Starting phenix.real_space_refine on Mon Sep 14 20:36:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5w9o_8790/09_2026/5w9o_8790.cif Found real_map, /net/cci-nas-00/data/ceres_data/5w9o_8790/09_2026/5w9o_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/5w9o_8790/09_2026/5w9o_8790.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5w9o_8790/09_2026/5w9o_8790.map" model { file = "/net/cci-nas-00/data/ceres_data/5w9o_8790/09_2026/5w9o_8790.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5w9o_8790/09_2026/5w9o_8790.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 7.22, per 1000 atoms: 0.22 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: 2.75 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.21 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: 8.62 Time building geometry restraints manager: 3.65 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: 0.01 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: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 31.950 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.070 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 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 are 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/Z covalent geometry : bond 0.01272 / 0.83 (33735) covalent geometry : angle 1.65911 / 1.14 (45876) SS BOND : bond 0.15146 / 9.18 ( 56) SS BOND : angle 7.48322 / 5.07 ( 112) hydrogen bonds : bond 0.19320 / 12.86 ( 1245) hydrogen bonds : angle 8.29564 / 5.88 ( 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: 0.8313 (tm-30) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.0693 time to fit residues: 6.9983 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 : 0.145 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 : 0.045 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: 0.0704 time to fit residues: 2.6718 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 : 0.034 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: 0.1185 time to fit residues: 2.9864 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 : 0.033 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 : 0.215 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: 0.7932 (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: 0.0884 time to fit residues: 9.9763 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 : 0.271 ------------------------------------------------------------------------------- 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... ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1104 ASN B 41 HIS ** 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: 7 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.086066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.073313 restraints weight = 13829.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.075025 restraints weight = 8423.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.076242 restraints weight = 5829.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.077113 restraints weight = 4465.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.077412 restraints weight = 3657.991| |-----------------------------------------------------------------------------| r_work (final): 0.3314 |-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: 0.5713 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 : 31.33 Ramachandran Plot: Outliers : 1.92 % Allowed : 5.39 % Favored : 92.69 % Rotamer: Outliers : 1.23 % Allowed : 2.71 % Favored : 96.06 % 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 are 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/Z covalent geometry : bond 0.01020 / 0.57 (33735) covalent geometry : angle 1.47908 / 0.85 (45876) SS BOND : bond 0.03674 / 2.55 ( 56) SS BOND : angle 5.90521 / 3.78 ( 112) hydrogen bonds : bond 0.49027 / 30.17 ( 1245) hydrogen bonds : angle 9.37254 / 6.91 ( 3231) *********************** REFINEMENT MACRO_CYCLE 2 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 133 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 128 time to evaluate : 0.084 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 756 GLU cc_start: 0.5318 (tm-30) cc_final: 0.3951 (pm20) REVERT: D 799 ILE cc_start: 0.9294 (mm) cc_final: 0.8702 (pt) REVERT: D 816 LYS cc_start: 0.8750 (mmmt) cc_final: 0.8506 (mmtm) REVERT: D 842 GLN cc_start: 0.8588 (mm-40) cc_final: 0.8219 (mm110) REVERT: D 905 TYR cc_start: 0.5915 (m-80) cc_final: 0.5685 (t80) REVERT: D 940 ASP cc_start: 0.6514 (t0) cc_final: 0.6025 (m-30) REVERT: D 977 PHE cc_start: 0.8176 (m-10) cc_final: 0.7826 (m-80) REVERT: D 1021 LYS cc_start: 0.9042 (mtpt) cc_final: 0.8788 (tptp) REVERT: D 1039 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8185 (mm-30) REVERT: D 1127 VAL cc_start: 0.8924 (p) cc_final: 0.8555 (p) REVERT: D 1134 LEU cc_start: 0.9507 (mt) cc_final: 0.9275 (mp) REVERT: D 1136 PHE cc_start: 0.8898 (m-80) cc_final: 0.8424 (m-10) outliers start: 5 outliers final: 0 residues processed: 132 average time/residue: 0.0854 time to fit residues: 13.1287 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 : 0.086 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: 0.6480 (p0) cc_final: 0.6258 (p0) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0431 time to fit residues: 1.1859 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 : 0.035 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: 0.0457 time to fit residues: 1.0869 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 : 0.036 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 : 0.219 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: 0.0778 time to fit residues: 8.8213 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 : 0.259 ------------------------------------------------------------------------------- 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: 0.5980 chunk 251 optimal weight: 10.0000 chunk 405 optimal weight: 0.0370 chunk 211 optimal weight: 8.9990 chunk 392 optimal weight: 20.0000 chunk 60 optimal weight: 3.9990 overall best weight: 3.7264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 HIS ** D 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 907 GLN ** D 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1104 ASN D1122 HIS ** D1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 HIS ** 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: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.080189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.067514 restraints weight = 15047.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.069317 restraints weight = 9042.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.070440 restraints weight = 6275.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.071320 restraints weight = 4872.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.071940 restraints weight = 4032.988| |-----------------------------------------------------------------------------| r_work (final): 0.3206 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.053245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.046577 restraints weight = 6700.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.047863 restraints weight = 4419.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.048760 restraints weight = 3212.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.049480 restraints weight = 2467.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.049990 restraints weight = 1959.506| |-----------------------------------------------------------------------------| r_work (final): 0.3130 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.066836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.058349 restraints weight = 5693.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.060129 restraints weight = 3778.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.061307 restraints weight = 2715.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.062165 restraints weight = 2089.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.062660 restraints weight = 1676.244| |-----------------------------------------------------------------------------| r_work (final): 0.3510 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.092065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.074964 restraints weight = 47341.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.073863 restraints weight = 40544.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.074133 restraints weight = 37097.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.074374 restraints weight = 30906.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.074608 restraints weight = 27209.574| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5839 moved from start: 4.5266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.226 33791 Z= 0.442 Angle : 1.288 24.211 45988 Z= 0.734 Chirality : 0.063 0.690 5091 Planarity : 0.008 0.121 5961 Dihedral : 9.379 138.115 4629 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 29.72 Ramachandran Plot: Outliers : 1.06 % Allowed : 6.10 % Favored : 92.83 % Rotamer: Outliers : 0.99 % Allowed : 4.02 % Favored : 94.99 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.37 % Twisted Proline : 1.47 % Twisted General : 2.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.13), residues: 4227 helix: 0.43 (0.20), residues: 702 sheet: 0.17 (0.15), residues: 1116 loop : -0.30 (0.13), residues: 2409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG L 652 TYR 0.076 0.003 TYR L 361 PHE 0.026 0.002 PHE J 327 TRP 0.012 0.001 TRP B 47 HIS 0.020 0.001 HIS L 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00795 / 0.44 (33735) covalent geometry : angle 1.26742 / 0.73 (45876) SS BOND : bond 0.03671 / 2.61 ( 56) SS BOND : angle 4.79448 / 3.12 ( 112) hydrogen bonds : bond 0.45235 / 26.95 ( 1245) hydrogen bonds : angle 9.05480 / 6.66 ( 3231) *********************** REFINEMENT MACRO_CYCLE 3 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 63 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: D 757 MET cc_start: 0.3821 (tpp) cc_final: 0.3371 (tpp) REVERT: D 809 TYR cc_start: 0.8673 (t80) cc_final: 0.8384 (t80) REVERT: D 842 GLN cc_start: 0.8697 (mm-40) cc_final: 0.8286 (mm-40) REVERT: D 1021 LYS cc_start: 0.9126 (mtpt) cc_final: 0.8896 (tptp) outliers start: 6 outliers final: 0 residues processed: 60 average time/residue: 0.0615 time to fit residues: 4.6840 Evaluate side-chains 39 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.171 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 : 0.038 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0485 time to fit residues: 1.0057 Evaluate side-chains 8 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.039 Evaluate side-chains 16 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 33 MET cc_start: 0.8753 (tpp) cc_final: 0.8538 (tpp) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0538 time to fit residues: 0.9734 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 72 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 65 SER cc_start: 0.7545 (t) cc_final: 0.7324 (t) REVERT: J 69 ILE cc_start: 0.8433 (tp) cc_final: 0.8108 (tp) REVERT: J 278 MET cc_start: 0.8836 (mmm) cc_final: 0.8604 (mmm) outliers start: 6 outliers final: 3 residues processed: 69 average time/residue: 0.0571 time to fit residues: 5.8016 Evaluate side-chains 47 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 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: 0.3980 chunk 14 optimal weight: 8.9990 chunk 294 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 414 optimal weight: 4.9990 chunk 272 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 289 optimal weight: 0.0270 chunk 217 optimal weight: 0.2980 chunk 248 optimal weight: 40.0000 overall best weight: 1.7442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN ** D1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3419 r_free = 0.3419 target = 0.082292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.069680 restraints weight = 14380.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.071501 restraints weight = 8557.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.072768 restraints weight = 5800.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.073625 restraints weight = 4378.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.074106 restraints weight = 3558.202| |-----------------------------------------------------------------------------| r_work (final): 0.3251 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.054386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.047985 restraints weight = 6368.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.049350 restraints weight = 4066.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.050326 restraints weight = 2857.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.050992 restraints weight = 2132.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.051564 restraints weight = 1680.101| |-----------------------------------------------------------------------------| r_work (final): 0.3146 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.067602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.058964 restraints weight = 5448.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.060871 restraints weight = 3471.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.062286 restraints weight = 2442.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.063189 restraints weight = 1812.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.063977 restraints weight = 1433.517| |-----------------------------------------------------------------------------| r_work (final): 0.3533 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.092288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.071236 restraints weight = 43584.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.072400 restraints weight = 28245.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.073190 restraints weight = 20909.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.073789 restraints weight = 16554.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.074130 restraints weight = 14058.390| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5807 moved from start: 4.5588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.168 33791 Z= 0.399 Angle : 1.200 28.876 45988 Z= 0.684 Chirality : 0.059 0.539 5091 Planarity : 0.007 0.075 5961 Dihedral : 9.032 131.669 4629 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 27.69 Ramachandran Plot: Outliers : 1.06 % Allowed : 6.53 % Favored : 92.41 % Rotamer: Outliers : 0.33 % Allowed : 2.87 % Favored : 96.80 % 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 are not related in a simple way. whole: -0.12 (0.13), residues: 4227 helix: 0.29 (0.19), residues: 741 sheet: 0.51 (0.15), residues: 1029 loop : -0.40 (0.13), residues: 2457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 62 TYR 0.060 0.003 TYR G 905 PHE 0.035 0.002 PHE J 385 TRP 0.013 0.001 TRP B 47 HIS 0.004 0.001 HIS K 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00678 / 0.39 (33735) covalent geometry : angle 1.17638 / 0.67 (45876) SS BOND : bond 0.03493 / 2.44 ( 56) SS BOND : angle 4.92451 / 3.13 ( 112) hydrogen bonds : bond 0.43505 / 26.00 ( 1245) hydrogen bonds : angle 8.86720 / 6.55 ( 3231) *********************** REFINEMENT MACRO_CYCLE 4 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 49 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.145 Fit side-chains REVERT: D 842 GLN cc_start: 0.8447 (mm-40) cc_final: 0.8025 (mm-40) REVERT: D 940 ASP cc_start: 0.7627 (t0) cc_final: 0.6755 (m-30) REVERT: D 1035 LYS cc_start: 0.8811 (ptmm) cc_final: 0.8461 (mtmm) outliers start: 1 outliers final: 0 residues processed: 48 average time/residue: 0.0562 time to fit residues: 3.5571 Evaluate side-chains 32 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.146 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 : 0.028 Fit side-chains REVERT: B 100 ASP cc_start: 0.5861 (m-30) cc_final: 0.5353 (p0) REVERT: B 100 ASP cc_start: 0.6353 (p0) cc_final: 0.6031 (m-30) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0295 time to fit residues: 0.6685 Evaluate side-chains 11 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.046 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 : 0.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 LEU cc_start: 0.8814 (pt) cc_final: 0.8608 (pt) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0457 time to fit residues: 0.7530 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 : 0.026 Evaluate side-chains 66 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 65 SER cc_start: 0.7538 (t) cc_final: 0.7245 (t) REVERT: J 278 MET cc_start: 0.8910 (mmm) cc_final: 0.8513 (mmm) REVERT: J 600 LEU cc_start: 0.7867 (mt) cc_final: 0.7178 (pp) REVERT: J 649 TYR cc_start: 0.8788 (m-80) cc_final: 0.8424 (m-80) REVERT: J 662 ILE cc_start: 0.7419 (mt) cc_final: 0.7111 (mt) outliers start: 3 outliers final: 1 residues processed: 65 average time/residue: 0.0577 time to fit residues: 5.4892 Evaluate side-chains 44 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.231 ------------------------------------------------------------------------------- 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: 3.9990 chunk 342 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 372 optimal weight: 8.9990 chunk 247 optimal weight: 10.0000 chunk 115 optimal weight: 0.4980 chunk 171 optimal weight: 8.9990 chunk 113 optimal weight: 0.0970 chunk 184 optimal weight: 20.0000 chunk 100 optimal weight: 3.9990 chunk 206 optimal weight: 7.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 HIS D 819 GLN ** D 836 HIS ** 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** J 348 HIS J 406 ASN J 618 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 = 0.3404 r_free = 0.3404 target = 0.081669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.068817 restraints weight = 14327.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.070546 restraints weight = 8579.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.071765 restraints weight = 5895.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.072560 restraints weight = 4487.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.073053 restraints weight = 3687.818| |-----------------------------------------------------------------------------| r_work (final): 0.3231 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.054327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.048051 restraints weight = 6689.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.049383 restraints weight = 4240.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.050293 restraints weight = 2963.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.051020 restraints weight = 2221.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.051519 restraints weight = 1720.993| |-----------------------------------------------------------------------------| r_work (final): 0.3167 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.067575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.058476 restraints weight = 5859.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.060436 restraints weight = 3770.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.061826 restraints weight = 2670.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.062858 restraints weight = 2015.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.063566 restraints weight = 1583.873| |-----------------------------------------------------------------------------| r_work (final): 0.3541 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.093097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.073362 restraints weight = 46586.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.074576 restraints weight = 30246.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.075418 restraints weight = 21798.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.075791 restraints weight = 17096.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.076366 restraints weight = 14807.802| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5903 moved from start: 4.5823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.172 33791 Z= 0.383 Angle : 1.131 28.960 45988 Z= 0.650 Chirality : 0.057 0.459 5091 Planarity : 0.007 0.088 5961 Dihedral : 8.911 131.726 4629 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 27.05 Ramachandran Plot: Outliers : 0.99 % Allowed : 6.32 % Favored : 92.69 % Rotamer: Outliers : 0.41 % Allowed : 2.46 % Favored : 97.13 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.37 % Twisted Proline : 1.47 % 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 are not related in a simple way. whole: -0.25 (0.13), residues: 4227 helix: 0.24 (0.19), residues: 741 sheet: 0.32 (0.15), residues: 1068 loop : -0.47 (0.14), residues: 2418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 629 TYR 0.067 0.002 TYR K 663 PHE 0.036 0.002 PHE K 327 TRP 0.010 0.001 TRP B 47 HIS 0.006 0.001 HIS G 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00643 / 0.38 (33735) covalent geometry : angle 1.12241 / 0.65 (45876) SS BOND : bond 0.03457 / 2.43 ( 56) SS BOND : angle 2.98792 / 2.02 ( 112) hydrogen bonds : bond 0.41843 / 24.89 ( 1245) hydrogen bonds : angle 8.62390 / 6.31 ( 3231) *********************** REFINEMENT MACRO_CYCLE 5 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 49 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: D 809 TYR cc_start: 0.8100 (t80) cc_final: 0.7893 (t80) REVERT: D 842 GLN cc_start: 0.8510 (mm-40) cc_final: 0.8019 (mm-40) REVERT: D 933 LYS cc_start: 0.8415 (tptt) cc_final: 0.7152 (mmtt) REVERT: D 940 ASP cc_start: 0.7692 (t0) cc_final: 0.6699 (m-30) REVERT: D 977 PHE cc_start: 0.7876 (m-80) cc_final: 0.7567 (m-80) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.0571 time to fit residues: 3.6083 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 : 0.091 Evaluate side-chains 17 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.035 Fit side-chains REVERT: B 100 ASP cc_start: 0.5720 (m-30) cc_final: 0.5109 (p0) REVERT: B 105 GLN cc_start: 0.8601 (pm20) cc_final: 0.7816 (pp30) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0386 time to fit residues: 0.7672 Evaluate side-chains 11 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.038 Evaluate side-chains 16 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.037 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0418 time to fit residues: 0.7812 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 68 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 148 MET cc_start: 0.7899 (tpt) cc_final: 0.7497 (tpp) REVERT: J 171 LEU cc_start: 0.8523 (mm) cc_final: 0.8086 (tp) REVERT: J 649 TYR cc_start: 0.8891 (m-80) cc_final: 0.8403 (m-80) REVERT: J 738 LEU cc_start: -0.5775 (OUTLIER) cc_final: -0.6104 (mp) outliers start: 5 outliers final: 1 residues processed: 67 average time/residue: 0.0515 time to fit residues: 5.1910 Evaluate side-chains 46 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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: 6.9990 chunk 31 optimal weight: 0.5980 chunk 345 optimal weight: 10.0000 chunk 249 optimal weight: 0.4980 chunk 41 optimal weight: 0.0970 chunk 110 optimal weight: 9.9990 chunk 330 optimal weight: 0.7980 chunk 194 optimal weight: 0.8980 chunk 196 optimal weight: 0.0370 chunk 364 optimal weight: 6.9990 chunk 306 optimal weight: 0.0370 overall best weight: 0.2534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 GLN D 927 GLN ** D1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 406 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.084356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.071092 restraints weight = 14278.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.072939 restraints weight = 8598.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.074215 restraints weight = 5913.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.074970 restraints weight = 4492.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.075620 restraints weight = 3732.360| |-----------------------------------------------------------------------------| r_work (final): 0.3282 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.054167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.047735 restraints weight = 6958.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.049157 restraints weight = 4440.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.050126 restraints weight = 3080.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.050848 restraints weight = 2281.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.051407 restraints weight = 1754.209| |-----------------------------------------------------------------------------| r_work (final): 0.3177 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.069556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.061020 restraints weight = 5620.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.062793 restraints weight = 3689.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.064094 restraints weight = 2624.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.065057 restraints weight = 1984.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.065674 restraints weight = 1549.965| |-----------------------------------------------------------------------------| r_work (final): 0.3580 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.094487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.075072 restraints weight = 46003.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.076270 restraints weight = 29658.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.077124 restraints weight = 21669.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.077760 restraints weight = 16999.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.078121 restraints weight = 14260.949| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5816 moved from start: 4.6082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.166 33791 Z= 0.377 Angle : 1.118 23.507 45988 Z= 0.643 Chirality : 0.056 0.516 5091 Planarity : 0.007 0.096 5961 Dihedral : 8.878 130.210 4629 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 25.48 Ramachandran Plot: Outliers : 0.85 % Allowed : 6.60 % Favored : 92.55 % Rotamer: Outliers : 0.08 % Allowed : 2.30 % Favored : 97.62 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 1.49 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.13), residues: 4227 helix: 0.35 (0.20), residues: 735 sheet: 0.37 (0.15), residues: 1065 loop : -0.45 (0.14), residues: 2427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG J 626 TYR 0.067 0.002 TYR K 663 PHE 0.046 0.002 PHE J 327 TRP 0.021 0.001 TRP L 253 HIS 0.010 0.001 HIS D 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00617 / 0.37 (33735) covalent geometry : angle 1.11018 / 0.64 (45876) SS BOND : bond 0.03331 / 2.34 ( 56) SS BOND : angle 2.85056 / 1.90 ( 112) hydrogen bonds : bond 0.40648 / 24.19 ( 1245) hydrogen bonds : angle 8.53874 / 6.26 ( 3231) *********************** REFINEMENT MACRO_CYCLE 6 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 48 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.134 Fit side-chains revert: symmetry clash REVERT: D 815 GLN cc_start: 0.8633 (mm-40) cc_final: 0.8411 (pm20) REVERT: D 842 GLN cc_start: 0.8344 (mm-40) cc_final: 0.7930 (mm-40) REVERT: D 933 LYS cc_start: 0.7874 (tptt) cc_final: 0.6908 (mmtt) REVERT: D 940 ASP cc_start: 0.7604 (t0) cc_final: 0.6293 (m-30) REVERT: D 977 PHE cc_start: 0.7894 (m-80) cc_final: 0.7455 (m-80) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.0537 time to fit residues: 3.4116 Evaluate side-chains 37 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.134 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: 0.6686 (p0) cc_final: 0.6426 (p0) REVERT: B 105 GLN cc_start: 0.8485 (pm20) cc_final: 0.7817 (pp30) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0375 time to fit residues: 0.8027 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 : 0.036 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: symmetry clash outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0424 time to fit residues: 0.7467 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 : 0.041 Evaluate side-chains 64 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 148 MET cc_start: 0.7850 (tpt) cc_final: 0.7467 (tpp) REVERT: J 171 LEU cc_start: 0.8495 (mm) cc_final: 0.8071 (tp) REVERT: J 172 LEU cc_start: 0.9129 (pt) cc_final: 0.8858 (pt) outliers start: 1 outliers final: 0 residues processed: 64 average time/residue: 0.0658 time to fit residues: 5.9985 Evaluate side-chains 46 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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: 0.5980 chunk 63 optimal weight: 3.9990 chunk 279 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 chunk 366 optimal weight: 9.9990 chunk 264 optimal weight: 0.0470 chunk 107 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 119 optimal weight: 0.0170 chunk 176 optimal weight: 0.0040 overall best weight: 0.3128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1122 HIS D1129 ASN J 406 ASN J 619 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.085611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.072510 restraints weight = 14422.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.074195 restraints weight = 8897.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.075405 restraints weight = 6280.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.076133 restraints weight = 4877.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.076837 restraints weight = 4101.203| |-----------------------------------------------------------------------------| r_work (final): 0.3309 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.055161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.049127 restraints weight = 7114.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.050425 restraints weight = 4562.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.051360 restraints weight = 3168.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.052039 restraints weight = 2326.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.052443 restraints weight = 1788.699| |-----------------------------------------------------------------------------| r_work (final): 0.3183 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.069804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.061009 restraints weight = 5518.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.062681 restraints weight = 3545.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.063921 restraints weight = 2586.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.064881 restraints weight = 2001.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.065472 restraints weight = 1596.416| |-----------------------------------------------------------------------------| r_work (final): 0.3584 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.094860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.076673 restraints weight = 46400.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.077097 restraints weight = 37013.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.077590 restraints weight = 28300.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.078229 restraints weight = 23702.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.078189 restraints weight = 20663.322| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5788 moved from start: 4.6297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.171 33791 Z= 0.370 Angle : 1.099 23.663 45988 Z= 0.629 Chirality : 0.056 0.562 5091 Planarity : 0.007 0.087 5961 Dihedral : 8.894 130.699 4629 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 25.25 Ramachandran Plot: Outliers : 0.71 % Allowed : 6.53 % Favored : 92.76 % Rotamer: Outliers : 0.16 % Allowed : 1.40 % Favored : 98.44 % Cbeta Deviations : 0.30 % 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 are not related in a simple way. whole: -0.25 (0.13), residues: 4227 helix: 0.44 (0.20), residues: 741 sheet: 0.53 (0.15), residues: 1005 loop : -0.63 (0.13), residues: 2481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG K 626 TYR 0.052 0.002 TYR K 663 PHE 0.042 0.002 PHE K 630 TRP 0.008 0.001 TRP E 47 HIS 0.007 0.001 HIS K 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.36 (33735) covalent geometry : angle 1.09080 / 0.63 (45876) SS BOND : bond 0.03278 / 2.30 ( 56) SS BOND : angle 2.86246 / 2.00 ( 112) hydrogen bonds : bond 0.39648 / 23.66 ( 1245) hydrogen bonds : angle 8.38527 / 6.12 ( 3231) *********************** REFINEMENT MACRO_CYCLE 7 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 53 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 842 GLN cc_start: 0.8363 (mm-40) cc_final: 0.7979 (mm-40) REVERT: D 853 VAL cc_start: 0.9060 (t) cc_final: 0.8849 (p) REVERT: D 874 LEU cc_start: 0.7879 (pt) cc_final: 0.7573 (tp) REVERT: D 933 LYS cc_start: 0.7762 (tptt) cc_final: 0.6759 (mmtt) REVERT: D 977 PHE cc_start: 0.7850 (m-80) cc_final: 0.7474 (m-80) outliers start: 1 outliers final: 0 residues processed: 53 average time/residue: 0.0577 time to fit residues: 3.9794 Evaluate side-chains 40 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.152 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 : 0.041 Fit side-chains REVERT: B 100 ASP cc_start: 0.5709 (m-30) cc_final: 0.4998 (p0) REVERT: B 100 ASP cc_start: 0.6702 (p0) cc_final: 0.6417 (p0) REVERT: B 105 GLN cc_start: 0.8346 (pm20) cc_final: 0.7793 (pp30) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0509 time to fit residues: 1.1105 Evaluate side-chains 16 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.043 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 : 0.038 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0440 time to fit residues: 0.7263 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 57 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 148 MET cc_start: 0.7833 (tpt) cc_final: 0.7378 (tpp) REVERT: J 169 LEU cc_start: 0.8569 (mp) cc_final: 0.8238 (mm) REVERT: J 171 LEU cc_start: 0.8481 (mm) cc_final: 0.8071 (tp) REVERT: J 488 LEU cc_start: 0.6777 (mt) cc_final: 0.6398 (mt) REVERT: J 672 THR cc_start: 0.7836 (t) cc_final: 0.7527 (t) outliers start: 1 outliers final: 0 residues processed: 57 average time/residue: 0.0654 time to fit residues: 5.3289 Evaluate side-chains 42 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.214 ------------------------------------------------------------------------------- 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: 8.9990 chunk 209 optimal weight: 0.0000 chunk 346 optimal weight: 8.9990 chunk 288 optimal weight: 2.9990 chunk 398 optimal weight: 20.0000 chunk 223 optimal weight: 10.0000 chunk 262 optimal weight: 0.0370 chunk 325 optimal weight: 0.0010 chunk 224 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 overall best weight: 0.8072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1122 HIS J 406 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.085440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.072014 restraints weight = 14355.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.073684 restraints weight = 8833.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.074959 restraints weight = 6255.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.075735 restraints weight = 4831.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.076407 restraints weight = 4044.797| |-----------------------------------------------------------------------------| r_work (final): 0.3297 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.054876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.049202 restraints weight = 7165.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.050505 restraints weight = 4638.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.051339 restraints weight = 3252.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.052019 restraints weight = 2412.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.052370 restraints weight = 1857.140| |-----------------------------------------------------------------------------| r_work (final): 0.3204 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.070255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.060620 restraints weight = 5517.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.062643 restraints weight = 3670.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.064115 restraints weight = 2650.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.065163 restraints weight = 2037.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.065939 restraints weight = 1642.695| |-----------------------------------------------------------------------------| r_work (final): 0.3623 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.095313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.077862 restraints weight = 48081.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.078997 restraints weight = 35126.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.080973 restraints weight = 25680.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.080411 restraints weight = 22305.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.080462 restraints weight = 17808.914| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5811 moved from start: 4.6474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.162 33791 Z= 0.363 Angle : 1.093 28.115 45988 Z= 0.618 Chirality : 0.059 0.655 5091 Planarity : 0.007 0.094 5961 Dihedral : 8.826 129.630 4629 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 24.06 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.88 % Favored : 92.55 % Rotamer: Outliers : 0.08 % Allowed : 0.82 % Favored : 99.10 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.37 % Twisted Proline : 0.00 % 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 are not related in a simple way. whole: -0.21 (0.13), residues: 4227 helix: 0.54 (0.20), residues: 735 sheet: 0.56 (0.15), residues: 1005 loop : -0.63 (0.13), residues: 2487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG J 626 TYR 0.053 0.002 TYR J 663 PHE 0.038 0.002 PHE L 327 TRP 0.013 0.001 TRP J 253 HIS 0.003 0.001 HIS G 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.36 (33735) covalent geometry : angle 1.08609 / 0.62 (45876) SS BOND : bond 0.03287 / 2.30 ( 56) SS BOND : angle 2.64832 / 1.81 ( 112) hydrogen bonds : bond 0.38404 / 22.99 ( 1245) hydrogen bonds : angle 8.33432 / 6.03 ( 3231) *********************** REFINEMENT MACRO_CYCLE 8 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 53 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.154 Fit side-chains revert: symmetry clash REVERT: D 842 GLN cc_start: 0.8309 (mm-40) cc_final: 0.7968 (mm-40) REVERT: D 874 LEU cc_start: 0.7839 (pt) cc_final: 0.7589 (tp) REVERT: D 933 LYS cc_start: 0.7658 (tptt) cc_final: 0.6637 (mmtt) REVERT: D 977 PHE cc_start: 0.7783 (m-80) cc_final: 0.7410 (m-80) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.0671 time to fit residues: 4.5192 Evaluate side-chains 39 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.141 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 : 0.042 Fit side-chains REVERT: B 43 LYS cc_start: 0.7594 (mmmt) cc_final: 0.7141 (mmmm) REVERT: B 100 ASP cc_start: 0.6048 (m-30) cc_final: 0.5362 (p0) REVERT: B 100 ASP cc_start: 0.6756 (p0) cc_final: 0.6306 (t0) REVERT: B 105 GLN cc_start: 0.8218 (pm20) cc_final: 0.7732 (pp30) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0403 time to fit residues: 0.9203 Evaluate side-chains 16 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.038 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 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 62 PHE cc_start: 0.8098 (m-80) cc_final: 0.7734 (m-80) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0460 time to fit residues: 0.6995 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 58 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 65 SER cc_start: 0.7337 (t) cc_final: 0.7124 (t) REVERT: J 148 MET cc_start: 0.7761 (tpt) cc_final: 0.7378 (tpp) REVERT: J 169 LEU cc_start: 0.8446 (mp) cc_final: 0.7810 (mp) REVERT: J 171 LEU cc_start: 0.8437 (mm) cc_final: 0.8114 (tp) REVERT: J 172 LEU cc_start: 0.9159 (pt) cc_final: 0.8905 (pt) REVERT: J 293 TYR cc_start: 0.6230 (t80) cc_final: 0.5860 (t80) REVERT: J 488 LEU cc_start: 0.6783 (mt) cc_final: 0.6407 (mt) REVERT: J 637 ASN cc_start: 0.8105 (t0) cc_final: 0.7550 (m-40) REVERT: J 661 VAL cc_start: 0.7680 (p) cc_final: 0.7248 (p) REVERT: J 672 THR cc_start: 0.7295 (t) cc_final: 0.7066 (m) outliers start: 1 outliers final: 1 residues processed: 58 average time/residue: 0.0571 time to fit residues: 5.0036 Evaluate side-chains 45 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 205 optimal weight: 0.9990 chunk 376 optimal weight: 6.9990 chunk 209 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 310 optimal weight: 0.0020 chunk 193 optimal weight: 20.0000 chunk 45 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 246 optimal weight: 4.9990 chunk 151 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1122 HIS ** D1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 406 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.086427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.072874 restraints weight = 14039.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.074665 restraints weight = 8631.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.075848 restraints weight = 6017.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.076748 restraints weight = 4686.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.077191 restraints weight = 3881.134| |-----------------------------------------------------------------------------| r_work (final): 0.3313 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.054424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.048642 restraints weight = 7143.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.049835 restraints weight = 4730.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.050719 restraints weight = 3418.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.051366 restraints weight = 2586.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.051807 restraints weight = 2026.103| |-----------------------------------------------------------------------------| r_work (final): 0.3191 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.069813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.060241 restraints weight = 5665.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.062342 restraints weight = 3670.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.063912 restraints weight = 2591.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.064937 restraints weight = 1970.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.065826 restraints weight = 1563.169| |-----------------------------------------------------------------------------| r_work (final): 0.3607 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.095301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.077916 restraints weight = 47336.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.079190 restraints weight = 33512.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.079671 restraints weight = 22672.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.079708 restraints weight = 26607.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.079820 restraints weight = 20106.611| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5769 moved from start: 4.6603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.213 33791 Z= 0.386 Angle : 1.140 22.987 45988 Z= 0.645 Chirality : 0.060 0.698 5091 Planarity : 0.007 0.093 5961 Dihedral : 8.972 130.344 4629 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 24.38 Ramachandran Plot: Outliers : 0.71 % Allowed : 7.17 % Favored : 92.12 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.61 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.37 % Twisted Proline : 2.94 % Twisted General : 1.86 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.13), residues: 4227 helix: 0.54 (0.20), residues: 744 sheet: 0.57 (0.15), residues: 1011 loop : -0.63 (0.13), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.054 0.001 ARG A 758 TYR 0.055 0.002 TYR K 663 PHE 0.043 0.002 PHE J 327 TRP 0.014 0.001 TRP C 35 HIS 0.005 0.001 HIS L 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00689 / 0.38 (33735) covalent geometry : angle 1.13046 / 0.64 (45876) SS BOND : bond 0.03549 / 2.53 ( 56) SS BOND : angle 3.12870 / 2.16 ( 112) hydrogen bonds : bond 0.37818 / 22.68 ( 1245) hydrogen bonds : angle 8.42811 / 6.08 ( 3231) *********************** REFINEMENT MACRO_CYCLE 9 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 50 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: D 842 GLN cc_start: 0.8324 (mm-40) cc_final: 0.7975 (mm-40) REVERT: D 874 LEU cc_start: 0.7872 (pt) cc_final: 0.7627 (tp) REVERT: D 933 LYS cc_start: 0.7636 (tptt) cc_final: 0.6760 (mttt) REVERT: D 977 PHE cc_start: 0.7810 (m-80) cc_final: 0.7445 (m-80) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0592 time to fit residues: 3.8808 Evaluate side-chains 36 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.125 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 : 0.040 Fit side-chains REVERT: B 37 VAL cc_start: 0.8990 (t) cc_final: 0.8692 (m) REVERT: B 43 LYS cc_start: 0.7374 (mmmt) cc_final: 0.7120 (mmmm) REVERT: B 100 ASP cc_start: 0.6581 (p0) cc_final: 0.6248 (t0) REVERT: B 105 GLN cc_start: 0.8285 (pm20) cc_final: 0.7775 (pp30) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0387 time to fit residues: 0.8725 Evaluate side-chains 16 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 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 : 0.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 33 MET cc_start: 0.8152 (tmm) cc_final: 0.7832 (tmm) REVERT: C 62 PHE cc_start: 0.8163 (m-80) cc_final: 0.7795 (m-80) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0438 time to fit residues: 0.7171 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 55 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 148 MET cc_start: 0.7648 (tpt) cc_final: 0.7400 (tpp) REVERT: J 169 LEU cc_start: 0.8426 (mp) cc_final: 0.7911 (mp) REVERT: J 171 LEU cc_start: 0.8371 (mm) cc_final: 0.8070 (tp) REVERT: J 488 LEU cc_start: 0.6601 (mt) cc_final: 0.6219 (mt) REVERT: J 637 ASN cc_start: 0.8064 (t0) cc_final: 0.6844 (m-40) REVERT: J 661 VAL cc_start: 0.7436 (p) cc_final: 0.7063 (p) REVERT: J 672 THR cc_start: 0.6680 (t) cc_final: 0.6446 (m) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0534 time to fit residues: 4.4359 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 : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 150 optimal weight: 7.9990 chunk 201 optimal weight: 30.0000 chunk 98 optimal weight: 0.7980 chunk 331 optimal weight: 0.7980 chunk 210 optimal weight: 8.9990 chunk 408 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 224 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 239 optimal weight: 0.0770 chunk 9 optimal weight: 6.9990 overall best weight: 3.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 808 GLN D 812 ASN D1122 HIS ** D1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 406 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.084846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.070539 restraints weight = 14506.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.072403 restraints weight = 8746.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.073728 restraints weight = 6056.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.074654 restraints weight = 4622.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.075282 restraints weight = 3802.917| |-----------------------------------------------------------------------------| r_work (final): 0.3269 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.053706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.047931 restraints weight = 7305.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.049059 restraints weight = 4826.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.049934 restraints weight = 3487.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.050471 restraints weight = 2657.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.050966 restraints weight = 2136.665| |-----------------------------------------------------------------------------| r_work (final): 0.3172 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.067528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.060548 restraints weight = 5283.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.062406 restraints weight = 3289.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.063584 restraints weight = 2249.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.064419 restraints weight = 1644.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.064972 restraints weight = 1252.670| |-----------------------------------------------------------------------------| r_work (final): 0.3586 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.095451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.078012 restraints weight = 46901.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.078706 restraints weight = 35294.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.079413 restraints weight = 26789.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.079370 restraints weight = 27500.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.079551 restraints weight = 22375.039| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5829 moved from start: 4.6631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.213 33791 Z= 0.396 Angle : 1.170 23.211 45988 Z= 0.655 Chirality : 0.060 0.562 5091 Planarity : 0.007 0.104 5961 Dihedral : 8.982 129.682 4629 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 26.23 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.59 % Favored : 91.77 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.53 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.37 % Twisted Proline : 2.94 % 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 are not related in a simple way. whole: -0.27 (0.13), residues: 4227 helix: 0.42 (0.19), residues: 747 sheet: 0.52 (0.15), residues: 1014 loop : -0.65 (0.13), residues: 2466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.049 0.001 ARG A 758 TYR 0.041 0.002 TYR L 663 PHE 0.040 0.002 PHE J 327 TRP 0.010 0.001 TRP C 35 HIS 0.006 0.002 HIS L 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00706 / 0.39 (33735) covalent geometry : angle 1.16478 / 0.65 (45876) SS BOND : bond 0.03402 / 2.40 ( 56) SS BOND : angle 2.53405 / 1.73 ( 112) hydrogen bonds : bond 0.36962 / 22.29 ( 1245) hydrogen bonds : angle 8.60032 / 6.09 ( 3231) ********************** REFINEMENT MACRO_CYCLE 10 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 41 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: D 842 GLN cc_start: 0.8354 (mm-40) cc_final: 0.8003 (mm-40) REVERT: D 874 LEU cc_start: 0.8134 (pt) cc_final: 0.7856 (tp) REVERT: D 933 LYS cc_start: 0.7551 (tptt) cc_final: 0.6718 (mmtt) REVERT: D 977 PHE cc_start: 0.7935 (m-80) cc_final: 0.7538 (m-80) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0657 time to fit residues: 3.4717 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 : 0.147 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 : 0.042 Fit side-chains REVERT: B 43 LYS cc_start: 0.7499 (mmmt) cc_final: 0.7227 (mmmm) REVERT: B 100 ASP cc_start: 0.6702 (p0) cc_final: 0.6386 (p0) REVERT: B 105 GLN cc_start: 0.7976 (pm20) cc_final: 0.7727 (pp30) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0406 time to fit residues: 0.8678 Evaluate side-chains 15 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.040 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 : 0.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 62 PHE cc_start: 0.7694 (m-80) cc_final: 0.7492 (m-80) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0445 time to fit residues: 0.7280 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 : 0.032 Evaluate side-chains 54 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 148 MET cc_start: 0.7800 (tpt) cc_final: 0.7592 (tpp) REVERT: J 169 LEU cc_start: 0.8650 (mp) cc_final: 0.8176 (mp) REVERT: J 171 LEU cc_start: 0.8495 (mm) cc_final: 0.8141 (tp) REVERT: J 172 LEU cc_start: 0.9202 (pt) cc_final: 0.8944 (pt) REVERT: J 452 MET cc_start: 0.0368 (ttp) cc_final: 0.0086 (ptm) REVERT: J 488 LEU cc_start: 0.6496 (mt) cc_final: 0.6093 (mt) REVERT: J 563 MET cc_start: 0.4902 (tmm) cc_final: 0.4532 (tpp) REVERT: J 637 ASN cc_start: 0.8127 (t0) cc_final: 0.7010 (m-40) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0571 time to fit residues: 4.6589 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 : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 42 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 18 optimal weight: 0.6980 chunk 70 optimal weight: 8.9990 chunk 356 optimal weight: 0.0980 chunk 23 optimal weight: 0.9980 chunk 324 optimal weight: 0.5980 chunk 191 optimal weight: 8.9990 chunk 123 optimal weight: 0.8980 chunk 302 optimal weight: 0.3980 chunk 128 optimal weight: 9.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 6 GLN D1023 GLN D1122 HIS ** D1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 406 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.087464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.073264 restraints weight = 14134.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.075089 restraints weight = 8795.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.076330 restraints weight = 6111.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.077122 restraints weight = 4682.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.077334 restraints weight = 3905.456| |-----------------------------------------------------------------------------| r_work (final): 0.3312 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.054501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.047757 restraints weight = 6975.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.049151 restraints weight = 4560.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.050133 restraints weight = 3248.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.050850 restraints weight = 2448.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.051391 restraints weight = 1921.328| |-----------------------------------------------------------------------------| r_work (final): 0.3199 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.069175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.060279 restraints weight = 5638.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.062290 restraints weight = 3666.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.063702 restraints weight = 2665.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.064756 restraints weight = 2050.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.065424 restraints weight = 1632.742| |-----------------------------------------------------------------------------| r_work (final): 0.3575 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.096439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.079358 restraints weight = 47237.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.080338 restraints weight = 36064.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.082329 restraints weight = 25630.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.081960 restraints weight = 23344.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.081930 restraints weight = 17583.097| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5714 moved from start: 4.6806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.172 33791 Z= 0.385 Angle : 1.151 26.808 45988 Z= 0.643 Chirality : 0.059 0.579 5091 Planarity : 0.007 0.114 5961 Dihedral : 9.009 130.784 4629 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 24.06 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.24 % Favored : 92.26 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.61 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.37 % Twisted Proline : 2.94 % 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 are not related in a simple way. whole: -0.14 (0.13), residues: 4227 helix: 0.55 (0.20), residues: 750 sheet: 0.66 (0.15), residues: 1002 loop : -0.59 (0.13), residues: 2475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.048 0.001 ARG D 758 TYR 0.050 0.002 TYR J 663 PHE 0.039 0.002 PHE J 327 TRP 0.007 0.001 TRP H 47 HIS 0.006 0.001 HIS K 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00673 / 0.38 (33735) covalent geometry : angle 1.14219 / 0.64 (45876) SS BOND : bond 0.03373 / 2.38 ( 56) SS BOND : angle 3.02860 / 2.09 ( 112) hydrogen bonds : bond 0.36031 / 21.66 ( 1245) hydrogen bonds : angle 8.62675 / 6.08 ( 3231) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3440.67 seconds wall clock time: 61 minutes 34.45 seconds (3694.45 seconds total)