B 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 91 through 94' Processing helix chain 'B' and resid 142 through 159 removed outlier: 4.043A pdb=" N ARG B 159 " --> pdb=" O PHE B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 192 removed outlier: 3.555A pdb=" N ARG B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 239 removed outlier: 3.877A pdb=" N ARG B 223 " --> pdb=" O LYS B 219 " (cutoff:3.500A) Proline residue: B 229 - end of helix Processing helix chain 'B' and resid 263 through 277 Processing helix chain 'B' and resid 340 through 349 Processing helix chain 'B' and resid 380 through 395 removed outlier: 5.102A pdb=" N GLU B 388 " --> pdb=" O HIS B 384 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ALA B 389 " --> pdb=" O LYS B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 417 Processing helix chain 'B' and resid 419 through 429 Processing helix chain 'B' and resid 441 through 446 Processing helix chain 'B' and resid 480 through 499 Processing helix chain 'B' and resid 530 through 534 Processing helix chain 'B' and resid 537 through 554 Processing helix chain 'B' and resid 557 through 581 Processing helix chain 'B' and resid 598 through 615 Processing helix chain 'B' and resid 617 through 619 No H-bonds generated for 'chain 'B' and resid 617 through 619' Processing helix chain 'B' and resid 627 through 638 Processing helix chain 'B' and resid 645 through 651 Processing helix chain 'B' and resid 663 through 667 Processing helix chain 'B' and resid 673 through 683 Processing helix chain 'B' and resid 704 through 708 removed outlier: 3.609A pdb=" N ILE B 708 " --> pdb=" O PRO B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 722 Processing helix chain 'B' and resid 735 through 752 Processing helix chain 'B' and resid 758 through 763 removed outlier: 3.779A pdb=" N LEU B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 766 through 778 Processing helix chain 'B' and resid 790 through 808 Processing helix chain 'B' and resid 811 through 813 No H-bonds generated for 'chain 'B' and resid 811 through 813' Processing helix chain 'B' and resid 821 through 823 No H-bonds generated for 'chain 'B' and resid 821 through 823' Processing helix chain 'B' and resid 824 through 840 Processing helix chain 'B' and resid 889 through 897 removed outlier: 3.563A pdb=" N ARG B 897 " --> pdb=" O CYS B 893 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 32 Processing helix chain 'C' and resid 34 through 54 Processing helix chain 'C' and resid 70 through 75 Processing helix chain 'C' and resid 77 through 88 Processing helix chain 'C' and resid 142 through 159 Processing helix chain 'C' and resid 161 through 165 removed outlier: 4.212A pdb=" N VAL C 164 " --> pdb=" O ARG C 161 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LYS C 165 " --> pdb=" O PRO C 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 161 through 165' Processing helix chain 'C' and resid 180 through 192 removed outlier: 3.661A pdb=" N ARG C 184 " --> pdb=" O GLU C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 238 removed outlier: 3.836A pdb=" N ARG C 223 " --> pdb=" O LYS C 219 " (cutoff:3.500A) Proline residue: C 229 - end of helix Processing helix chain 'C' and resid 263 through 277 Processing helix chain 'C' and resid 340 through 350 Processing helix chain 'C' and resid 380 through 395 removed outlier: 4.929A pdb=" N GLU C 388 " --> pdb=" O HIS C 384 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ALA C 389 " --> pdb=" O LYS C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 417 Processing helix chain 'C' and resid 419 through 429 Processing helix chain 'C' and resid 441 through 446 Processing helix chain 'C' and resid 480 through 499 Processing helix chain 'C' and resid 530 through 534 Processing helix chain 'C' and resid 537 through 554 Processing helix chain 'C' and resid 557 through 581 Processing helix chain 'C' and resid 582 through 585 Processing helix chain 'C' and resid 598 through 615 Processing helix chain 'C' and resid 617 through 619 No H-bonds generated for 'chain 'C' and resid 617 through 619' Processing helix chain 'C' and resid 627 through 638 Processing helix chain 'C' and resid 645 through 651 Processing helix chain 'C' and resid 663 through 667 Processing helix chain 'C' and resid 673 through 683 Processing helix chain 'C' and resid 704 through 708 removed outlier: 3.912A pdb=" N ILE C 708 " --> pdb=" O PRO C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 718 through 722 Processing helix chain 'C' and resid 735 through 752 Processing helix chain 'C' and resid 760 through 765 removed outlier: 3.696A pdb=" N PHE C 765 " --> pdb=" O LEU C 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 766 through 778 Processing helix chain 'C' and resid 790 through 808 Processing helix chain 'C' and resid 811 through 813 No H-bonds generated for 'chain 'C' and resid 811 through 813' Processing helix chain 'C' and resid 821 through 823 No H-bonds generated for 'chain 'C' and resid 821 through 823' Processing helix chain 'C' and resid 824 through 840 Processing helix chain 'C' and resid 866 through 869 Processing helix chain 'C' and resid 889 through 897 removed outlier: 3.549A pdb=" N ARG C 897 " --> pdb=" O CYS C 893 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 16 through 22 removed outlier: 6.140A pdb=" N GLU B 63 " --> pdb=" O VAL B 19 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ARG B 21 " --> pdb=" O GLU B 63 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 131 through 134 Processing sheet with id=AA3, first strand: chain 'B' and resid 178 through 179 removed outlier: 6.318A pdb=" N VAL C 17 " --> pdb=" O LYS C 61 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N GLU C 63 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N VAL C 19 " --> pdb=" O GLU C 63 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 195 through 197 removed outlier: 6.176A pdb=" N LEU B 196 " --> pdb=" O TYR B 300 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N GLN B 301 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LEU B 305 " --> pdb=" O GLN B 301 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA B 211 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 195 through 197 removed outlier: 6.176A pdb=" N LEU B 196 " --> pdb=" O TYR B 300 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N GLN B 301 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LEU B 305 " --> pdb=" O GLN B 301 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 280 through 281 removed outlier: 3.657A pdb=" N VAL B 320 " --> pdb=" O PHE B 281 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 329 through 332 Processing sheet with id=AA8, first strand: chain 'B' and resid 403 through 405 removed outlier: 6.207A pdb=" N GLN B 403 " --> pdb=" O VAL B 436 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N PHE B 438 " --> pdb=" O GLN B 403 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LYS B 405 " --> pdb=" O PHE B 438 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS B 456 " --> pdb=" O ILE B 472 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 641 through 644 removed outlier: 6.131A pdb=" N ILE B 621 " --> pdb=" O GLN B 641 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL B 643 " --> pdb=" O ILE B 621 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N TYR B 623 " --> pdb=" O VAL B 643 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU B 589 " --> pdb=" O LEU B 701 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU B 703 " --> pdb=" O LEU B 589 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILE B 591 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N LYS B 726 " --> pdb=" O GLU B 588 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N PHE B 590 " --> pdb=" O LYS B 726 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ILE B 728 " --> pdb=" O PHE B 590 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N TYR B 592 " --> pdb=" O ILE B 728 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 782 through 789 removed outlier: 6.457A pdb=" N THR B 874 " --> pdb=" O HIS B 901 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N TYR B 903 " --> pdb=" O THR B 874 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL B 876 " --> pdb=" O TYR B 903 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N LEU B 905 " --> pdb=" O VAL B 876 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLY B 878 " --> pdb=" O LEU B 905 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N GLU B 907 " --> pdb=" O GLY B 878 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N SER B 880 " --> pdb=" O GLU B 907 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N SER B 850 " --> pdb=" O LEU B 862 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N SER B 864 " --> pdb=" O SER B 850 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 131 through 134 Processing sheet with id=AB3, first strand: chain 'C' and resid 195 through 197 removed outlier: 6.148A pdb=" N LEU C 196 " --> pdb=" O TYR C 300 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY C 307 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA C 211 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 195 through 197 removed outlier: 6.148A pdb=" N LEU C 196 " --> pdb=" O TYR C 300 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY C 307 " --> pdb=" O VAL C 299 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 280 through 281 Processing sheet with id=AB6, first strand: chain 'C' and resid 329 through 331 Processing sheet with id=AB7, first strand: chain 'C' and resid 403 through 405 removed outlier: 6.265A pdb=" N GLN C 403 " --> pdb=" O VAL C 436 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N PHE C 438 " --> pdb=" O GLN C 403 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LYS C 405 " --> pdb=" O PHE C 438 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N CYS C 456 " --> pdb=" O ILE C 472 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL C 467 " --> pdb=" O ILE C 509 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ARG C 511 " --> pdb=" O VAL C 467 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU C 469 " --> pdb=" O ARG C 511 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE C 513 " --> pdb=" O LEU C 469 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N THR C 471 " --> pdb=" O ILE C 513 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 641 through 644 removed outlier: 6.154A pdb=" N ILE C 621 " --> pdb=" O GLN C 641 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL C 643 " --> pdb=" O ILE C 621 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N TYR C 623 " --> pdb=" O VAL C 643 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU C 589 " --> pdb=" O LEU C 701 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LEU C 703 " --> pdb=" O LEU C 589 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE C 591 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N LYS C 726 " --> pdb=" O GLU C 588 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N PHE C 590 " --> pdb=" O LYS C 726 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ILE C 728 " --> pdb=" O PHE C 590 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TYR C 592 " --> pdb=" O ILE C 728 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 782 through 789 removed outlier: 3.848A pdb=" N ASN C 788 " --> pdb=" O TYR C 906 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N THR C 874 " --> pdb=" O ILE C 899 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N SER C 850 " --> pdb=" O LEU C 862 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N SER C 864 " --> pdb=" O SER C 850 " (cutoff:3.500A) 683 hydrogen bonds defined for protein. 1950 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 3.15 Time building geometry restraints manager: 1.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4654 1.34 - 1.46: 2939 1.46 - 1.58: 7432 1.58 - 1.70: 61 1.70 - 1.82: 140 Bond restraints: 15226 Sorted by residual: bond pdb=" CB LYS B 165 " pdb=" CG LYS B 165 " ideal model delta sigma weight residual 1.520 1.573 -0.053 3.00e-02 1.11e+03 3.13e+00 bond pdb=" CB PRO C 169 " pdb=" CG PRO C 169 " ideal model delta sigma weight residual 1.492 1.563 -0.071 5.00e-02 4.00e+02 1.99e+00 bond pdb=" CB PRO B 169 " pdb=" CG PRO B 169 " ideal model delta sigma weight residual 1.492 1.560 -0.068 5.00e-02 4.00e+02 1.83e+00 bond pdb=" C HIS B 168 " pdb=" N PRO B 169 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.75e+00 bond pdb=" C HIS C 168 " pdb=" N PRO C 169 " ideal model delta sigma weight residual 1.334 1.360 -0.027 2.34e-02 1.83e+03 1.28e+00 ... (remaining 15221 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 20418 2.12 - 4.24: 251 4.24 - 6.37: 27 6.37 - 8.49: 4 8.49 - 10.61: 2 Bond angle restraints: 20702 Sorted by residual: angle pdb=" CB LYS B 165 " pdb=" CG LYS B 165 " pdb=" CD LYS B 165 " ideal model delta sigma weight residual 111.30 120.18 -8.88 2.30e+00 1.89e-01 1.49e+01 angle pdb=" CB MET B 676 " pdb=" CG MET B 676 " pdb=" SD MET B 676 " ideal model delta sigma weight residual 112.70 123.31 -10.61 3.00e+00 1.11e-01 1.25e+01 angle pdb=" CA LYS B 165 " pdb=" CB LYS B 165 " pdb=" CG LYS B 165 " ideal model delta sigma weight residual 114.10 120.87 -6.77 2.00e+00 2.50e-01 1.15e+01 angle pdb=" CB GLU C 407 " pdb=" CG GLU C 407 " pdb=" CD GLU C 407 " ideal model delta sigma weight residual 112.60 117.21 -4.61 1.70e+00 3.46e-01 7.35e+00 angle pdb=" CB GLU B 652 " pdb=" CG GLU B 652 " pdb=" CD GLU B 652 " ideal model delta sigma weight residual 112.60 117.11 -4.51 1.70e+00 3.46e-01 7.04e+00 ... (remaining 20697 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.26: 7848 18.26 - 36.52: 1025 36.52 - 54.78: 348 54.78 - 73.03: 93 73.03 - 91.29: 31 Dihedral angle restraints: 9345 sinusoidal: 4153 harmonic: 5192 Sorted by residual: dihedral pdb=" O4' U A 18 " pdb=" C1' U A 18 " pdb=" N1 U A 18 " pdb=" C2 U A 18 " ideal model delta sinusoidal sigma weight residual -128.00 -70.02 -57.98 1 1.70e+01 3.46e-03 1.56e+01 dihedral pdb=" CA ASP C 97 " pdb=" CB ASP C 97 " pdb=" CG ASP C 97 " pdb=" OD1 ASP C 97 " ideal model delta sinusoidal sigma weight residual -30.00 -86.47 56.47 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CA ASP B 249 " pdb=" CB ASP B 249 " pdb=" CG ASP B 249 " pdb=" OD1 ASP B 249 " ideal model delta sinusoidal sigma weight residual -30.00 -85.05 55.05 1 2.00e+01 2.50e-03 1.03e+01 ... (remaining 9342 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1590 0.040 - 0.080: 544 0.080 - 0.120: 182 0.120 - 0.159: 22 0.159 - 0.199: 1 Chirality restraints: 2339 Sorted by residual: chirality pdb=" CA PRO C 169 " pdb=" N PRO C 169 " pdb=" C PRO C 169 " pdb=" CB PRO C 169 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.93e-01 chirality pdb=" C3' C A 8 " pdb=" C4' C A 8 " pdb=" O3' C A 8 " pdb=" C2' C A 8 " both_signs ideal model delta sigma weight residual False -2.48 -2.64 0.16 2.00e-01 2.50e+01 6.35e-01 chirality pdb=" CA ILE B 177 " pdb=" N ILE B 177 " pdb=" C ILE B 177 " pdb=" CB ILE B 177 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.96e-01 ... (remaining 2336 not shown) Planarity restraints: 2521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 168 " -0.058 5.00e-02 4.00e+02 8.86e-02 1.26e+01 pdb=" N PRO B 169 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO B 169 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 169 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 168 " 0.057 5.00e-02 4.00e+02 8.67e-02 1.20e+01 pdb=" N PRO C 169 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO C 169 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO C 169 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 165 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.80e+00 pdb=" C LYS B 165 " 0.048 2.00e-02 2.50e+03 pdb=" O LYS B 165 " -0.018 2.00e-02 2.50e+03 pdb=" N LYS B 166 " -0.016 2.00e-02 2.50e+03 ... (remaining 2518 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 6580 2.96 - 3.45: 14397 3.45 - 3.93: 25625 3.93 - 4.42: 29178 4.42 - 4.90: 46380 Nonbonded interactions: 122160 Sorted by model distance: nonbonded pdb=" O5' C A 8 " pdb=" O4' C A 8 " model vdw 2.477 2.432 nonbonded pdb=" O5' U A 19 " pdb=" O4' U A 19 " model vdw 2.514 2.432 nonbonded pdb=" O5' U A 18 " pdb=" O4' U A 18 " model vdw 2.517 2.432 nonbonded pdb=" O5' A A 15 " pdb=" O4' A A 15 " model vdw 2.527 2.432 nonbonded pdb=" N GLU C 286 " pdb=" OE1 GLU C 286 " model vdw 2.534 3.120 ... (remaining 122155 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 'B' selection = chain 'C' } 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: 1.170 Set stop_for_unknowns flag: 0.010 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.790 Find NCS groups from input model: 0.200 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: 0.010 Load rotamer database and sin/cos tables:6.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 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 0.071 15234 Z= 0.171 Angle : 0.601 10.609 20708 Z= 0.313 Chirality : 0.044 0.199 2339 Planarity : 0.005 0.089 2521 Dihedral : 18.979 91.293 5977 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.17 % Favored : 96.60 % Rotamer: Outliers : 1.70 % Allowed : 27.42 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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 aren not related in a simple way. whole: 1.07 (0.20), residues: 1764 helix: 1.79 (0.19), residues: 708 sheet: 0.96 (0.32), residues: 268 loop : -0.35 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 214 TYR 0.014 0.002 TYR C 308 PHE 0.018 0.002 PHE B 594 TRP 0.011 0.002 TRP C 329 HIS 0.005 0.001 HIS C 514 Details of bonding type rmsd covalent geometry : bond 0.00411 (15226) covalent geometry : angle 0.60015 (20702) hydrogen bonds : bond 0.17046 ( 690) hydrogen bonds : angle 6.12301 ( 1994) metal coordination : bond 0.01095 ( 8) metal coordination : angle 1.86041 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 195 time to evaluate : 0.612 Fit side-chains REVERT: B 5 LYS cc_start: 0.6104 (tmtp) cc_final: 0.5744 (pttm) REVERT: B 156 ARG cc_start: 0.7140 (ttt90) cc_final: 0.6832 (mtp180) REVERT: B 180 GLU cc_start: 0.7856 (tt0) cc_final: 0.7347 (mp0) REVERT: B 197 MET cc_start: 0.7585 (tpp) cc_final: 0.7316 (mmp) REVERT: B 540 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7319 (mm-30) REVERT: B 657 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8068 (mmtp) REVERT: B 740 LYS cc_start: 0.8061 (ptmt) cc_final: 0.7735 (tptp) REVERT: B 761 THR cc_start: 0.7386 (t) cc_final: 0.6939 (m) REVERT: B 820 ARG cc_start: 0.6970 (tpt90) cc_final: 0.6559 (ttt-90) REVERT: B 821 ARG cc_start: 0.7196 (mtp85) cc_final: 0.6760 (ptm160) REVERT: B 866 GLN cc_start: 0.6847 (pt0) cc_final: 0.6535 (tm-30) REVERT: B 890 HIS cc_start: 0.6818 (p-80) cc_final: 0.6611 (p90) REVERT: C 31 LYS cc_start: 0.7810 (ptpp) cc_final: 0.7329 (mtmt) REVERT: C 63 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8089 (tm-30) REVERT: C 94 LYS cc_start: 0.8426 (mtpp) cc_final: 0.8037 (tptt) REVERT: C 148 GLU cc_start: 0.8019 (tt0) cc_final: 0.7808 (tt0) REVERT: C 180 GLU cc_start: 0.7692 (tt0) cc_final: 0.6915 (mp0) REVERT: C 223 ARG cc_start: 0.7506 (mmt90) cc_final: 0.7120 (mmp80) REVERT: C 261 LYS cc_start: 0.5974 (mtpt) cc_final: 0.5689 (ttmm) REVERT: C 452 GLN cc_start: 0.7539 (pt0) cc_final: 0.7234 (tm-30) REVERT: C 453 ASN cc_start: 0.8033 (m110) cc_final: 0.7244 (t0) REVERT: C 491 GLN cc_start: 0.8542 (mm-40) cc_final: 0.8268 (mm110) REVERT: C 538 GLU cc_start: 0.8164 (mp0) cc_final: 0.7377 (tt0) REVERT: C 650 GLN cc_start: 0.7622 (mt0) cc_final: 0.7315 (mt0) REVERT: C 669 SER cc_start: 0.6168 (p) cc_final: 0.5249 (t) REVERT: C 676 MET cc_start: 0.8131 (tpp) cc_final: 0.7745 (tpp) REVERT: C 748 ARG cc_start: 0.6848 (ttp80) cc_final: 0.6571 (tmm160) REVERT: C 772 GLU cc_start: 0.6390 (mt-10) cc_final: 0.5784 (mm-30) REVERT: C 788 ASN cc_start: 0.7743 (m-40) cc_final: 0.7223 (t0) outliers start: 27 outliers final: 12 residues processed: 216 average time/residue: 0.7928 time to fit residues: 184.7255 Evaluate side-chains 192 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 178 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 657 LYS Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 597 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 98 optimal weight: 0.0870 chunk 107 optimal weight: 0.0770 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 103 HIS B 452 GLN B 636 GLN B 695 HIS ** B 733 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 793 GLN C 72 GLN C 575 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.158253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.119665 restraints weight = 15553.736| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.73 r_work: 0.2997 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.0713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 15234 Z= 0.140 Angle : 0.534 7.243 20708 Z= 0.277 Chirality : 0.042 0.197 2339 Planarity : 0.004 0.087 2521 Dihedral : 12.514 91.377 2407 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.46 % Favored : 96.32 % Rotamer: Outliers : 4.53 % Allowed : 23.40 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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 aren not related in a simple way. whole: 1.03 (0.20), residues: 1764 helix: 1.86 (0.19), residues: 708 sheet: 0.84 (0.32), residues: 268 loop : -0.43 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 531 TYR 0.011 0.001 TYR C 308 PHE 0.014 0.001 PHE B 190 TRP 0.007 0.001 TRP B 329 HIS 0.005 0.001 HIS C 514 Details of bonding type rmsd covalent geometry : bond 0.00319 (15226) covalent geometry : angle 0.53250 (20702) hydrogen bonds : bond 0.04901 ( 690) hydrogen bonds : angle 4.48894 ( 1994) metal coordination : bond 0.01120 ( 8) metal coordination : angle 2.06498 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 183 time to evaluate : 0.584 Fit side-chains REVERT: B 5 LYS cc_start: 0.6182 (tmtp) cc_final: 0.5835 (pttm) REVERT: B 27 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7665 (mp0) REVERT: B 63 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7830 (tm-30) REVERT: B 180 GLU cc_start: 0.7864 (tt0) cc_final: 0.7512 (mp0) REVERT: B 249 ASP cc_start: 0.6160 (OUTLIER) cc_final: 0.5950 (t70) REVERT: B 407 GLU cc_start: 0.7457 (tp30) cc_final: 0.7217 (tp30) REVERT: B 411 LYS cc_start: 0.7957 (mmtm) cc_final: 0.7652 (mptm) REVERT: B 531 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.8227 (tpp80) REVERT: B 540 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7300 (mm-30) REVERT: B 609 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7622 (mppt) REVERT: B 657 LYS cc_start: 0.8320 (mmmm) cc_final: 0.8113 (mmtp) REVERT: B 661 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8409 (mtt) REVERT: B 740 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7736 (tptp) REVERT: B 761 THR cc_start: 0.7461 (t) cc_final: 0.7003 (m) REVERT: B 821 ARG cc_start: 0.7222 (mtp85) cc_final: 0.6718 (ptm160) REVERT: B 823 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6573 (pm20) REVERT: B 866 GLN cc_start: 0.6954 (pt0) cc_final: 0.6560 (tm-30) REVERT: C 10 MET cc_start: 0.6812 (OUTLIER) cc_final: 0.5425 (mmt) REVERT: C 23 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8688 (mt) REVERT: C 31 LYS cc_start: 0.7722 (ptpp) cc_final: 0.7503 (ttpp) REVERT: C 94 LYS cc_start: 0.8453 (mtpp) cc_final: 0.8072 (tptt) REVERT: C 148 GLU cc_start: 0.8076 (tt0) cc_final: 0.7854 (tt0) REVERT: C 173 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6379 (mp) REVERT: C 180 GLU cc_start: 0.7715 (tt0) cc_final: 0.6928 (mp0) REVERT: C 223 ARG cc_start: 0.7478 (mmt90) cc_final: 0.7114 (mmp80) REVERT: C 261 LYS cc_start: 0.5921 (mtpt) cc_final: 0.5636 (ttmm) REVERT: C 452 GLN cc_start: 0.7672 (pt0) cc_final: 0.7289 (tm-30) REVERT: C 491 GLN cc_start: 0.8548 (mm-40) cc_final: 0.8283 (mm110) REVERT: C 650 GLN cc_start: 0.7626 (mt0) cc_final: 0.7361 (mm110) REVERT: C 669 SER cc_start: 0.6208 (p) cc_final: 0.5341 (t) REVERT: C 788 ASN cc_start: 0.7775 (m-40) cc_final: 0.7244 (t0) REVERT: C 820 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.6679 (mtp-110) outliers start: 72 outliers final: 21 residues processed: 234 average time/residue: 0.7903 time to fit residues: 199.4844 Evaluate side-chains 207 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 531 ARG Chi-restraints excluded: chain B residue 609 LYS Chi-restraints excluded: chain B residue 661 MET Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 740 LYS Chi-restraints excluded: chain B residue 823 GLU Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 861 VAL Chi-restraints excluded: chain B residue 864 SER Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 36 CYS Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain C residue 820 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 56 optimal weight: 9.9990 chunk 121 optimal weight: 8.9990 chunk 149 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 72 optimal weight: 0.0070 chunk 39 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 2 optimal weight: 20.0000 chunk 135 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 overall best weight: 2.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 452 GLN B 636 GLN B 793 GLN C 575 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.157711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.119590 restraints weight = 15738.329| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.68 r_work: 0.2986 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 15234 Z= 0.150 Angle : 0.530 8.148 20708 Z= 0.274 Chirality : 0.042 0.198 2339 Planarity : 0.004 0.087 2521 Dihedral : 12.304 89.845 2391 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.57 % Favored : 96.20 % Rotamer: Outliers : 4.40 % Allowed : 23.52 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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 aren not related in a simple way. whole: 1.04 (0.20), residues: 1764 helix: 1.89 (0.19), residues: 706 sheet: 0.77 (0.32), residues: 262 loop : -0.41 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 748 TYR 0.016 0.002 TYR C 308 PHE 0.014 0.001 PHE B 190 TRP 0.006 0.001 TRP B 329 HIS 0.006 0.001 HIS C 514 Details of bonding type rmsd covalent geometry : bond 0.00348 (15226) covalent geometry : angle 0.52850 (20702) hydrogen bonds : bond 0.04763 ( 690) hydrogen bonds : angle 4.34459 ( 1994) metal coordination : bond 0.01150 ( 8) metal coordination : angle 1.99092 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 186 time to evaluate : 0.600 Fit side-chains REVERT: B 5 LYS cc_start: 0.6229 (tmtp) cc_final: 0.5978 (pttp) REVERT: B 23 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8504 (mp) REVERT: B 27 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7670 (mp0) REVERT: B 31 LYS cc_start: 0.7924 (mmtm) cc_final: 0.7662 (mmmt) REVERT: B 63 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7880 (tm-30) REVERT: B 156 ARG cc_start: 0.7346 (ttt90) cc_final: 0.6996 (mtp180) REVERT: B 180 GLU cc_start: 0.7933 (tt0) cc_final: 0.7551 (mp0) REVERT: B 197 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.7482 (mmp) REVERT: B 249 ASP cc_start: 0.6180 (OUTLIER) cc_final: 0.5970 (t70) REVERT: B 531 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8260 (tpp80) REVERT: B 540 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7248 (mm-30) REVERT: B 581 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7453 (mt-10) REVERT: B 609 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7613 (mppt) REVERT: B 657 LYS cc_start: 0.8308 (mmmm) cc_final: 0.8033 (mmtt) REVERT: B 661 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8438 (mtt) REVERT: B 740 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7753 (tptp) REVERT: B 761 THR cc_start: 0.7493 (t) cc_final: 0.7043 (m) REVERT: B 821 ARG cc_start: 0.7312 (mtp85) cc_final: 0.6738 (ptm160) REVERT: B 823 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6583 (pm20) REVERT: B 866 GLN cc_start: 0.7038 (pt0) cc_final: 0.6590 (tm-30) REVERT: C 10 MET cc_start: 0.6820 (OUTLIER) cc_final: 0.5470 (mmt) REVERT: C 23 ILE cc_start: 0.8950 (OUTLIER) cc_final: 0.8690 (mt) REVERT: C 31 LYS cc_start: 0.7778 (ptpp) cc_final: 0.7256 (mtmt) REVERT: C 94 LYS cc_start: 0.8482 (mtpp) cc_final: 0.8074 (tptt) REVERT: C 134 ASP cc_start: 0.8136 (t0) cc_final: 0.7829 (t0) REVERT: C 148 GLU cc_start: 0.8118 (tt0) cc_final: 0.7890 (tt0) REVERT: C 173 LEU cc_start: 0.7207 (OUTLIER) cc_final: 0.6436 (mp) REVERT: C 180 GLU cc_start: 0.7671 (tt0) cc_final: 0.6901 (mp0) REVERT: C 223 ARG cc_start: 0.7609 (mmt90) cc_final: 0.7226 (mmp80) REVERT: C 258 LYS cc_start: 0.7149 (mmtm) cc_final: 0.6816 (mmmm) REVERT: C 261 LYS cc_start: 0.5995 (mtpt) cc_final: 0.5678 (ttmm) REVERT: C 452 GLN cc_start: 0.7657 (pt0) cc_final: 0.7273 (tm-30) REVERT: C 491 GLN cc_start: 0.8535 (mm-40) cc_final: 0.8271 (mm110) REVERT: C 558 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8994 (tp) REVERT: C 650 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.7365 (mm-40) REVERT: C 669 SER cc_start: 0.6125 (p) cc_final: 0.5313 (t) REVERT: C 767 GLU cc_start: 0.6540 (OUTLIER) cc_final: 0.6255 (mp0) REVERT: C 788 ASN cc_start: 0.7814 (m-40) cc_final: 0.7230 (t0) REVERT: C 820 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7380 (mmm-85) outliers start: 70 outliers final: 26 residues processed: 237 average time/residue: 0.7779 time to fit residues: 199.3509 Evaluate side-chains 219 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 175 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 285 CYS Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 531 ARG Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 609 LYS Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 661 MET Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 740 LYS Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 823 GLU Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 861 VAL Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 36 CYS Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 650 GLN Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain C residue 767 GLU Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 820 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 44 optimal weight: 0.6980 chunk 157 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 155 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 167 optimal weight: 9.9990 chunk 78 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 chunk 136 optimal weight: 8.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 452 GLN B 636 GLN B 707 GLN B 793 GLN C 575 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.159894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.121959 restraints weight = 15674.589| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.66 r_work: 0.3015 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 15234 Z= 0.101 Angle : 0.475 8.540 20708 Z= 0.246 Chirality : 0.040 0.199 2339 Planarity : 0.004 0.088 2521 Dihedral : 11.959 87.953 2389 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.34 % Favored : 96.37 % Rotamer: Outliers : 4.21 % Allowed : 23.84 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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 aren not related in a simple way. whole: 1.17 (0.20), residues: 1764 helix: 2.05 (0.19), residues: 706 sheet: 0.74 (0.31), residues: 268 loop : -0.36 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 748 TYR 0.014 0.001 TYR C 308 PHE 0.012 0.001 PHE B 155 TRP 0.005 0.001 TRP B 112 HIS 0.005 0.000 HIS C 514 Details of bonding type rmsd covalent geometry : bond 0.00223 (15226) covalent geometry : angle 0.47380 (20702) hydrogen bonds : bond 0.03892 ( 690) hydrogen bonds : angle 4.17950 ( 1994) metal coordination : bond 0.00628 ( 8) metal coordination : angle 1.88125 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 194 time to evaluate : 0.618 Fit side-chains REVERT: B 5 LYS cc_start: 0.6231 (tmtp) cc_final: 0.5959 (pttp) REVERT: B 23 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8457 (mp) REVERT: B 27 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7699 (mp0) REVERT: B 63 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.7907 (tm-30) REVERT: B 68 THR cc_start: 0.7584 (p) cc_final: 0.7099 (m) REVERT: B 156 ARG cc_start: 0.7397 (ttt90) cc_final: 0.7032 (mtp180) REVERT: B 180 GLU cc_start: 0.7890 (tt0) cc_final: 0.7507 (mp0) REVERT: B 197 MET cc_start: 0.7725 (OUTLIER) cc_final: 0.7479 (mmp) REVERT: B 249 ASP cc_start: 0.6139 (OUTLIER) cc_final: 0.5936 (t70) REVERT: B 285 CYS cc_start: 0.6016 (OUTLIER) cc_final: 0.5774 (m) REVERT: B 407 GLU cc_start: 0.7399 (tp30) cc_final: 0.7113 (tp30) REVERT: B 531 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8242 (tpp80) REVERT: B 540 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7297 (mm-30) REVERT: B 661 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8466 (mtt) REVERT: B 676 MET cc_start: 0.8009 (tpp) cc_final: 0.7780 (tpp) REVERT: B 740 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7716 (tptp) REVERT: B 761 THR cc_start: 0.7457 (t) cc_final: 0.6995 (m) REVERT: B 788 ASN cc_start: 0.6595 (OUTLIER) cc_final: 0.6362 (t0) REVERT: B 821 ARG cc_start: 0.7223 (mtp85) cc_final: 0.6296 (ptm160) REVERT: B 823 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.6512 (pm20) REVERT: B 824 ASP cc_start: 0.7377 (m-30) cc_final: 0.6908 (m-30) REVERT: B 866 GLN cc_start: 0.6966 (pt0) cc_final: 0.6520 (tm-30) REVERT: C 10 MET cc_start: 0.6952 (OUTLIER) cc_final: 0.5617 (mtt) REVERT: C 23 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8691 (mt) REVERT: C 31 LYS cc_start: 0.7738 (ptpp) cc_final: 0.7238 (mtmt) REVERT: C 78 GLN cc_start: 0.8222 (tt0) cc_final: 0.8003 (mt0) REVERT: C 94 LYS cc_start: 0.8445 (mtpp) cc_final: 0.8073 (tptt) REVERT: C 134 ASP cc_start: 0.8151 (t0) cc_final: 0.7848 (t0) REVERT: C 148 GLU cc_start: 0.8109 (tt0) cc_final: 0.7855 (tt0) REVERT: C 173 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6412 (mp) REVERT: C 180 GLU cc_start: 0.7600 (tt0) cc_final: 0.6875 (mp0) REVERT: C 202 LEU cc_start: 0.7987 (mp) cc_final: 0.7707 (mt) REVERT: C 223 ARG cc_start: 0.7552 (mmt90) cc_final: 0.7169 (mmp80) REVERT: C 258 LYS cc_start: 0.7137 (mmtm) cc_final: 0.6727 (mmmm) REVERT: C 261 LYS cc_start: 0.5931 (mtpt) cc_final: 0.5585 (ttmm) REVERT: C 491 GLN cc_start: 0.8514 (mm-40) cc_final: 0.8250 (mm110) REVERT: C 540 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7298 (mm-30) REVERT: C 558 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8916 (tp) REVERT: C 649 MET cc_start: 0.8276 (mmm) cc_final: 0.8073 (mmp) REVERT: C 650 GLN cc_start: 0.7573 (mt0) cc_final: 0.7361 (mm110) REVERT: C 669 SER cc_start: 0.6056 (p) cc_final: 0.5245 (t) REVERT: C 788 ASN cc_start: 0.7760 (m-40) cc_final: 0.7195 (t0) REVERT: C 820 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7348 (mmm-85) REVERT: C 827 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.6457 (ptm160) outliers start: 67 outliers final: 18 residues processed: 243 average time/residue: 0.7969 time to fit residues: 209.2382 Evaluate side-chains 215 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 180 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 285 CYS Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 531 ARG Chi-restraints excluded: chain B residue 661 MET Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 740 LYS Chi-restraints excluded: chain B residue 788 ASN Chi-restraints excluded: chain B residue 823 GLU Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 36 CYS Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 820 ARG Chi-restraints excluded: chain C residue 827 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 154 optimal weight: 7.9990 chunk 116 optimal weight: 7.9990 chunk 75 optimal weight: 0.6980 chunk 128 optimal weight: 0.7980 chunk 143 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 141 optimal weight: 0.9980 chunk 163 optimal weight: 20.0000 chunk 73 optimal weight: 0.3980 chunk 86 optimal weight: 4.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 452 GLN B 636 GLN B 707 GLN B 793 GLN C 575 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.159883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.122632 restraints weight = 15675.248| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.67 r_work: 0.3011 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 15234 Z= 0.112 Angle : 0.486 9.172 20708 Z= 0.250 Chirality : 0.041 0.198 2339 Planarity : 0.004 0.088 2521 Dihedral : 11.812 87.042 2388 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.46 % Favored : 96.26 % Rotamer: Outliers : 3.71 % Allowed : 24.21 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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 aren not related in a simple way. whole: 1.17 (0.20), residues: 1764 helix: 2.05 (0.19), residues: 708 sheet: 0.74 (0.32), residues: 264 loop : -0.37 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 531 TYR 0.012 0.001 TYR C 308 PHE 0.011 0.001 PHE B 155 TRP 0.005 0.001 TRP B 329 HIS 0.003 0.001 HIS C 514 Details of bonding type rmsd covalent geometry : bond 0.00258 (15226) covalent geometry : angle 0.48434 (20702) hydrogen bonds : bond 0.04005 ( 690) hydrogen bonds : angle 4.13121 ( 1994) metal coordination : bond 0.00969 ( 8) metal coordination : angle 2.02968 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 185 time to evaluate : 0.548 Fit side-chains REVERT: B 5 LYS cc_start: 0.6270 (tmtp) cc_final: 0.6006 (pttp) REVERT: B 23 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8465 (mp) REVERT: B 27 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7627 (mp0) REVERT: B 31 LYS cc_start: 0.7900 (mmtm) cc_final: 0.7619 (mmmt) REVERT: B 63 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7869 (tm-30) REVERT: B 68 THR cc_start: 0.7579 (p) cc_final: 0.7089 (m) REVERT: B 156 ARG cc_start: 0.7384 (ttt90) cc_final: 0.7027 (mtp180) REVERT: B 180 GLU cc_start: 0.7887 (tt0) cc_final: 0.7510 (mp0) REVERT: B 197 MET cc_start: 0.7723 (OUTLIER) cc_final: 0.7481 (mmp) REVERT: B 407 GLU cc_start: 0.7293 (tp30) cc_final: 0.7065 (tp30) REVERT: B 531 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8236 (tpp80) REVERT: B 540 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7300 (mm-30) REVERT: B 581 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7309 (mt-10) REVERT: B 609 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7513 (mppt) REVERT: B 661 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8437 (mtt) REVERT: B 676 MET cc_start: 0.7903 (tpp) cc_final: 0.7606 (tpp) REVERT: B 740 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7718 (tptp) REVERT: B 761 THR cc_start: 0.7438 (t) cc_final: 0.6971 (m) REVERT: B 788 ASN cc_start: 0.6588 (OUTLIER) cc_final: 0.6354 (t0) REVERT: B 821 ARG cc_start: 0.7134 (mtp85) cc_final: 0.6278 (ptm160) REVERT: B 823 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6446 (pm20) REVERT: B 824 ASP cc_start: 0.7400 (m-30) cc_final: 0.6910 (m-30) REVERT: B 866 GLN cc_start: 0.6928 (pt0) cc_final: 0.6488 (tm-30) REVERT: C 10 MET cc_start: 0.6938 (OUTLIER) cc_final: 0.5703 (mtt) REVERT: C 23 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8684 (mt) REVERT: C 31 LYS cc_start: 0.7715 (ptpp) cc_final: 0.7258 (mtmt) REVERT: C 63 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8111 (tm-30) REVERT: C 94 LYS cc_start: 0.8450 (mtpp) cc_final: 0.8091 (tptt) REVERT: C 134 ASP cc_start: 0.8157 (t0) cc_final: 0.7850 (t0) REVERT: C 148 GLU cc_start: 0.8083 (tt0) cc_final: 0.7837 (tt0) REVERT: C 173 LEU cc_start: 0.7135 (OUTLIER) cc_final: 0.6440 (mp) REVERT: C 180 GLU cc_start: 0.7606 (tt0) cc_final: 0.6904 (mp0) REVERT: C 202 LEU cc_start: 0.7983 (mp) cc_final: 0.7684 (mt) REVERT: C 223 ARG cc_start: 0.7610 (mmt90) cc_final: 0.7201 (mmp80) REVERT: C 258 LYS cc_start: 0.7120 (mmtm) cc_final: 0.6705 (mmmm) REVERT: C 261 LYS cc_start: 0.5967 (mtpt) cc_final: 0.5633 (ttmm) REVERT: C 491 GLN cc_start: 0.8523 (mm-40) cc_final: 0.8257 (mm110) REVERT: C 540 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7331 (mm-30) REVERT: C 558 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8915 (tp) REVERT: C 650 GLN cc_start: 0.7549 (mt0) cc_final: 0.7289 (mm110) REVERT: C 669 SER cc_start: 0.6056 (p) cc_final: 0.5239 (t) REVERT: C 788 ASN cc_start: 0.7765 (m-40) cc_final: 0.7181 (t0) REVERT: C 820 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.7329 (mmm-85) REVERT: C 827 ARG cc_start: 0.7046 (OUTLIER) cc_final: 0.6467 (ptm160) outliers start: 59 outliers final: 19 residues processed: 230 average time/residue: 0.7289 time to fit residues: 181.1739 Evaluate side-chains 212 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 175 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 285 CYS Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 531 ARG Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 609 LYS Chi-restraints excluded: chain B residue 661 MET Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 740 LYS Chi-restraints excluded: chain B residue 788 ASN Chi-restraints excluded: chain B residue 823 GLU Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 36 CYS Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 820 ARG Chi-restraints excluded: chain C residue 827 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 124 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 152 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN B 452 GLN B 636 GLN B 666 ASN ** B 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 707 GLN B 793 GLN C 575 GLN C 714 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.156525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.119020 restraints weight = 15543.732| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.63 r_work: 0.2977 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 15234 Z= 0.206 Angle : 0.585 9.513 20708 Z= 0.302 Chirality : 0.044 0.200 2339 Planarity : 0.005 0.086 2521 Dihedral : 11.967 88.010 2388 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.63 % Favored : 96.03 % Rotamer: Outliers : 4.21 % Allowed : 23.90 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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 aren not related in a simple way. whole: 0.89 (0.20), residues: 1764 helix: 1.83 (0.19), residues: 704 sheet: 0.68 (0.32), residues: 262 loop : -0.55 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 531 TYR 0.017 0.002 TYR C 231 PHE 0.015 0.002 PHE B 155 TRP 0.009 0.002 TRP B 329 HIS 0.005 0.001 HIS C 901 Details of bonding type rmsd covalent geometry : bond 0.00496 (15226) covalent geometry : angle 0.58368 (20702) hydrogen bonds : bond 0.05080 ( 690) hydrogen bonds : angle 4.32834 ( 1994) metal coordination : bond 0.01438 ( 8) metal coordination : angle 2.25307 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 177 time to evaluate : 0.643 Fit side-chains revert: symmetry clash REVERT: B 5 LYS cc_start: 0.6381 (tmtp) cc_final: 0.6092 (pttp) REVERT: B 23 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8515 (mp) REVERT: B 27 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7689 (mp0) REVERT: B 63 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.7988 (tm-30) REVERT: B 156 ARG cc_start: 0.7303 (ttt90) cc_final: 0.6977 (mtp180) REVERT: B 180 GLU cc_start: 0.7925 (tt0) cc_final: 0.7522 (mp0) REVERT: B 197 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7462 (mmp) REVERT: B 540 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7305 (mm-30) REVERT: B 581 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7477 (mt-10) REVERT: B 609 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7579 (mppt) REVERT: B 661 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8386 (mtt) REVERT: B 676 MET cc_start: 0.7882 (tpp) cc_final: 0.7564 (tpp) REVERT: B 740 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7737 (tptp) REVERT: B 761 THR cc_start: 0.7467 (t) cc_final: 0.7066 (m) REVERT: B 821 ARG cc_start: 0.7218 (mtp85) cc_final: 0.6632 (ptm160) REVERT: B 866 GLN cc_start: 0.7073 (pt0) cc_final: 0.6666 (tm-30) REVERT: C 10 MET cc_start: 0.6825 (OUTLIER) cc_final: 0.5601 (mtt) REVERT: C 23 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8695 (mt) REVERT: C 31 LYS cc_start: 0.7761 (ptpp) cc_final: 0.7475 (ttpp) REVERT: C 63 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8124 (tm-30) REVERT: C 94 LYS cc_start: 0.8450 (mtpp) cc_final: 0.8054 (tptt) REVERT: C 134 ASP cc_start: 0.8135 (t0) cc_final: 0.7854 (t0) REVERT: C 148 GLU cc_start: 0.8130 (tt0) cc_final: 0.7908 (tt0) REVERT: C 173 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.6539 (mp) REVERT: C 180 GLU cc_start: 0.7632 (tt0) cc_final: 0.6896 (mp0) REVERT: C 202 LEU cc_start: 0.7943 (mp) cc_final: 0.7685 (mt) REVERT: C 223 ARG cc_start: 0.7709 (mmt90) cc_final: 0.7284 (mmp80) REVERT: C 258 LYS cc_start: 0.7201 (mmtm) cc_final: 0.6753 (mmmm) REVERT: C 452 GLN cc_start: 0.7694 (pt0) cc_final: 0.7194 (tm-30) REVERT: C 491 GLN cc_start: 0.8519 (mm-40) cc_final: 0.8237 (mm110) REVERT: C 650 GLN cc_start: 0.7596 (mt0) cc_final: 0.7283 (mm110) REVERT: C 669 SER cc_start: 0.6126 (p) cc_final: 0.5330 (t) REVERT: C 788 ASN cc_start: 0.7803 (m-40) cc_final: 0.7133 (t0) REVERT: C 820 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.7408 (mmm-85) outliers start: 67 outliers final: 28 residues processed: 229 average time/residue: 0.7696 time to fit residues: 190.4153 Evaluate side-chains 214 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 173 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 285 CYS Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 609 LYS Chi-restraints excluded: chain B residue 661 MET Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 740 LYS Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 861 VAL Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 36 CYS Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 184 ARG Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 627 SER Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 820 ARG Chi-restraints excluded: chain C residue 827 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 107 optimal weight: 50.0000 chunk 93 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 164 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 135 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 452 GLN B 636 GLN B 666 ASN ** B 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 707 GLN ** B 733 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 793 GLN C 575 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.156372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.118955 restraints weight = 15609.290| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.63 r_work: 0.2975 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 15234 Z= 0.199 Angle : 0.580 8.875 20708 Z= 0.300 Chirality : 0.044 0.203 2339 Planarity : 0.005 0.088 2521 Dihedral : 11.972 88.505 2388 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.80 % Favored : 95.86 % Rotamer: Outliers : 4.40 % Allowed : 24.21 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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 aren not related in a simple way. whole: 0.75 (0.20), residues: 1764 helix: 1.72 (0.19), residues: 704 sheet: 0.57 (0.32), residues: 262 loop : -0.62 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 531 TYR 0.016 0.002 TYR C 231 PHE 0.018 0.002 PHE B 155 TRP 0.009 0.002 TRP B 329 HIS 0.006 0.001 HIS C 514 Details of bonding type rmsd covalent geometry : bond 0.00478 (15226) covalent geometry : angle 0.57893 (20702) hydrogen bonds : bond 0.05001 ( 690) hydrogen bonds : angle 4.34819 ( 1994) metal coordination : bond 0.01402 ( 8) metal coordination : angle 1.99884 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 174 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: B 5 LYS cc_start: 0.6406 (tmtp) cc_final: 0.6177 (pttp) REVERT: B 23 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8523 (mp) REVERT: B 27 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7650 (mp0) REVERT: B 31 LYS cc_start: 0.7891 (mmtm) cc_final: 0.7658 (mmmt) REVERT: B 63 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.7961 (tm-30) REVERT: B 156 ARG cc_start: 0.7333 (ttt90) cc_final: 0.6990 (mtp180) REVERT: B 180 GLU cc_start: 0.7923 (tt0) cc_final: 0.7537 (mp0) REVERT: B 197 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7460 (mmp) REVERT: B 540 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7381 (mm-30) REVERT: B 581 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7442 (mt-10) REVERT: B 609 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7641 (mppt) REVERT: B 661 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8383 (mtt) REVERT: B 740 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7758 (tptp) REVERT: B 761 THR cc_start: 0.7463 (t) cc_final: 0.7054 (m) REVERT: B 821 ARG cc_start: 0.7236 (mtp85) cc_final: 0.6585 (ptm160) REVERT: B 866 GLN cc_start: 0.6975 (pt0) cc_final: 0.6619 (tm-30) REVERT: C 10 MET cc_start: 0.6881 (OUTLIER) cc_final: 0.5659 (mtt) REVERT: C 23 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8696 (mt) REVERT: C 31 LYS cc_start: 0.7822 (ptpp) cc_final: 0.7525 (ttpp) REVERT: C 94 LYS cc_start: 0.8448 (mtpp) cc_final: 0.8048 (tptt) REVERT: C 134 ASP cc_start: 0.8083 (t0) cc_final: 0.7789 (t0) REVERT: C 148 GLU cc_start: 0.8123 (tt0) cc_final: 0.7894 (tt0) REVERT: C 168 HIS cc_start: 0.2995 (OUTLIER) cc_final: 0.2148 (m90) REVERT: C 173 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6579 (mp) REVERT: C 180 GLU cc_start: 0.7667 (tt0) cc_final: 0.6943 (mp0) REVERT: C 202 LEU cc_start: 0.7963 (mp) cc_final: 0.7722 (mt) REVERT: C 223 ARG cc_start: 0.7740 (mmt90) cc_final: 0.7285 (mmp80) REVERT: C 258 LYS cc_start: 0.7225 (mmtm) cc_final: 0.6751 (mmmm) REVERT: C 261 LYS cc_start: 0.6257 (mtpt) cc_final: 0.5813 (ttmm) REVERT: C 452 GLN cc_start: 0.7587 (pt0) cc_final: 0.7127 (tm-30) REVERT: C 650 GLN cc_start: 0.7512 (mt0) cc_final: 0.7279 (mm110) REVERT: C 669 SER cc_start: 0.6192 (p) cc_final: 0.5233 (t) REVERT: C 788 ASN cc_start: 0.7830 (m-40) cc_final: 0.7058 (t0) REVERT: C 789 LEU cc_start: 0.8171 (mt) cc_final: 0.7958 (mp) REVERT: C 820 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7084 (mmm160) outliers start: 70 outliers final: 34 residues processed: 226 average time/residue: 0.7635 time to fit residues: 186.9599 Evaluate side-chains 217 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 170 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 285 CYS Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 609 LYS Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 661 MET Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 740 LYS Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 813 LYS Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 861 VAL Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 36 CYS Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 184 ARG Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 695 HIS Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 820 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 66 optimal weight: 8.9990 chunk 104 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 172 optimal weight: 0.0470 chunk 78 optimal weight: 6.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN B 452 GLN B 636 GLN ** B 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 707 GLN ** B 733 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 793 GLN C 575 GLN C 793 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.158944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.121040 restraints weight = 15535.185| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.65 r_work: 0.3024 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 15234 Z= 0.102 Angle : 0.488 8.596 20708 Z= 0.253 Chirality : 0.040 0.202 2339 Planarity : 0.004 0.088 2521 Dihedral : 11.648 86.409 2388 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.34 % Favored : 96.32 % Rotamer: Outliers : 3.40 % Allowed : 25.41 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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 aren not related in a simple way. whole: 1.01 (0.20), residues: 1764 helix: 1.97 (0.19), residues: 708 sheet: 0.60 (0.32), residues: 264 loop : -0.48 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 531 TYR 0.014 0.001 TYR C 308 PHE 0.012 0.001 PHE B 567 TRP 0.006 0.001 TRP B 112 HIS 0.003 0.001 HIS C 514 Details of bonding type rmsd covalent geometry : bond 0.00225 (15226) covalent geometry : angle 0.48764 (20702) hydrogen bonds : bond 0.03862 ( 690) hydrogen bonds : angle 4.17671 ( 1994) metal coordination : bond 0.00512 ( 8) metal coordination : angle 1.72732 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 181 time to evaluate : 0.717 Fit side-chains REVERT: B 5 LYS cc_start: 0.6391 (tmtp) cc_final: 0.6088 (pttp) REVERT: B 23 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8456 (mp) REVERT: B 27 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7666 (mp0) REVERT: B 31 LYS cc_start: 0.7866 (mmtm) cc_final: 0.7466 (mtmm) REVERT: B 156 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.6994 (mtp180) REVERT: B 180 GLU cc_start: 0.7859 (tt0) cc_final: 0.7507 (mp0) REVERT: B 192 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7142 (mtpt) REVERT: B 260 GLU cc_start: 0.6096 (OUTLIER) cc_final: 0.5896 (pm20) REVERT: B 540 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7305 (mm-30) REVERT: B 661 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8449 (mtt) REVERT: B 740 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7716 (tptp) REVERT: B 761 THR cc_start: 0.7428 (t) cc_final: 0.7012 (m) REVERT: B 821 ARG cc_start: 0.7053 (mtp85) cc_final: 0.6521 (ptm160) REVERT: B 866 GLN cc_start: 0.6985 (pt0) cc_final: 0.6537 (tm-30) REVERT: C 10 MET cc_start: 0.6932 (OUTLIER) cc_final: 0.5629 (mtt) REVERT: C 23 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8690 (mt) REVERT: C 31 LYS cc_start: 0.7721 (ptpp) cc_final: 0.7216 (mtmt) REVERT: C 94 LYS cc_start: 0.8434 (mtpp) cc_final: 0.8071 (tptt) REVERT: C 134 ASP cc_start: 0.8123 (t0) cc_final: 0.7848 (t0) REVERT: C 148 GLU cc_start: 0.8072 (tt0) cc_final: 0.7825 (tt0) REVERT: C 173 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6465 (mp) REVERT: C 180 GLU cc_start: 0.7590 (tt0) cc_final: 0.6873 (mp0) REVERT: C 202 LEU cc_start: 0.7924 (mp) cc_final: 0.7683 (mt) REVERT: C 223 ARG cc_start: 0.7711 (mmt90) cc_final: 0.7277 (mmp80) REVERT: C 258 LYS cc_start: 0.7188 (mmtm) cc_final: 0.6720 (mmmm) REVERT: C 261 LYS cc_start: 0.6211 (mtpt) cc_final: 0.5814 (ttmm) REVERT: C 540 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7353 (mm-30) REVERT: C 558 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8918 (tp) REVERT: C 650 GLN cc_start: 0.7570 (mt0) cc_final: 0.7343 (mm110) REVERT: C 669 SER cc_start: 0.6078 (p) cc_final: 0.5272 (t) REVERT: C 676 MET cc_start: 0.8192 (tpp) cc_final: 0.7867 (tpp) REVERT: C 788 ASN cc_start: 0.7808 (m-40) cc_final: 0.7157 (t0) REVERT: C 820 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.7036 (mmm160) outliers start: 54 outliers final: 23 residues processed: 221 average time/residue: 0.8009 time to fit residues: 191.5279 Evaluate side-chains 206 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 171 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 285 CYS Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 385 LYS Chi-restraints excluded: chain B residue 661 MET Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 740 LYS Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 36 CYS Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain C residue 785 THR Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 820 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 127 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 144 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 153 optimal weight: 0.3980 chunk 111 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 175 optimal weight: 9.9990 chunk 173 optimal weight: 0.4980 chunk 149 optimal weight: 0.5980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 452 GLN B 636 GLN ** B 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 793 GLN C 575 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.158089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.120636 restraints weight = 15623.237| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.67 r_work: 0.2993 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 15234 Z= 0.131 Angle : 0.521 8.514 20708 Z= 0.268 Chirality : 0.041 0.201 2339 Planarity : 0.004 0.087 2521 Dihedral : 11.674 86.281 2388 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.68 % Favored : 95.98 % Rotamer: Outliers : 2.83 % Allowed : 25.91 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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 aren not related in a simple way. whole: 1.02 (0.20), residues: 1764 helix: 1.97 (0.19), residues: 706 sheet: 0.60 (0.32), residues: 264 loop : -0.47 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 800 TYR 0.014 0.001 TYR C 308 PHE 0.016 0.001 PHE B 155 TRP 0.006 0.001 TRP B 329 HIS 0.006 0.001 HIS C 514 Details of bonding type rmsd covalent geometry : bond 0.00309 (15226) covalent geometry : angle 0.51977 (20702) hydrogen bonds : bond 0.04219 ( 690) hydrogen bonds : angle 4.17180 ( 1994) metal coordination : bond 0.00888 ( 8) metal coordination : angle 1.82069 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 173 time to evaluate : 0.716 Fit side-chains REVERT: B 5 LYS cc_start: 0.6408 (tmtp) cc_final: 0.6140 (pttp) REVERT: B 23 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8478 (mp) REVERT: B 27 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7684 (mp0) REVERT: B 31 LYS cc_start: 0.7871 (mmtm) cc_final: 0.7466 (mtmm) REVERT: B 63 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7832 (tm-30) REVERT: B 156 ARG cc_start: 0.7348 (OUTLIER) cc_final: 0.6983 (mtp180) REVERT: B 180 GLU cc_start: 0.7870 (tt0) cc_final: 0.7506 (mp0) REVERT: B 192 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7138 (mtpt) REVERT: B 260 GLU cc_start: 0.6084 (OUTLIER) cc_final: 0.5844 (pp20) REVERT: B 540 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7302 (mm-30) REVERT: B 661 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8439 (mtt) REVERT: B 740 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7685 (tptp) REVERT: B 761 THR cc_start: 0.7414 (t) cc_final: 0.7004 (m) REVERT: B 788 ASN cc_start: 0.6623 (OUTLIER) cc_final: 0.6390 (t0) REVERT: B 800 ARG cc_start: 0.7399 (mtm110) cc_final: 0.6954 (mtm-85) REVERT: B 821 ARG cc_start: 0.7040 (mtp85) cc_final: 0.6504 (ptm160) REVERT: B 866 GLN cc_start: 0.6988 (pt0) cc_final: 0.6535 (tm-30) REVERT: C 10 MET cc_start: 0.6890 (OUTLIER) cc_final: 0.5708 (mtt) REVERT: C 23 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8690 (mt) REVERT: C 31 LYS cc_start: 0.7740 (ptpp) cc_final: 0.7265 (mtmt) REVERT: C 94 LYS cc_start: 0.8438 (mtpp) cc_final: 0.8073 (tptt) REVERT: C 134 ASP cc_start: 0.8113 (t0) cc_final: 0.7833 (t0) REVERT: C 148 GLU cc_start: 0.8100 (tt0) cc_final: 0.7846 (tt0) REVERT: C 173 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6478 (mp) REVERT: C 180 GLU cc_start: 0.7626 (tt0) cc_final: 0.6899 (mp0) REVERT: C 202 LEU cc_start: 0.7950 (mp) cc_final: 0.7686 (mt) REVERT: C 223 ARG cc_start: 0.7702 (mmt90) cc_final: 0.7254 (mmp80) REVERT: C 258 LYS cc_start: 0.7180 (mmtm) cc_final: 0.6708 (mmmm) REVERT: C 261 LYS cc_start: 0.6239 (mtpt) cc_final: 0.5839 (ttmm) REVERT: C 491 GLN cc_start: 0.8512 (mm-40) cc_final: 0.8247 (mm110) REVERT: C 540 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7318 (mm-30) REVERT: C 558 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8942 (tp) REVERT: C 650 GLN cc_start: 0.7592 (mt0) cc_final: 0.7333 (mm110) REVERT: C 669 SER cc_start: 0.6086 (p) cc_final: 0.5278 (t) REVERT: C 676 MET cc_start: 0.8196 (tpp) cc_final: 0.7879 (tpp) REVERT: C 820 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7056 (mmm160) outliers start: 45 outliers final: 23 residues processed: 211 average time/residue: 0.7430 time to fit residues: 170.2865 Evaluate side-chains 207 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 170 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 285 CYS Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 661 MET Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 740 LYS Chi-restraints excluded: chain B residue 788 ASN Chi-restraints excluded: chain B residue 813 LYS Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 36 CYS Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 785 THR Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 820 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 109 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 1 optimal weight: 20.0000 chunk 41 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 123 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN B 452 GLN B 636 GLN ** B 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 793 GLN C 575 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.157729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.119014 restraints weight = 15502.959| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.74 r_work: 0.2984 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 15234 Z= 0.138 Angle : 0.534 8.365 20708 Z= 0.274 Chirality : 0.042 0.201 2339 Planarity : 0.004 0.086 2521 Dihedral : 11.675 86.185 2388 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.85 % Favored : 95.80 % Rotamer: Outliers : 2.52 % Allowed : 26.23 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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 aren not related in a simple way. whole: 0.99 (0.20), residues: 1764 helix: 1.95 (0.19), residues: 708 sheet: 0.62 (0.32), residues: 262 loop : -0.51 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 800 TYR 0.015 0.001 TYR C 308 PHE 0.018 0.001 PHE B 155 TRP 0.007 0.001 TRP B 856 HIS 0.003 0.001 HIS C 859 Details of bonding type rmsd covalent geometry : bond 0.00327 (15226) covalent geometry : angle 0.53261 (20702) hydrogen bonds : bond 0.04337 ( 690) hydrogen bonds : angle 4.19171 ( 1994) metal coordination : bond 0.00957 ( 8) metal coordination : angle 1.91291 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 172 time to evaluate : 0.635 Fit side-chains REVERT: B 5 LYS cc_start: 0.6445 (tmtp) cc_final: 0.6184 (pttp) REVERT: B 10 MET cc_start: 0.6936 (ptm) cc_final: 0.6655 (ptp) REVERT: B 23 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8486 (mp) REVERT: B 27 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7693 (mp0) REVERT: B 31 LYS cc_start: 0.7895 (mmtm) cc_final: 0.7513 (mtmm) REVERT: B 63 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7859 (tm-30) REVERT: B 156 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.7001 (mtp180) REVERT: B 180 GLU cc_start: 0.7877 (tt0) cc_final: 0.7529 (mp0) REVERT: B 192 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7171 (mtpt) REVERT: B 540 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7339 (mm-30) REVERT: B 609 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7483 (mppt) REVERT: B 661 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8469 (mtt) REVERT: B 740 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7707 (tptp) REVERT: B 761 THR cc_start: 0.7419 (t) cc_final: 0.7013 (m) REVERT: B 788 ASN cc_start: 0.6638 (OUTLIER) cc_final: 0.6408 (t0) REVERT: B 821 ARG cc_start: 0.7078 (mtp85) cc_final: 0.6521 (ptm160) REVERT: B 866 GLN cc_start: 0.7021 (pt0) cc_final: 0.6560 (tm-30) REVERT: C 10 MET cc_start: 0.6863 (OUTLIER) cc_final: 0.5706 (mtt) REVERT: C 23 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8688 (mt) REVERT: C 31 LYS cc_start: 0.7739 (ptpp) cc_final: 0.7259 (mtmt) REVERT: C 94 LYS cc_start: 0.8444 (mtpp) cc_final: 0.8071 (tptt) REVERT: C 134 ASP cc_start: 0.8137 (t0) cc_final: 0.7830 (t0) REVERT: C 148 GLU cc_start: 0.8116 (tt0) cc_final: 0.7870 (tt0) REVERT: C 173 LEU cc_start: 0.7156 (OUTLIER) cc_final: 0.6461 (mp) REVERT: C 180 GLU cc_start: 0.7660 (tt0) cc_final: 0.6919 (mp0) REVERT: C 202 LEU cc_start: 0.7945 (mp) cc_final: 0.7690 (mt) REVERT: C 223 ARG cc_start: 0.7719 (mmt90) cc_final: 0.7191 (mmp80) REVERT: C 258 LYS cc_start: 0.7150 (mmtm) cc_final: 0.6691 (mmmm) REVERT: C 261 LYS cc_start: 0.6256 (mtpt) cc_final: 0.5849 (ttmm) REVERT: C 491 GLN cc_start: 0.8524 (mm-40) cc_final: 0.8261 (mm110) REVERT: C 558 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.9001 (tp) REVERT: C 650 GLN cc_start: 0.7595 (mt0) cc_final: 0.7308 (mm-40) REVERT: C 669 SER cc_start: 0.6081 (p) cc_final: 0.5274 (t) REVERT: C 676 MET cc_start: 0.8143 (tpp) cc_final: 0.7755 (tpp) REVERT: C 820 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7380 (mmm-85) outliers start: 40 outliers final: 23 residues processed: 205 average time/residue: 0.7781 time to fit residues: 172.9671 Evaluate side-chains 204 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 167 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 285 CYS Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 609 LYS Chi-restraints excluded: chain B residue 661 MET Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 740 LYS Chi-restraints excluded: chain B residue 788 ASN Chi-restraints excluded: chain B residue 813 LYS Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 861 VAL Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 36 CYS Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain C residue 785 THR Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 820 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 29 optimal weight: 0.9980 chunk 158 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 153 optimal weight: 7.9990 chunk 172 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 chunk 3 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 164 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN B 452 GLN B 636 GLN ** B 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 793 GLN C 575 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.156969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.118846 restraints weight = 15543.254| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.67 r_work: 0.2981 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 15234 Z= 0.153 Angle : 0.553 8.361 20708 Z= 0.285 Chirality : 0.042 0.201 2339 Planarity : 0.005 0.084 2521 Dihedral : 11.718 86.545 2388 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.85 % Favored : 95.86 % Rotamer: Outliers : 2.77 % Allowed : 26.10 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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 aren not related in a simple way. whole: 0.94 (0.20), residues: 1764 helix: 1.91 (0.19), residues: 706 sheet: 0.65 (0.32), residues: 260 loop : -0.55 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 800 TYR 0.015 0.002 TYR C 308 PHE 0.021 0.001 PHE B 155 TRP 0.008 0.001 TRP B 856 HIS 0.007 0.001 HIS C 514 Details of bonding type rmsd covalent geometry : bond 0.00364 (15226) covalent geometry : angle 0.55224 (20702) hydrogen bonds : bond 0.04525 ( 690) hydrogen bonds : angle 4.22937 ( 1994) metal coordination : bond 0.01109 ( 8) metal coordination : angle 1.94920 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5802.15 seconds wall clock time: 99 minutes 42.05 seconds (5982.05 seconds total)