Starting phenix.real_space_refine on Tue Aug 26 03:53:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5w9o_8790/08_2025/5w9o_8790.cif Found real_map, /net/cci-nas-00/data/ceres_data/5w9o_8790/08_2025/5w9o_8790.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5w9o_8790/08_2025/5w9o_8790.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5w9o_8790/08_2025/5w9o_8790.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5w9o_8790/08_2025/5w9o_8790.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5w9o_8790/08_2025/5w9o_8790.map" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 180 5.16 5 C 20904 2.51 5 N 5475 2.21 5 O 6399 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32958 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3545 Classifications: {'peptide': 463} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 437} Chain breaks: 1 Chain: "B" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "C" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 835 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3545 Classifications: {'peptide': 463} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 437} Chain breaks: 1 Chain: "E" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "F" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 835 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "G" Number of atoms: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3545 Classifications: {'peptide': 463} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 437} Chain breaks: 1 Chain: "H" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "I" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 835 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "J" Number of atoms: 5658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5658 Classifications: {'peptide': 726} Link IDs: {'CIS': 3, 'PTRANS': 36, 'TRANS': 686} Chain: "K" Number of atoms: 5658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5658 Classifications: {'peptide': 726} Link IDs: {'CIS': 5, 'PTRANS': 36, 'TRANS': 684} Chain: "L" Number of atoms: 5658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5658 Classifications: {'peptide': 726} Link IDs: {'CIS': 5, 'PTRANS': 36, 'TRANS': 684} Time building chain proxies: 8.47, per 1000 atoms: 0.26 Number of scatterers: 32958 At special positions: 0 Unit cell: (154.02, 154.02, 222.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 180 16.00 O 6399 8.00 N 5475 7.00 C 20904 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=56, symmetry=0 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS A 828 " distance=2.03 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.03 Simple disulfide: pdb=" SG CYS A 912 " - pdb=" SG CYS A 925 " distance=2.06 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.03 Simple disulfide: pdb=" SG CYS A1156 " - pdb=" SG CYS A1164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 806 " - pdb=" SG CYS D 828 " distance=2.03 Simple disulfide: pdb=" SG CYS D 811 " - pdb=" SG CYS D 817 " distance=2.02 Simple disulfide: pdb=" SG CYS D 912 " - pdb=" SG CYS D 925 " distance=2.17 Simple disulfide: pdb=" SG CYS D1156 " - pdb=" SG CYS D1164 " distance=2.39 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.02 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.15 Simple disulfide: pdb=" SG CYS G 806 " - pdb=" SG CYS G 828 " distance=2.03 Simple disulfide: pdb=" SG CYS G 811 " - pdb=" SG CYS G 817 " distance=2.03 Simple disulfide: pdb=" SG CYS G 912 " - pdb=" SG CYS G 925 " distance=2.08 Simple disulfide: pdb=" SG CYS G1106 " - pdb=" SG CYS G1117 " distance=2.03 Simple disulfide: pdb=" SG CYS G1156 " - pdb=" SG CYS G1164 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.11 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 30 " - pdb=" SG CYS J 195 " distance=2.01 Simple disulfide: pdb=" SG CYS J 176 " - pdb=" SG CYS J 214 " distance=2.60 Simple disulfide: pdb=" SG CYS J 185 " - pdb=" SG CYS J 237 " distance=2.04 Simple disulfide: pdb=" SG CYS J 339 " - pdb=" SG CYS J 349 " distance=2.03 Simple disulfide: pdb=" SG CYS J 383 " - pdb=" SG CYS J 407 " distance=1.82 Simple disulfide: pdb=" SG CYS J 425 " - pdb=" SG CYS J 478 " distance=2.02 Simple disulfide: pdb=" SG CYS J 437 " - pdb=" SG CYS J 585 " distance=2.19 Simple disulfide: pdb=" SG CYS J 503 " - pdb=" SG CYS J 526 " distance=2.02 Simple disulfide: pdb=" SG CYS J 603 " - pdb=" SG CYS J 654 " distance=2.02 Simple disulfide: pdb=" SG CYS J 620 " - pdb=" SG CYS J 650 " distance=1.94 Simple disulfide: pdb=" SG CYS J 679 " - pdb=" SG CYS J 713 " distance=2.04 Simple disulfide: pdb=" SG CYS J 727 " - pdb=" SG CYS J 736 " distance=2.02 Simple disulfide: pdb=" SG CYS K 30 " - pdb=" SG CYS K 195 " distance=2.20 Simple disulfide: pdb=" SG CYS K 176 " - pdb=" SG CYS K 214 " distance=2.40 Simple disulfide: pdb=" SG CYS K 185 " - pdb=" SG CYS K 237 " distance=2.15 Simple disulfide: pdb=" SG CYS K 339 " - pdb=" SG CYS K 349 " distance=2.04 Simple disulfide: pdb=" SG CYS K 383 " - pdb=" SG CYS K 407 " distance=2.07 Simple disulfide: pdb=" SG CYS K 425 " - pdb=" SG CYS K 478 " distance=2.14 Simple disulfide: pdb=" SG CYS K 437 " - pdb=" SG CYS K 585 " distance=2.13 Simple disulfide: pdb=" SG CYS K 503 " - pdb=" SG CYS K 526 " distance=2.02 Simple disulfide: pdb=" SG CYS K 603 " - pdb=" SG CYS K 654 " distance=2.06 Simple disulfide: pdb=" SG CYS K 620 " - pdb=" SG CYS K 650 " distance=2.01 Simple disulfide: pdb=" SG CYS K 679 " - pdb=" SG CYS K 713 " distance=2.03 Simple disulfide: pdb=" SG CYS K 727 " - pdb=" SG CYS K 736 " distance=2.02 Simple disulfide: pdb=" SG CYS L 30 " - pdb=" SG CYS L 195 " distance=2.02 Simple disulfide: pdb=" SG CYS L 176 " - pdb=" SG CYS L 214 " distance=2.55 Simple disulfide: pdb=" SG CYS L 185 " - pdb=" SG CYS L 237 " distance=2.12 Simple disulfide: pdb=" SG CYS L 339 " - pdb=" SG CYS L 349 " distance=2.03 Simple disulfide: pdb=" SG CYS L 383 " - pdb=" SG CYS L 407 " distance=2.31 Simple disulfide: pdb=" SG CYS L 425 " - pdb=" SG CYS L 478 " distance=1.99 Simple disulfide: pdb=" SG CYS L 437 " - pdb=" SG CYS L 585 " distance=2.06 Simple disulfide: pdb=" SG CYS L 503 " - pdb=" SG CYS L 526 " distance=2.02 Simple disulfide: pdb=" SG CYS L 603 " - pdb=" SG CYS L 654 " distance=2.12 Simple disulfide: pdb=" SG CYS L 620 " - pdb=" SG CYS L 650 " distance=1.66 Simple disulfide: pdb=" SG CYS L 679 " - pdb=" SG CYS L 713 " distance=2.03 Simple disulfide: pdb=" SG CYS L 727 " - pdb=" SG CYS L 736 " distance=2.02 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: 3.66 Conformation dependent library (CDL) restraints added in 2.1 seconds Enol-peptide restraints added in 1.7 microseconds 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7902 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 76 sheets defined 22.5% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.97 Creating SS restraints... Processing helix chain 'A' and resid 814 through 821 Processing helix chain 'A' and resid 824 through 854 removed outlier: 3.578A pdb=" N CYS A 828 " --> pdb=" O TYR A 824 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER A 852 " --> pdb=" O ASN A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 898 Processing helix chain 'A' and resid 907 through 912 Processing helix chain 'A' and resid 922 through 931 removed outlier: 3.586A pdb=" N ALA A 926 " --> pdb=" O ASP A 922 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TYR A 928 " --> pdb=" O ILE A 924 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL A 929 " --> pdb=" O CYS A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 953 Processing helix chain 'A' and resid 971 through 982 Processing helix chain 'A' and resid 986 through 993 Processing helix chain 'A' and resid 993 through 1007 Processing helix chain 'A' and resid 1008 through 1011 Processing helix chain 'A' and resid 1016 through 1040 removed outlier: 3.545A pdb=" N LEU A1033 " --> pdb=" O ASN A1029 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1058 Processing helix chain 'A' and resid 1059 through 1104 removed outlier: 4.694A pdb=" N ALA A1065 " --> pdb=" O PRO A1061 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN A1066 " --> pdb=" O GLU A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1200 No H-bonds generated for 'chain 'A' and resid 1198 through 1200' Processing helix chain 'B' and resid 28 through 31 Processing helix chain 'B' and resid 61 through 64 Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'D' and resid 814 through 821 Processing helix chain 'D' and resid 824 through 854 removed outlier: 3.660A pdb=" N CYS D 828 " --> pdb=" O TYR D 824 " (cutoff:3.500A) Processing helix chain 'D' and resid 888 through 898 Processing helix chain 'D' and resid 907 through 912 Processing helix chain 'D' and resid 922 through 931 removed outlier: 5.003A pdb=" N TYR D 928 " --> pdb=" O ILE D 924 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL D 929 " --> pdb=" O CYS D 925 " (cutoff:3.500A) Processing helix chain 'D' and resid 940 through 953 Processing helix chain 'D' and resid 971 through 982 Processing helix chain 'D' and resid 986 through 993 Processing helix chain 'D' and resid 993 through 1007 Processing helix chain 'D' and resid 1008 through 1010 No H-bonds generated for 'chain 'D' and resid 1008 through 1010' Processing helix chain 'D' and resid 1016 through 1039 Processing helix chain 'D' and resid 1040 through 1042 No H-bonds generated for 'chain 'D' and resid 1040 through 1042' Processing helix chain 'D' and resid 1050 through 1058 Processing helix chain 'D' and resid 1059 through 1104 removed outlier: 3.947A pdb=" N ALA D1065 " --> pdb=" O PRO D1061 " (cutoff:3.500A) Processing helix chain 'D' and resid 1198 through 1200 No H-bonds generated for 'chain 'D' and resid 1198 through 1200' Processing helix chain 'E' and resid 28 through 32 removed outlier: 4.142A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 64 Processing helix chain 'E' and resid 73 through 75 No H-bonds generated for 'chain 'E' and resid 73 through 75' Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'G' and resid 814 through 821 Processing helix chain 'G' and resid 824 through 854 removed outlier: 3.548A pdb=" N CYS G 828 " --> pdb=" O TYR G 824 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER G 852 " --> pdb=" O ASN G 848 " (cutoff:3.500A) Processing helix chain 'G' and resid 888 through 898 Processing helix chain 'G' and resid 908 through 912 Processing helix chain 'G' and resid 922 through 931 removed outlier: 3.600A pdb=" N ALA G 926 " --> pdb=" O ASP G 922 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N TYR G 928 " --> pdb=" O ILE G 924 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL G 929 " --> pdb=" O CYS G 925 " (cutoff:3.500A) Processing helix chain 'G' and resid 940 through 953 Processing helix chain 'G' and resid 971 through 982 Processing helix chain 'G' and resid 986 through 993 Processing helix chain 'G' and resid 993 through 1006 Processing helix chain 'G' and resid 1007 through 1010 Processing helix chain 'G' and resid 1016 through 1040 removed outlier: 3.717A pdb=" N LEU G1040 " --> pdb=" O LEU G1036 " (cutoff:3.500A) Processing helix chain 'G' and resid 1050 through 1058 Processing helix chain 'G' and resid 1059 through 1104 removed outlier: 3.831A pdb=" N ALA G1065 " --> pdb=" O PRO G1061 " (cutoff:3.500A) Processing helix chain 'G' and resid 1198 through 1200 No H-bonds generated for 'chain 'G' and resid 1198 through 1200' Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.988A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 73 through 76 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'J' and resid 37 through 41 Processing helix chain 'J' and resid 49 through 53 Processing helix chain 'J' and resid 104 through 108 Processing helix chain 'J' and resid 222 through 230 Processing helix chain 'J' and resid 303 through 307 Processing helix chain 'J' and resid 342 through 351 Processing helix chain 'J' and resid 385 through 390 removed outlier: 3.868A pdb=" N LEU J 388 " --> pdb=" O PHE J 385 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER J 390 " --> pdb=" O PRO J 387 " (cutoff:3.500A) Processing helix chain 'J' and resid 395 through 399 removed outlier: 3.657A pdb=" N PHE J 399 " --> pdb=" O VAL J 396 " (cutoff:3.500A) Processing helix chain 'J' and resid 410 through 415 Processing helix chain 'J' and resid 416 through 418 No H-bonds generated for 'chain 'J' and resid 416 through 418' Processing helix chain 'J' and resid 429 through 436 removed outlier: 3.897A pdb=" N ALA J 434 " --> pdb=" O PRO J 430 " (cutoff:3.500A) Processing helix chain 'J' and resid 449 through 456 removed outlier: 4.839A pdb=" N SER J 454 " --> pdb=" O SER J 451 " (cutoff:3.500A) Processing helix chain 'J' and resid 462 through 468 Processing helix chain 'J' and resid 524 through 529 Processing helix chain 'J' and resid 546 through 550 Processing helix chain 'J' and resid 694 through 702 removed outlier: 4.933A pdb=" N ARG J 700 " --> pdb=" O MET J 696 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 41 removed outlier: 4.230A pdb=" N ASP K 41 " --> pdb=" O THR K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 53 Processing helix chain 'K' and resid 104 through 108 Processing helix chain 'K' and resid 222 through 230 Processing helix chain 'K' and resid 342 through 351 Processing helix chain 'K' and resid 385 through 390 removed outlier: 3.630A pdb=" N SER K 390 " --> pdb=" O PRO K 387 " (cutoff:3.500A) Processing helix chain 'K' and resid 410 through 416 removed outlier: 3.611A pdb=" N LEU K 414 " --> pdb=" O ASN K 410 " (cutoff:3.500A) Processing helix chain 'K' and resid 431 through 436 Processing helix chain 'K' and resid 449 through 456 removed outlier: 4.898A pdb=" N SER K 454 " --> pdb=" O SER K 451 " (cutoff:3.500A) Processing helix chain 'K' and resid 462 through 468 Processing helix chain 'K' and resid 524 through 529 Processing helix chain 'K' and resid 675 through 678 removed outlier: 4.167A pdb=" N ALA K 678 " --> pdb=" O GLY K 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 675 through 678' Processing helix chain 'K' and resid 694 through 702 removed outlier: 3.576A pdb=" N LYS K 698 " --> pdb=" O ARG K 694 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ARG K 700 " --> pdb=" O MET K 696 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 41 Processing helix chain 'L' and resid 49 through 53 Processing helix chain 'L' and resid 104 through 107 Processing helix chain 'L' and resid 222 through 230 Processing helix chain 'L' and resid 268 through 273 removed outlier: 4.096A pdb=" N LEU L 273 " --> pdb=" O ARG L 269 " (cutoff:3.500A) Processing helix chain 'L' and resid 303 through 307 removed outlier: 3.770A pdb=" N ARG L 307 " --> pdb=" O GLN L 304 " (cutoff:3.500A) Processing helix chain 'L' and resid 342 through 351 Processing helix chain 'L' and resid 385 through 389 Processing helix chain 'L' and resid 410 through 416 removed outlier: 4.007A pdb=" N LEU L 414 " --> pdb=" O ASN L 410 " (cutoff:3.500A) Processing helix chain 'L' and resid 429 through 436 Processing helix chain 'L' and resid 449 through 456 removed outlier: 4.517A pdb=" N SER L 454 " --> pdb=" O SER L 451 " (cutoff:3.500A) Processing helix chain 'L' and resid 462 through 468 Processing helix chain 'L' and resid 524 through 529 Processing helix chain 'L' and resid 546 through 550 Processing helix chain 'L' and resid 694 through 702 removed outlier: 3.538A pdb=" N LYS L 698 " --> pdb=" O ARG L 694 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ARG L 700 " --> pdb=" O MET L 696 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 719 through 724 removed outlier: 7.390A pdb=" N LEU A 759 " --> pdb=" O SER J 720 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU J 722 " --> pdb=" O LEU A 759 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 768 through 769 removed outlier: 5.752A pdb=" N ILE A 768 " --> pdb=" O SER D 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 777 through 782 removed outlier: 5.872A pdb=" N VAL A1150 " --> pdb=" O LYS A1174 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N PHE A1172 " --> pdb=" O ALA A1152 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 785 through 796 Processing sheet with id=AA5, first strand: chain 'A' and resid 802 through 804 Processing sheet with id=AA6, first strand: chain 'A' and resid 857 through 858 Processing sheet with id=AA7, first strand: chain 'A' and resid 1202 through 1204 removed outlier: 6.477A pdb=" N CYS A1156 " --> pdb=" O ILE A1214 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 3 through 6 removed outlier: 5.665A pdb=" N VAL B 16 " --> pdb=" O ARG B 82B" (cutoff:3.500A) removed outlier: 4.226A pdb=" N ARG B 82B" --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA B 78 " --> pdb=" O CYS B 22 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 57 through 59 removed outlier: 6.686A pdb=" N SER B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TRP B 36 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL B 50 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE B 34 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.517A pdb=" N TYR B 98 " --> pdb=" O VAL B 100B" (cutoff:3.500A) removed outlier: 7.551A pdb=" N VAL B 100B" --> pdb=" O TYR B 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.837A pdb=" N MET C 33 " --> pdb=" O SER C 49 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N SER C 49 " --> pdb=" O MET C 33 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 719 through 724 removed outlier: 7.285A pdb=" N LEU D 759 " --> pdb=" O SER K 720 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU K 722 " --> pdb=" O LEU D 759 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 768 through 769 removed outlier: 5.675A pdb=" N ILE D 768 " --> pdb=" O SER G 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 777 through 782 removed outlier: 5.712A pdb=" N VAL D1150 " --> pdb=" O LYS D1174 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N PHE D1172 " --> pdb=" O ALA D1152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 785 through 796 Processing sheet with id=AB8, first strand: chain 'D' and resid 802 through 804 Processing sheet with id=AB9, first strand: chain 'D' and resid 1155 through 1157 removed outlier: 6.498A pdb=" N CYS D1156 " --> pdb=" O ILE D1214 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 1164 through 1167 removed outlier: 3.947A pdb=" N CYS D1164 " --> pdb=" O VAL D1205 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AC3, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.385A pdb=" N SER E 44 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N CYS E 92 " --> pdb=" O TRP E 103 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TRP E 103 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ARG E 94 " --> pdb=" O ASP E 101 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N TYR E 98 " --> pdb=" O VAL E 100B" (cutoff:3.500A) removed outlier: 7.542A pdb=" N VAL E 100B" --> pdb=" O TYR E 98 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.385A pdb=" N SER E 44 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AC6, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.210A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N MET F 33 " --> pdb=" O SER F 49 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N SER F 49 " --> pdb=" O MET F 33 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 719 through 724 removed outlier: 7.246A pdb=" N LEU G 759 " --> pdb=" O SER L 720 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU L 722 " --> pdb=" O LEU G 759 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 777 through 782 removed outlier: 5.989A pdb=" N VAL G1150 " --> pdb=" O LYS G1174 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE G1172 " --> pdb=" O ALA G1152 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 785 through 796 Processing sheet with id=AD1, first strand: chain 'G' and resid 802 through 804 Processing sheet with id=AD2, first strand: chain 'G' and resid 1165 through 1167 Processing sheet with id=AD3, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.763A pdb=" N LYS H 23 " --> pdb=" O GLN H 5 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.360A pdb=" N SER H 44 " --> pdb=" O SER H 40 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 96 through 99 removed outlier: 4.609A pdb=" N TYR H 98 " --> pdb=" O VAL H 100B" (cutoff:3.500A) removed outlier: 7.511A pdb=" N VAL H 100B" --> pdb=" O TYR H 98 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.327A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N MET I 33 " --> pdb=" O SER I 49 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER I 49 " --> pdb=" O MET I 33 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 19 through 22 Processing sheet with id=AD8, first strand: chain 'J' and resid 33 through 35 Processing sheet with id=AD9, first strand: chain 'J' and resid 68 through 76 removed outlier: 6.448A pdb=" N SER J 267 " --> pdb=" O GLN J 280 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N GLN J 280 " --> pdb=" O SER J 267 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 83 through 85 removed outlier: 3.665A pdb=" N ARG J 335 " --> pdb=" O ASP J 326 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 88 through 89 removed outlier: 7.363A pdb=" N SER J 88 " --> pdb=" O ILE J 300 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 92 through 93 Processing sheet with id=AE4, first strand: chain 'J' and resid 110 through 111 removed outlier: 4.298A pdb=" N ALA J 146 " --> pdb=" O ILE J 296 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 126 through 127 removed outlier: 4.000A pdb=" N SER J 126 " --> pdb=" O ILE J 140 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA J 309 " --> pdb=" O THR J 139 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 153 through 154 Processing sheet with id=AE7, first strand: chain 'J' and resid 187 through 189 Processing sheet with id=AE8, first strand: chain 'J' and resid 359 through 366 removed outlier: 4.193A pdb=" N VAL J 659 " --> pdb=" O VAL J 363 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N SER J 365 " --> pdb=" O VAL J 657 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL J 657 " --> pdb=" O SER J 365 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 374 through 376 Processing sheet with id=AF1, first strand: chain 'J' and resid 400 through 404 removed outlier: 6.790A pdb=" N THR J 483 " --> pdb=" O VAL J 420 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N VAL J 420 " --> pdb=" O THR J 483 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 513 through 515 removed outlier: 5.402A pdb=" N SER J 498 " --> pdb=" O VAL J 561 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL J 561 " --> pdb=" O SER J 498 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ILE J 500 " --> pdb=" O SER J 559 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N SER J 559 " --> pdb=" O ILE J 500 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 617 through 618 removed outlier: 5.218A pdb=" N VAL J 639 " --> pdb=" O LEU J 651 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL J 631 " --> pdb=" O VAL J 639 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 33 through 35 removed outlier: 6.002A pdb=" N ASP K 34 " --> pdb=" O VAL K 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'K' and resid 68 through 75 removed outlier: 3.620A pdb=" N ARG K 335 " --> pdb=" O ASP K 326 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 83 through 85 removed outlier: 6.476A pdb=" N SER K 267 " --> pdb=" O GLN K 280 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N GLN K 280 " --> pdb=" O SER K 267 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 88 through 89 removed outlier: 7.414A pdb=" N SER K 88 " --> pdb=" O ILE K 300 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR K 206 " --> pdb=" O SER K 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'K' and resid 92 through 93 Processing sheet with id=AF9, first strand: chain 'K' and resid 110 through 111 removed outlier: 4.466A pdb=" N ALA K 146 " --> pdb=" O ILE K 296 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ILE K 186 " --> pdb=" O CYS K 237 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N CYS K 237 " --> pdb=" O ILE K 186 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N GLU K 188 " --> pdb=" O ARG K 235 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ARG K 235 " --> pdb=" O GLU K 188 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 126 through 127 removed outlier: 4.325A pdb=" N SER K 126 " --> pdb=" O ILE K 140 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 153 through 154 Processing sheet with id=AG3, first strand: chain 'K' and resid 359 through 366 removed outlier: 4.083A pdb=" N VAL K 659 " --> pdb=" O VAL K 363 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N SER K 365 " --> pdb=" O VAL K 657 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL K 657 " --> pdb=" O SER K 365 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 374 through 375 Processing sheet with id=AG5, first strand: chain 'K' and resid 381 through 382 removed outlier: 6.130A pdb=" N VAL K 381 " --> pdb=" O ASN K 408 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N CYS K 407 " --> pdb=" O CYS K 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'K' and resid 400 through 404 removed outlier: 3.563A pdb=" N LYS K 400 " --> pdb=" O TYR K 445 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR K 483 " --> pdb=" O VAL K 420 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N VAL K 420 " --> pdb=" O THR K 483 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 513 through 515 removed outlier: 5.451A pdb=" N SER K 498 " --> pdb=" O VAL K 561 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL K 561 " --> pdb=" O SER K 498 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ILE K 500 " --> pdb=" O SER K 559 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N SER K 559 " --> pdb=" O ILE K 500 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 617 through 618 removed outlier: 5.500A pdb=" N VAL K 639 " --> pdb=" O LEU K 651 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL K 631 " --> pdb=" O VAL K 639 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 33 through 35 Processing sheet with id=AH1, first strand: chain 'L' and resid 68 through 75 removed outlier: 3.615A pdb=" N ARG L 335 " --> pdb=" O ASP L 326 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'L' and resid 83 through 85 removed outlier: 6.251A pdb=" N SER L 267 " --> pdb=" O GLN L 280 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N GLN L 280 " --> pdb=" O SER L 267 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 88 through 89 removed outlier: 7.366A pdb=" N SER L 88 " --> pdb=" O ILE L 300 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR L 206 " --> pdb=" O SER L 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'L' and resid 92 through 93 Processing sheet with id=AH5, first strand: chain 'L' and resid 109 through 111 removed outlier: 4.477A pdb=" N ALA L 146 " --> pdb=" O ILE L 296 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU L 180 " --> pdb=" O TYR L 241 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TYR L 241 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA L 182 " --> pdb=" O PHE L 239 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N PHE L 239 " --> pdb=" O ALA L 182 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N TYR L 184 " --> pdb=" O CYS L 237 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N CYS L 237 " --> pdb=" O TYR L 184 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'L' and resid 126 through 127 removed outlier: 4.478A pdb=" N SER L 126 " --> pdb=" O ILE L 140 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA L 309 " --> pdb=" O THR L 139 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'L' and resid 153 through 154 Processing sheet with id=AH8, first strand: chain 'L' and resid 359 through 366 removed outlier: 4.436A pdb=" N VAL L 659 " --> pdb=" O VAL L 363 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N SER L 365 " --> pdb=" O VAL L 657 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL L 657 " --> pdb=" O SER L 365 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'L' and resid 371 through 375 removed outlier: 6.409A pdb=" N GLY L 372 " --> pdb=" O GLU L 605 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N SER L 607 " --> pdb=" O GLY L 372 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL L 374 " --> pdb=" O SER L 607 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'L' and resid 381 through 382 removed outlier: 6.362A pdb=" N VAL L 381 " --> pdb=" O ASN L 408 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N CYS L 407 " --> pdb=" O CYS L 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI1 Processing sheet with id=AI2, first strand: chain 'L' and resid 400 through 404 removed outlier: 3.538A pdb=" N LYS L 400 " --> pdb=" O TYR L 445 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR L 483 " --> pdb=" O VAL L 420 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VAL L 420 " --> pdb=" O THR L 483 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'L' and resid 513 through 515 removed outlier: 5.436A pdb=" N SER L 498 " --> pdb=" O VAL L 561 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL L 561 " --> pdb=" O SER L 498 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ILE L 500 " --> pdb=" O SER L 559 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N SER L 559 " --> pdb=" O ILE L 500 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'L' and resid 617 through 618 removed outlier: 5.440A pdb=" N VAL L 639 " --> pdb=" O LEU L 651 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL L 631 " --> pdb=" O VAL L 639 " (cutoff:3.500A) 1257 hydrogen bonds defined for protein. 3231 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.35 Time building geometry restraints manager: 4.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 9899 1.34 - 1.48: 9621 1.48 - 1.61: 13968 1.61 - 1.75: 1 1.75 - 1.89: 246 Bond restraints: 33735 Sorted by residual: bond pdb=" N CYS L 585 " pdb=" CA CYS L 585 " ideal model delta sigma weight residual 1.456 1.372 0.083 8.70e-03 1.32e+04 9.19e+01 bond pdb=" CA VAL L 584 " pdb=" C VAL L 584 " ideal model delta sigma weight residual 1.524 1.424 0.100 1.23e-02 6.61e+03 6.61e+01 bond pdb=" CA CYS J 437 " pdb=" C CYS J 437 " ideal model delta sigma weight residual 1.523 1.619 -0.096 1.30e-02 5.92e+03 5.50e+01 bond pdb=" C CYS L 437 " pdb=" O CYS L 437 " ideal model delta sigma weight residual 1.235 1.314 -0.079 1.18e-02 7.18e+03 4.50e+01 bond pdb=" C CYS K 437 " pdb=" N TYR K 438 " ideal model delta sigma weight residual 1.331 1.400 -0.069 1.22e-02 6.72e+03 3.21e+01 ... (remaining 33730 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 42121 2.85 - 5.69: 3168 5.69 - 8.54: 502 8.54 - 11.38: 78 11.38 - 14.23: 7 Bond angle restraints: 45876 Sorted by residual: angle pdb=" C GLN I 42 " pdb=" N PRO I 43 " pdb=" CA PRO I 43 " ideal model delta sigma weight residual 119.66 127.76 -8.10 7.20e-01 1.93e+00 1.26e+02 angle pdb=" C TYR J 144 " pdb=" N PRO J 145 " pdb=" CA PRO J 145 " ideal model delta sigma weight residual 120.31 130.17 -9.86 9.80e-01 1.04e+00 1.01e+02 angle pdb=" C VAL C 58 " pdb=" N PRO C 59 " pdb=" CA PRO C 59 " ideal model delta sigma weight residual 119.92 130.59 -10.67 1.07e+00 8.73e-01 9.94e+01 angle pdb=" N GLN L 688 " pdb=" CA GLN L 688 " pdb=" C GLN L 688 " ideal model delta sigma weight residual 111.28 122.12 -10.84 1.09e+00 8.42e-01 9.88e+01 angle pdb=" O CYS L 437 " pdb=" C CYS L 437 " pdb=" N TYR L 438 " ideal model delta sigma weight residual 123.19 111.65 11.54 1.17e+00 7.31e-01 9.72e+01 ... (remaining 45871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 19360 17.70 - 35.41: 488 35.41 - 53.11: 184 53.11 - 70.81: 82 70.81 - 88.51: 22 Dihedral angle restraints: 20136 sinusoidal: 7746 harmonic: 12390 Sorted by residual: dihedral pdb=" CB CYS I 23 " pdb=" SG CYS I 23 " pdb=" SG CYS I 88 " pdb=" CB CYS I 88 " ideal model delta sinusoidal sigma weight residual 93.00 175.48 -82.48 1 1.00e+01 1.00e-02 8.34e+01 dihedral pdb=" CB CYS K 176 " pdb=" SG CYS K 176 " pdb=" SG CYS K 214 " pdb=" CB CYS K 214 " ideal model delta sinusoidal sigma weight residual 93.00 173.88 -80.88 1 1.00e+01 1.00e-02 8.08e+01 dihedral pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " pdb=" SG CYS F 88 " pdb=" CB CYS F 88 " ideal model delta sinusoidal sigma weight residual 93.00 168.92 -75.92 1 1.00e+01 1.00e-02 7.27e+01 ... (remaining 20133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 3629 0.081 - 0.161: 1255 0.161 - 0.242: 185 0.242 - 0.322: 20 0.322 - 0.403: 2 Chirality restraints: 5091 Sorted by residual: chirality pdb=" CB ILE F 2 " pdb=" CA ILE F 2 " pdb=" CG1 ILE F 2 " pdb=" CG2 ILE F 2 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" CA PHE G 850 " pdb=" N PHE G 850 " pdb=" C PHE G 850 " pdb=" CB PHE G 850 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CA GLN L 688 " pdb=" N GLN L 688 " pdb=" C GLN L 688 " pdb=" CB GLN L 688 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 5088 not shown) Planarity restraints: 5961 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 47 " -0.076 2.00e-02 2.50e+03 3.79e-02 3.58e+01 pdb=" CG TRP B 47 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP B 47 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP B 47 " 0.044 2.00e-02 2.50e+03 pdb=" NE1 TRP B 47 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP B 47 " 0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP B 47 " 0.052 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 47 " -0.034 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 47 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 47 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS K 603 " 0.028 2.00e-02 2.50e+03 5.70e-02 3.25e+01 pdb=" C CYS K 603 " -0.099 2.00e-02 2.50e+03 pdb=" O CYS K 603 " 0.038 2.00e-02 2.50e+03 pdb=" N VAL K 604 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 22 " -0.027 2.00e-02 2.50e+03 5.48e-02 3.00e+01 pdb=" C CYS B 22 " 0.095 2.00e-02 2.50e+03 pdb=" O CYS B 22 " -0.036 2.00e-02 2.50e+03 pdb=" N LYS B 23 " -0.031 2.00e-02 2.50e+03 ... (remaining 5958 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.04: 15 2.04 - 2.75: 5247 2.75 - 3.47: 45893 3.47 - 4.18: 80520 4.18 - 4.90: 136470 Nonbonded interactions: 268145 Sorted by model distance: nonbonded pdb=" OH TYR A 905 " pdb=" CA PRO A 936 " model vdw 1.325 3.470 nonbonded pdb=" OH TYR D 905 " pdb=" CA PRO D 936 " model vdw 1.497 3.470 nonbonded pdb=" OH TYR K 448 " pdb=" O MET K 452 " model vdw 1.540 3.040 nonbonded pdb=" OH TYR D 905 " pdb=" N PRO D 936 " model vdw 1.546 3.120 nonbonded pdb=" CE2 PHE K 506 " pdb=" CG2 VAL K 555 " model vdw 1.580 3.760 ... (remaining 268140 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints Number of NCS constrained groups: 4 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } pdb_interpretation.ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } Set refine NCS operators NCS operators will be refined. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 38.220 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.090 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 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 : 0.014 0.571 33791 Z= 0.881 Angle : 1.698 32.244 45988 Z= 1.152 Chirality : 0.076 0.403 5091 Planarity : 0.010 0.122 5961 Dihedral : 10.487 88.515 12066 Min Nonbonded Distance : 1.325 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.71 % Allowed : 3.88 % Favored : 95.41 % Rotamer: Outliers : 0.08 % Allowed : 0.33 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.47 % 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: 1.29 (0.13), residues: 4227 helix: -0.52 (0.16), residues: 670 sheet: 0.65 (0.15), residues: 1000 loop : 1.60 (0.13), residues: 2557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 96 TYR 0.059 0.004 TYR G 909 PHE 0.030 0.002 PHE I 98 TRP 0.076 0.005 TRP B 47 HIS 0.006 0.001 HIS G1146 Details of bonding type rmsd covalent geometry : bond 0.01272 (33735) covalent geometry : angle 1.65911 (45876) SS BOND : bond 0.15146 ( 56) SS BOND : angle 7.48322 ( 112) hydrogen bonds : bond 0.19320 ( 1245) hydrogen bonds : angle 8.29564 ( 3231) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.139 Fit side-chains REVERT: A 928 TYR cc_start: 0.7830 (m-80) cc_final: 0.6867 (t80) REVERT: A 943 MET cc_start: 0.9187 (mtp) cc_final: 0.8551 (tpt) REVERT: A 1008 MET cc_start: 0.9130 (mmm) cc_final: 0.8579 (mmp) REVERT: A 1039 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8387 (mm-30) REVERT: A 1068 ASP cc_start: 0.9074 (m-30) cc_final: 0.8779 (p0) REVERT: A 1105 GLU cc_start: 0.8556 (tt0) cc_final: 0.8314 (tm-30) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.0662 time to fit residues: 6.6594 Evaluate side-chains 25 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.153 Evaluate side-chains 35 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 100 ASP cc_start: 0.6415 (m-30) cc_final: 0.5616 (t0) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0691 time to fit residues: 2.6189 Evaluate side-chains 12 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.038 Evaluate side-chains 24 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1216 time to fit residues: 3.0560 Evaluate side-chains 11 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.036 Evaluate side-chains 88 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 41 ASP cc_start: 0.7899 (t0) cc_final: 0.7487 (m-30) REVERT: J 172 LEU cc_start: 0.9173 (tp) cc_final: 0.8923 (pt) REVERT: J 287 TYR cc_start: 0.7595 (p90) cc_final: 0.7342 (p90) REVERT: J 338 ASP cc_start: 0.8232 (t0) cc_final: 0.7933 (t0) REVERT: J 726 ASP cc_start: 0.6209 (t0) cc_final: 0.5392 (p0) outliers start: 2 outliers final: 0 residues processed: 87 average time/residue: 0.0982 time to fit residues: 10.9308 Evaluate side-chains 50 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 197 optimal weight: 0.0670 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 0.0030 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.0050 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 8.9990 overall best weight: 0.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1104 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 111 GLN J 167 HIS J 319 GLN J 408 ASN J 636 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.086006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.073323 restraints weight = 13766.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.075046 restraints weight = 8369.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.076249 restraints weight = 5780.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.077119 restraints weight = 4428.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.077420 restraints weight = 3635.091| |-----------------------------------------------------------------------------| r_work (final): 0.3315 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.055252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.049228 restraints weight = 6465.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.050514 restraints weight = 4111.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.051507 restraints weight = 2878.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.052174 restraints weight = 2094.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.052678 restraints weight = 1600.244| |-----------------------------------------------------------------------------| r_work (final): 0.3227 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.067810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.058692 restraints weight = 5533.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.060495 restraints weight = 3771.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.061881 restraints weight = 2767.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.063040 restraints weight = 2116.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.063804 restraints weight = 1638.277| |-----------------------------------------------------------------------------| r_work (final): 0.3528 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.091707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.071899 restraints weight = 45680.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.072925 restraints weight = 29281.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.073665 restraints weight = 21175.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.074047 restraints weight = 16814.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.074380 restraints weight = 14309.750| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5732 moved from start: 4.4599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.260 33791 Z= 0.578 Angle : 1.506 33.992 45988 Z= 0.859 Chirality : 0.076 1.141 5091 Planarity : 0.010 0.114 5961 Dihedral : 9.505 138.364 4629 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 31.46 Ramachandran Plot: Outliers : 1.92 % Allowed : 5.39 % Favored : 92.69 % Rotamer: Outliers : 1.31 % Allowed : 2.71 % Favored : 95.98 % Cbeta Deviations : 0.53 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.37 % Twisted Proline : 1.47 % Twisted General : 1.41 % 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: 0.23 (0.13), residues: 4227 helix: 0.59 (0.20), residues: 660 sheet: 0.51 (0.15), residues: 966 loop : -0.02 (0.13), residues: 2601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG J 626 TYR 0.066 0.004 TYR K 663 PHE 0.086 0.003 PHE L 723 TRP 0.017 0.001 TRP E 47 HIS 0.008 0.001 HIS K 167 Details of bonding type rmsd covalent geometry : bond 0.01020 (33735) covalent geometry : angle 1.47908 (45876) SS BOND : bond 0.03674 ( 56) SS BOND : angle 5.90521 ( 112) hydrogen bonds : bond 0.49027 ( 1245) hydrogen bonds : angle 9.37254 ( 3231) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 756 GLU cc_start: 0.5311 (tm-30) cc_final: 0.3947 (pm20) REVERT: D 799 ILE cc_start: 0.9293 (mm) cc_final: 0.8701 (pt) REVERT: D 816 LYS cc_start: 0.8736 (mmmt) cc_final: 0.8501 (mmtm) REVERT: D 842 GLN cc_start: 0.8590 (mm-40) cc_final: 0.8221 (mm110) REVERT: D 905 TYR cc_start: 0.5893 (m-80) cc_final: 0.5679 (t80) REVERT: D 940 ASP cc_start: 0.6510 (t0) cc_final: 0.6024 (m-30) REVERT: D 977 PHE cc_start: 0.8171 (m-10) cc_final: 0.7823 (m-80) REVERT: D 1021 LYS cc_start: 0.9040 (mtpt) cc_final: 0.8790 (tptp) REVERT: D 1039 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8184 (mm-30) REVERT: D 1127 VAL cc_start: 0.8923 (p) cc_final: 0.8558 (p) REVERT: D 1134 LEU cc_start: 0.9509 (mt) cc_final: 0.9277 (mp) REVERT: D 1136 PHE cc_start: 0.8899 (m-80) cc_final: 0.8424 (m-10) outliers start: 6 outliers final: 0 residues processed: 133 average time/residue: 0.0905 time to fit residues: 14.0162 Evaluate side-chains 59 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.154 Evaluate side-chains 24 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.039 Fit side-chains REVERT: B 100 ASP cc_start: 0.6277 (m-30) cc_final: 0.5910 (t0) REVERT: B 100 ASP cc_start: 0.6481 (p0) cc_final: 0.6258 (p0) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0451 time to fit residues: 1.2345 Evaluate side-chains 9 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.038 Evaluate side-chains 21 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0475 time to fit residues: 1.1257 Evaluate side-chains 14 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.039 Evaluate side-chains 87 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 171 LEU cc_start: 0.8464 (mm) cc_final: 0.8050 (tt) REVERT: J 287 TYR cc_start: 0.6313 (p90) cc_final: 0.6099 (p90) REVERT: J 384 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7310 (m-30) REVERT: J 635 TYR cc_start: 0.7217 (OUTLIER) cc_final: 0.5751 (m-80) outliers start: 10 outliers final: 0 residues processed: 84 average time/residue: 0.0835 time to fit residues: 9.3581 Evaluate side-chains 49 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 272 optimal weight: 10.0000 chunk 382 optimal weight: 5.9990 chunk 295 optimal weight: 7.9990 chunk 165 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 251 optimal weight: 20.0000 chunk 405 optimal weight: 0.0370 chunk 211 optimal weight: 3.9990 chunk 392 optimal weight: 20.0000 chunk 60 optimal weight: 7.9990 overall best weight: 5.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 796 GLN ** D 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 815 GLN D 907 GLN ** D 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN C 89 GLN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 81 HIS ** J 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.080756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.068390 restraints weight = 15039.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.070058 restraints weight = 8974.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.071250 restraints weight = 6240.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.072100 restraints weight = 4788.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.072565 restraints weight = 3945.288| |-----------------------------------------------------------------------------| r_work (final): 0.3222 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.054640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.048366 restraints weight = 7217.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.049562 restraints weight = 4828.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.050505 restraints weight = 3534.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.051203 restraints weight = 2675.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.051745 restraints weight = 2096.020| |-----------------------------------------------------------------------------| r_work (final): 0.3165 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.066174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.057852 restraints weight = 5631.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.059581 restraints weight = 3657.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.060875 restraints weight = 2600.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.061764 restraints weight = 1955.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.062438 restraints weight = 1542.537| |-----------------------------------------------------------------------------| r_work (final): 0.3492 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.091120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.074270 restraints weight = 47154.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.073215 restraints weight = 37094.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.073201 restraints weight = 33926.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.073336 restraints weight = 30641.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.073472 restraints weight = 27253.373| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5750 moved from start: 4.5177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.185 33791 Z= 0.538 Angle : 1.631 31.847 45988 Z= 0.887 Chirality : 0.079 0.958 5091 Planarity : 0.013 0.334 5961 Dihedral : 10.079 133.228 4629 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 34.00 Ramachandran Plot: Outliers : 1.63 % Allowed : 6.32 % Favored : 92.05 % Rotamer: Outliers : 1.97 % Allowed : 5.34 % Favored : 92.69 % Cbeta Deviations : 0.53 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.37 % Twisted Proline : 1.47 % Twisted General : 1.63 % 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 (0.13), residues: 4227 helix: -1.02 (0.18), residues: 708 sheet: 0.05 (0.15), residues: 1056 loop : -0.70 (0.13), residues: 2463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.050 0.002 ARG G 758 TYR 0.155 0.006 TYR G 809 PHE 0.051 0.005 PHE G 850 TRP 0.037 0.003 TRP B 47 HIS 0.022 0.003 HIS A 836 Details of bonding type rmsd covalent geometry : bond 0.01027 (33735) covalent geometry : angle 1.61464 (45876) SS BOND : bond 0.03248 ( 56) SS BOND : angle 4.88856 ( 112) hydrogen bonds : bond 0.47482 ( 1245) hydrogen bonds : angle 9.46790 ( 3231) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 816 LYS cc_start: 0.8875 (mmmt) cc_final: 0.8474 (mmtm) REVERT: D 842 GLN cc_start: 0.8682 (mm-40) cc_final: 0.8404 (mm-40) REVERT: D 905 TYR cc_start: 0.6105 (m-80) cc_final: 0.5831 (t80) REVERT: D 939 MET cc_start: 0.6962 (ptp) cc_final: 0.6756 (ptp) REVERT: D 940 ASP cc_start: 0.6615 (t0) cc_final: 0.6225 (m-30) REVERT: D 1021 LYS cc_start: 0.9030 (mtpt) cc_final: 0.8826 (tptp) REVERT: D 1036 LEU cc_start: 0.8928 (mt) cc_final: 0.8576 (mt) REVERT: D 1039 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7754 (mm-30) REVERT: D 1177 ASN cc_start: 0.8934 (t0) cc_final: 0.8482 (t0) outliers start: 16 outliers final: 5 residues processed: 74 average time/residue: 0.0687 time to fit residues: 6.3126 Evaluate side-chains 47 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.133 Evaluate side-chains 24 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.036 Fit side-chains REVERT: B 62 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8502 (mttp) REVERT: B 100 ASP cc_start: 0.6399 (p0) cc_final: 0.6146 (m-30) outliers start: 3 outliers final: 0 residues processed: 22 average time/residue: 0.0526 time to fit residues: 1.3050 Evaluate side-chains 12 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 11 time to evaluate : 0.041 Evaluate side-chains 17 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0568 time to fit residues: 1.0902 Evaluate side-chains 13 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.035 Evaluate side-chains 68 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 171 LEU cc_start: 0.8542 (mm) cc_final: 0.8210 (tt) REVERT: J 343 ASP cc_start: 0.7976 (m-30) cc_final: 0.7662 (m-30) REVERT: J 637 ASN cc_start: 0.8211 (t0) cc_final: 0.7658 (m-40) outliers start: 5 outliers final: 1 residues processed: 65 average time/residue: 0.0569 time to fit residues: 5.4987 Evaluate side-chains 42 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 121 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 294 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 87 optimal weight: 0.3980 chunk 414 optimal weight: 2.9990 chunk 272 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 289 optimal weight: 0.0000 chunk 217 optimal weight: 0.0020 chunk 248 optimal weight: 0.4980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 974 GLN ** D1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.082143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.069907 restraints weight = 14757.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.071537 restraints weight = 9224.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.072628 restraints weight = 6546.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.073495 restraints weight = 5140.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.074022 restraints weight = 4263.131| |-----------------------------------------------------------------------------| r_work (final): 0.3258 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.053512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.047857 restraints weight = 7217.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.049046 restraints weight = 4552.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.049850 restraints weight = 3201.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.050477 restraints weight = 2427.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.050943 restraints weight = 1889.674| |-----------------------------------------------------------------------------| r_work (final): 0.3161 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.066722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.058681 restraints weight = 5279.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.060595 restraints weight = 3342.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.061868 restraints weight = 2283.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.062788 restraints weight = 1677.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.063524 restraints weight = 1301.789| |-----------------------------------------------------------------------------| r_work (final): 0.3549 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.091158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.073875 restraints weight = 47040.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.073510 restraints weight = 36090.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.072923 restraints weight = 35127.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.073211 restraints weight = 32542.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.073355 restraints weight = 27909.333| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5753 moved from start: 4.5314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.191 33791 Z= 0.537 Angle : 1.663 36.292 45988 Z= 0.887 Chirality : 0.075 0.742 5091 Planarity : 0.013 0.371 5961 Dihedral : 9.911 133.368 4629 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 34.23 Ramachandran Plot: Outliers : 1.42 % Allowed : 6.81 % Favored : 91.77 % Rotamer: Outliers : 1.07 % Allowed : 3.61 % Favored : 95.32 % Cbeta Deviations : 0.53 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.37 % Twisted Proline : 1.47 % Twisted General : 1.41 % 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: -1.18 (0.12), residues: 4227 helix: -1.18 (0.18), residues: 705 sheet: -0.15 (0.15), residues: 1047 loop : -0.91 (0.12), residues: 2475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.041 0.001 ARG A 758 TYR 0.086 0.006 TYR D 909 PHE 0.061 0.005 PHE D 850 TRP 0.038 0.003 TRP B 47 HIS 0.026 0.002 HIS A 836 Details of bonding type rmsd covalent geometry : bond 0.01041 (33735) covalent geometry : angle 1.63002 (45876) SS BOND : bond 0.03505 ( 56) SS BOND : angle 6.90416 ( 112) hydrogen bonds : bond 0.47208 ( 1245) hydrogen bonds : angle 9.42882 ( 3231) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 793 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7820 (mt-10) REVERT: D 842 GLN cc_start: 0.8750 (mm-40) cc_final: 0.8432 (mm-40) REVERT: D 940 ASP cc_start: 0.6830 (t0) cc_final: 0.6419 (m-30) REVERT: D 1021 LYS cc_start: 0.9066 (mtpt) cc_final: 0.8715 (tptp) REVERT: D 1036 LEU cc_start: 0.9155 (mt) cc_final: 0.8662 (tt) outliers start: 8 outliers final: 1 residues processed: 59 average time/residue: 0.0634 time to fit residues: 4.7754 Evaluate side-chains 34 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.150 Evaluate side-chains 18 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.041 Fit side-chains REVERT: B 100 ASP cc_start: 0.6502 (p0) cc_final: 0.6102 (m-30) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0359 time to fit residues: 0.7861 Evaluate side-chains 10 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.038 Evaluate side-chains 17 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 LEU cc_start: 0.8981 (pt) cc_final: 0.8771 (pt) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0427 time to fit residues: 0.8431 Evaluate side-chains 14 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.035 Evaluate side-chains 61 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 171 LEU cc_start: 0.8536 (mm) cc_final: 0.8132 (tt) REVERT: J 278 MET cc_start: 0.9098 (mmm) cc_final: 0.7637 (mmm) REVERT: J 293 TYR cc_start: 0.5644 (t80) cc_final: 0.5432 (t80) REVERT: J 343 ASP cc_start: 0.7965 (m-30) cc_final: 0.7649 (m-30) outliers start: 5 outliers final: 1 residues processed: 60 average time/residue: 0.0676 time to fit residues: 5.7839 Evaluate side-chains 43 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 304 optimal weight: 0.0370 chunk 342 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 372 optimal weight: 8.9990 chunk 247 optimal weight: 6.9990 chunk 115 optimal weight: 0.0670 chunk 171 optimal weight: 0.0470 chunk 113 optimal weight: 2.9990 chunk 184 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 206 optimal weight: 0.0270 overall best weight: 0.6354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 766 HIS D 796 GLN ** D1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1031 GLN ** D1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1212 GLN Total number of N/Q/H flips: 4 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.083422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.070552 restraints weight = 14439.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.072360 restraints weight = 8781.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.073614 restraints weight = 6075.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.074317 restraints weight = 4598.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.074999 restraints weight = 3823.291| |-----------------------------------------------------------------------------| r_work (final): 0.3264 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.053247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.047766 restraints weight = 7245.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.048978 restraints weight = 4613.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.049855 restraints weight = 3199.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.050479 restraints weight = 2331.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.050917 restraints weight = 1773.093| |-----------------------------------------------------------------------------| r_work (final): 0.3172 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.067153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.059001 restraints weight = 5695.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.060803 restraints weight = 3537.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.062159 restraints weight = 2449.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.063082 restraints weight = 1811.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.063867 restraints weight = 1407.489| |-----------------------------------------------------------------------------| r_work (final): 0.3525 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.092102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.074048 restraints weight = 47011.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.075014 restraints weight = 34702.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.075137 restraints weight = 23827.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.075109 restraints weight = 17790.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.075157 restraints weight = 16725.128| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5690 moved from start: 4.5557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.170 33791 Z= 0.442 Angle : 1.417 23.609 45988 Z= 0.778 Chirality : 0.073 0.956 5091 Planarity : 0.010 0.096 5961 Dihedral : 9.676 133.727 4629 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 30.73 Ramachandran Plot: Outliers : 1.14 % Allowed : 8.16 % Favored : 90.70 % Rotamer: Outliers : 0.74 % Allowed : 4.35 % Favored : 94.91 % Cbeta Deviations : 0.46 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.37 % Twisted Proline : 1.47 % Twisted General : 1.93 % 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: -1.32 (0.12), residues: 4227 helix: -0.97 (0.18), residues: 705 sheet: -0.12 (0.14), residues: 1077 loop : -1.19 (0.13), residues: 2445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.044 0.002 ARG G 758 TYR 0.117 0.005 TYR B 27 PHE 0.116 0.005 PHE L 327 TRP 0.037 0.003 TRP H 47 HIS 0.028 0.003 HIS D 836 Details of bonding type rmsd covalent geometry : bond 0.00788 (33735) covalent geometry : angle 1.40486 (45876) SS BOND : bond 0.03454 ( 56) SS BOND : angle 4.07208 ( 112) hydrogen bonds : bond 0.45889 ( 1245) hydrogen bonds : angle 9.29272 ( 3231) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 757 MET cc_start: 0.3824 (tpt) cc_final: 0.3487 (tpt) REVERT: D 940 ASP cc_start: 0.7023 (t0) cc_final: 0.6321 (m-30) REVERT: D 1021 LYS cc_start: 0.9130 (mtpt) cc_final: 0.8802 (tptp) REVERT: D 1036 LEU cc_start: 0.8873 (mt) cc_final: 0.8616 (mt) REVERT: D 1110 GLN cc_start: 0.8902 (tt0) cc_final: 0.8413 (tt0) outliers start: 6 outliers final: 0 residues processed: 57 average time/residue: 0.0641 time to fit residues: 4.6441 Evaluate side-chains 34 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.144 Evaluate side-chains 20 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.038 Fit side-chains REVERT: B 100 ASP cc_start: 0.6556 (p0) cc_final: 0.5987 (m-30) outliers start: 1 outliers final: 0 residues processed: 20 average time/residue: 0.0446 time to fit residues: 1.0316 Evaluate side-chains 13 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.062 Evaluate side-chains 17 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 62 PHE cc_start: 0.8312 (m-10) cc_final: 0.8076 (m-10) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0383 time to fit residues: 0.7617 Evaluate side-chains 11 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.035 Evaluate side-chains 65 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 171 LEU cc_start: 0.8408 (mm) cc_final: 0.8071 (tp) REVERT: J 278 MET cc_start: 0.9070 (mmm) cc_final: 0.8601 (mmm) REVERT: J 293 TYR cc_start: 0.5626 (t80) cc_final: 0.5326 (t80) REVERT: J 501 ASN cc_start: 0.6067 (m-40) cc_final: 0.5771 (m110) REVERT: J 637 ASN cc_start: 0.8043 (t0) cc_final: 0.7373 (m-40) outliers start: 2 outliers final: 0 residues processed: 64 average time/residue: 0.0583 time to fit residues: 5.5153 Evaluate side-chains 44 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 345 optimal weight: 0.0010 chunk 249 optimal weight: 8.9990 chunk 41 optimal weight: 0.0470 chunk 110 optimal weight: 0.3980 chunk 330 optimal weight: 8.9990 chunk 194 optimal weight: 0.7980 chunk 196 optimal weight: 0.0470 chunk 364 optimal weight: 2.9990 chunk 306 optimal weight: 4.9990 overall best weight: 0.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.082915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.070231 restraints weight = 14227.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.072040 restraints weight = 8563.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.073252 restraints weight = 5873.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.074096 restraints weight = 4481.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.074676 restraints weight = 3683.226| |-----------------------------------------------------------------------------| r_work (final): 0.3266 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.054133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.048887 restraints weight = 7272.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.050266 restraints weight = 4370.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.051077 restraints weight = 2885.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.051712 restraints weight = 2054.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.052104 restraints weight = 1517.566| |-----------------------------------------------------------------------------| r_work (final): 0.3201 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.066848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.057646 restraints weight = 5514.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.059485 restraints weight = 3560.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.060593 restraints weight = 2561.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.061547 restraints weight = 2034.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.061547 restraints weight = 1646.362| |-----------------------------------------------------------------------------| r_work (final): 0.3464 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.091816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.074814 restraints weight = 46693.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.074142 restraints weight = 34835.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.074386 restraints weight = 32631.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.074783 restraints weight = 27543.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.074785 restraints weight = 23214.738| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5764 moved from start: 4.5615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.176 33791 Z= 0.485 Angle : 1.483 27.918 45988 Z= 0.809 Chirality : 0.073 0.917 5091 Planarity : 0.010 0.119 5961 Dihedral : 9.602 133.481 4629 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 33.04 Ramachandran Plot: Outliers : 1.14 % Allowed : 8.30 % Favored : 90.56 % Rotamer: Outliers : 0.41 % Allowed : 2.22 % Favored : 97.37 % Cbeta Deviations : 0.53 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.37 % Twisted Proline : 1.47 % Twisted General : 1.78 % 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: -1.46 (0.12), residues: 4227 helix: -1.11 (0.18), residues: 705 sheet: -0.30 (0.15), residues: 1068 loop : -1.23 (0.13), residues: 2454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.123 0.002 ARG A1057 TYR 0.168 0.006 TYR D 928 PHE 0.115 0.005 PHE A 778 TRP 0.037 0.003 TRP B 47 HIS 0.029 0.004 HIS D 836 Details of bonding type rmsd covalent geometry : bond 0.00905 (33735) covalent geometry : angle 1.46244 (45876) SS BOND : bond 0.03400 ( 56) SS BOND : angle 5.14439 ( 112) hydrogen bonds : bond 0.45834 ( 1245) hydrogen bonds : angle 9.34779 ( 3231) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 757 MET cc_start: 0.3828 (tpt) cc_final: 0.3573 (tpt) REVERT: D 857 GLN cc_start: 0.8620 (pm20) cc_final: 0.7146 (mm-40) REVERT: D 977 PHE cc_start: 0.7790 (m-80) cc_final: 0.7472 (m-80) REVERT: D 1021 LYS cc_start: 0.9187 (mtpt) cc_final: 0.8840 (tptp) REVERT: D 1036 LEU cc_start: 0.8749 (mt) cc_final: 0.8460 (mt) REVERT: D 1184 TRP cc_start: 0.8625 (m100) cc_final: 0.8415 (m100) outliers start: 4 outliers final: 2 residues processed: 52 average time/residue: 0.0576 time to fit residues: 3.9584 Evaluate side-chains 38 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.178 Evaluate side-chains 18 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.041 Fit side-chains revert: symmetry clash REVERT: B 100 ASP cc_start: 0.6553 (p0) cc_final: 0.6052 (m-30) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0352 time to fit residues: 0.7572 Evaluate side-chains 14 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.038 Evaluate side-chains 17 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 46 LEU cc_start: 0.8754 (pt) cc_final: 0.8499 (pt) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0422 time to fit residues: 0.8195 Evaluate side-chains 12 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.034 Evaluate side-chains 54 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 65 SER cc_start: 0.6903 (t) cc_final: 0.6686 (t) REVERT: J 171 LEU cc_start: 0.8572 (mm) cc_final: 0.8150 (tp) REVERT: J 278 MET cc_start: 0.9052 (mmm) cc_final: 0.8548 (mmm) REVERT: J 293 TYR cc_start: 0.5763 (t80) cc_final: 0.5490 (t80) REVERT: J 501 ASN cc_start: 0.5922 (m-40) cc_final: 0.5536 (m110) REVERT: J 637 ASN cc_start: 0.8322 (t0) cc_final: 0.7563 (m-40) outliers start: 1 outliers final: 0 residues processed: 53 average time/residue: 0.0609 time to fit residues: 4.7846 Evaluate side-chains 44 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 342 optimal weight: 6.9990 chunk 63 optimal weight: 50.0000 chunk 279 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 366 optimal weight: 20.0000 chunk 264 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 119 optimal weight: 0.0870 chunk 176 optimal weight: 10.0000 overall best weight: 2.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.082151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.069532 restraints weight = 14732.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.071085 restraints weight = 9125.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.072248 restraints weight = 6493.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.072944 restraints weight = 5032.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.073555 restraints weight = 4232.679| |-----------------------------------------------------------------------------| r_work (final): 0.3240 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.053539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.047876 restraints weight = 7106.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.049166 restraints weight = 4333.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.050079 restraints weight = 2940.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.050680 restraints weight = 2115.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.051099 restraints weight = 1620.280| |-----------------------------------------------------------------------------| r_work (final): 0.3180 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.066998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.058584 restraints weight = 5779.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.060202 restraints weight = 3825.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.061429 restraints weight = 2792.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.062259 restraints weight = 2144.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.062264 restraints weight = 1747.703| |-----------------------------------------------------------------------------| r_work (final): 0.3491 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.092301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.072406 restraints weight = 46716.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.073600 restraints weight = 29996.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.074464 restraints weight = 21381.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.074998 restraints weight = 16699.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.075317 restraints weight = 14003.367| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5759 moved from start: 4.5727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.165 33791 Z= 0.424 Angle : 1.409 35.448 45988 Z= 0.765 Chirality : 0.072 0.969 5091 Planarity : 0.010 0.090 5961 Dihedral : 9.393 132.616 4629 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 28.90 Ramachandran Plot: Outliers : 1.14 % Allowed : 8.02 % Favored : 90.84 % Rotamer: Outliers : 0.33 % Allowed : 2.22 % Favored : 97.45 % Cbeta Deviations : 0.46 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.37 % Twisted Proline : 1.47 % Twisted General : 1.41 % 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: -1.63 (0.12), residues: 4227 helix: -1.03 (0.18), residues: 690 sheet: -0.31 (0.15), residues: 1005 loop : -1.44 (0.12), residues: 2532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.043 0.001 ARG D 758 TYR 0.127 0.004 TYR D 809 PHE 0.064 0.005 PHE A 850 TRP 0.037 0.003 TRP B 47 HIS 0.029 0.003 HIS G 836 Details of bonding type rmsd covalent geometry : bond 0.00769 (33735) covalent geometry : angle 1.39568 (45876) SS BOND : bond 0.03395 ( 56) SS BOND : angle 4.12117 ( 112) hydrogen bonds : bond 0.44885 ( 1245) hydrogen bonds : angle 9.20687 ( 3231) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: D 857 GLN cc_start: 0.8674 (pm20) cc_final: 0.7120 (mm-40) REVERT: D 977 PHE cc_start: 0.7821 (m-80) cc_final: 0.7537 (m-80) REVERT: D 1021 LYS cc_start: 0.9176 (mtpt) cc_final: 0.8866 (tptp) REVERT: D 1036 LEU cc_start: 0.8951 (mt) cc_final: 0.8693 (mt) outliers start: 4 outliers final: 1 residues processed: 52 average time/residue: 0.0601 time to fit residues: 4.0768 Evaluate side-chains 30 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.139 Evaluate side-chains 19 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.038 Fit side-chains REVERT: B 100 ASP cc_start: 0.6813 (p0) cc_final: 0.6197 (m-30) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0350 time to fit residues: 0.7992 Evaluate side-chains 12 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.038 Evaluate side-chains 15 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.034 Fit side-chains revert: symmetry clash REVERT: C 46 LEU cc_start: 0.8810 (pt) cc_final: 0.8609 (pt) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0405 time to fit residues: 0.7122 Evaluate side-chains 11 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.032 Evaluate side-chains 56 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 65 SER cc_start: 0.6806 (t) cc_final: 0.6588 (t) REVERT: J 148 MET cc_start: 0.7658 (tpt) cc_final: 0.7355 (tpp) REVERT: J 171 LEU cc_start: 0.8326 (mm) cc_final: 0.8018 (tp) REVERT: J 278 MET cc_start: 0.9084 (mmm) cc_final: 0.8709 (mmm) REVERT: J 290 ILE cc_start: 0.9185 (mm) cc_final: 0.8960 (mm) REVERT: J 293 TYR cc_start: 0.5644 (t80) cc_final: 0.5276 (t80) REVERT: J 343 ASP cc_start: 0.8315 (m-30) cc_final: 0.7998 (m-30) REVERT: J 637 ASN cc_start: 0.8324 (t0) cc_final: 0.7402 (m-40) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.0608 time to fit residues: 5.0124 Evaluate side-chains 41 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 313 optimal weight: 0.0040 chunk 209 optimal weight: 0.0770 chunk 346 optimal weight: 0.0770 chunk 288 optimal weight: 0.2980 chunk 398 optimal weight: 8.9990 chunk 223 optimal weight: 5.9990 chunk 262 optimal weight: 0.8980 chunk 325 optimal weight: 7.9990 chunk 224 optimal weight: 0.0370 chunk 32 optimal weight: 0.9980 chunk 91 optimal weight: 40.0000 overall best weight: 0.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 812 ASN D1029 ASN ** D1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.083422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.070626 restraints weight = 14373.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.072231 restraints weight = 8926.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.073266 restraints weight = 6306.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.074061 restraints weight = 4961.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.074730 restraints weight = 4144.144| |-----------------------------------------------------------------------------| r_work (final): 0.3259 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.052597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.046331 restraints weight = 6971.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.047583 restraints weight = 4428.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.048443 restraints weight = 3106.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.049091 restraints weight = 2325.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.049580 restraints weight = 1820.987| |-----------------------------------------------------------------------------| r_work (final): 0.3147 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.067931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.059651 restraints weight = 5538.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.061551 restraints weight = 3381.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.062785 restraints weight = 2327.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.063838 restraints weight = 1728.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.063838 restraints weight = 1329.638| |-----------------------------------------------------------------------------| r_work (final): 0.3512 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.092380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.072461 restraints weight = 47047.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.073629 restraints weight = 30188.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.074442 restraints weight = 21683.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.075074 restraints weight = 17054.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.075373 restraints weight = 14187.360| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5844 moved from start: 4.5801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.167 33791 Z= 0.440 Angle : 1.433 34.508 45988 Z= 0.774 Chirality : 0.073 1.008 5091 Planarity : 0.010 0.237 5961 Dihedral : 9.425 132.168 4629 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 29.63 Ramachandran Plot: Outliers : 1.21 % Allowed : 7.88 % Favored : 90.92 % Rotamer: Outliers : 0.16 % Allowed : 1.81 % Favored : 98.03 % Cbeta Deviations : 0.46 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 1.71 % 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: -1.72 (0.12), residues: 4227 helix: -1.07 (0.18), residues: 690 sheet: -0.45 (0.15), residues: 1044 loop : -1.49 (0.12), residues: 2493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.062 0.001 ARG G 758 TYR 0.068 0.005 TYR C 28 PHE 0.072 0.005 PHE G 778 TRP 0.036 0.003 TRP E 47 HIS 0.030 0.003 HIS D 836 Details of bonding type rmsd covalent geometry : bond 0.00800 (33735) covalent geometry : angle 1.41540 (45876) SS BOND : bond 0.03362 ( 56) SS BOND : angle 4.70828 ( 112) hydrogen bonds : bond 0.44718 ( 1245) hydrogen bonds : angle 9.14953 ( 3231) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: D 757 MET cc_start: 0.2750 (tpt) cc_final: 0.0273 (ptt) REVERT: D 857 GLN cc_start: 0.8491 (pm20) cc_final: 0.7561 (mm-40) REVERT: D 977 PHE cc_start: 0.7648 (m-80) cc_final: 0.7374 (m-80) REVERT: D 1021 LYS cc_start: 0.9159 (mtpt) cc_final: 0.8862 (tptp) REVERT: D 1035 LYS cc_start: 0.8974 (tmmt) cc_final: 0.8771 (mttp) outliers start: 2 outliers final: 0 residues processed: 49 average time/residue: 0.0579 time to fit residues: 3.7271 Evaluate side-chains 29 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.138 Evaluate side-chains 18 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.039 Fit side-chains REVERT: B 100 ASP cc_start: 0.6837 (p0) cc_final: 0.6219 (m-30) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0358 time to fit residues: 0.7756 Evaluate side-chains 13 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.039 Evaluate side-chains 14 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.035 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0409 time to fit residues: 0.6769 Evaluate side-chains 11 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.035 Evaluate side-chains 53 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 65 SER cc_start: 0.7192 (t) cc_final: 0.6920 (t) REVERT: J 148 MET cc_start: 0.7760 (tpt) cc_final: 0.7376 (tpp) REVERT: J 171 LEU cc_start: 0.8441 (mm) cc_final: 0.8037 (tp) REVERT: J 278 MET cc_start: 0.9088 (mmm) cc_final: 0.8666 (mmm) REVERT: J 293 TYR cc_start: 0.5894 (t80) cc_final: 0.5518 (t80) REVERT: J 343 ASP cc_start: 0.8266 (m-30) cc_final: 0.7998 (m-30) REVERT: J 563 MET cc_start: 0.2701 (tmm) cc_final: 0.2435 (ttt) REVERT: J 637 ASN cc_start: 0.8574 (t0) cc_final: 0.7560 (m-40) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.0620 time to fit residues: 4.8554 Evaluate side-chains 40 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 794, in minimization_ncs weight = real_space_weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 394, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 126, in refine minimized = mmtbx.refinement.minimization_ncs_constraints.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 424, in __init__ minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 456, in compute_functional_and_gradients t,g = self.target_and_grads_object.target_and_gradients( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 242, in target_and_gradients t_restraints, g_restraints = restraints_target_and_grads( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 110, in restraints_target_and_grads ef = restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.2776 > 50: distance: 1 - 2: 5.145 distance: 2 - 3: 4.106 distance: 2 - 8: 5.232 distance: 4 - 5: 3.973 distance: 5 - 6: 3.766 distance: 8 - 9: 5.470 distance: 9 - 10: 17.148 distance: 9 - 12: 14.866 distance: 10 - 11: 23.099 distance: 10 - 14: 17.541 distance: 14 - 15: 10.599 distance: 15 - 16: 18.671 distance: 15 - 18: 5.219 distance: 16 - 17: 4.157 distance: 16 - 22: 18.981 distance: 18 - 19: 17.537 distance: 19 - 20: 12.305 distance: 19 - 21: 3.499 distance: 22 - 23: 5.068 distance: 23 - 24: 4.815 distance: 23 - 26: 4.749 distance: 24 - 25: 16.492 distance: 24 - 29: 17.160 distance: 26 - 27: 4.496 distance: 26 - 28: 6.881 distance: 29 - 30: 5.697 distance: 30 - 31: 5.573 distance: 30 - 33: 7.566 distance: 31 - 32: 30.086 distance: 31 - 40: 20.196 distance: 33 - 34: 3.584 distance: 34 - 35: 10.822 distance: 34 - 36: 7.527 distance: 35 - 37: 3.372 distance: 36 - 38: 11.120 distance: 37 - 39: 15.571 distance: 38 - 39: 10.757 distance: 40 - 41: 9.949 distance: 41 - 42: 11.917 distance: 42 - 43: 51.278 distance: 42 - 44: 39.040 distance: 44 - 45: 21.373 distance: 45 - 46: 38.683 distance: 45 - 48: 32.487 distance: 46 - 47: 13.465 distance: 46 - 49: 43.876 distance: 49 - 50: 34.350 distance: 50 - 51: 24.520 distance: 50 - 53: 32.887 distance: 51 - 52: 13.626 distance: 51 - 57: 13.122 distance: 53 - 54: 14.161 distance: 53 - 55: 22.458 distance: 54 - 56: 23.096 distance: 57 - 58: 16.231 distance: 58 - 59: 22.019 distance: 58 - 61: 11.467 distance: 59 - 60: 19.942 distance: 59 - 63: 41.629 distance: 61 - 62: 16.943 distance: 63 - 64: 14.973 distance: 64 - 65: 16.305 distance: 64 - 67: 18.108 distance: 65 - 66: 13.291