Starting phenix.real_space_refine on Mon Dec 22 03:34:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5w9l_8787/12_2025/5w9l_8787.cif Found real_map, /net/cci-nas-00/data/ceres_data/5w9l_8787/12_2025/5w9l_8787.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5w9l_8787/12_2025/5w9l_8787.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5w9l_8787/12_2025/5w9l_8787.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5w9l_8787/12_2025/5w9l_8787.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5w9l_8787/12_2025/5w9l_8787.map" } resolution = 4.8 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= 0.003 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 171 5.16 5 C 19747 2.51 5 N 5164 2.21 5 O 6036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 223 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5913/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31118 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3488 Classifications: {'peptide': 456} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 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: "B" 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: "C" 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: "J" 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: 7.03, per 1000 atoms: 0.23 Number of scatterers: 31118 At special positions: 0 Unit cell: (155.04, 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 171 16.00 O 6036 8.00 N 5164 7.00 C 19747 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=55, symmetry=0 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS A 828 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.03 Simple disulfide: pdb=" SG CYS A1156 " - pdb=" SG CYS A1164 " distance=2.07 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=2.03 Simple disulfide: pdb=" SG CYS D 912 " - pdb=" SG CYS D 925 " distance=2.09 Simple disulfide: pdb=" SG CYS D1106 " - pdb=" SG CYS D1117 " distance=2.04 Simple disulfide: pdb=" SG CYS D1156 " - pdb=" SG CYS D1164 " distance=2.01 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=2.02 Simple disulfide: pdb=" SG CYS G 806 " - pdb=" SG CYS G 828 " distance=2.02 Simple disulfide: pdb=" SG CYS G 811 " - pdb=" SG CYS G 817 " distance=2.02 Simple disulfide: pdb=" SG CYS G 912 " - pdb=" SG CYS G 925 " distance=2.10 Simple disulfide: pdb=" SG CYS G1106 " - pdb=" SG CYS G1117 " distance=2.03 Simple disulfide: pdb=" SG CYS G1156 " - pdb=" SG CYS G1164 " distance=2.28 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 195 " distance=2.04 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 214 " distance=2.06 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 237 " distance=2.04 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 349 " distance=2.04 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS B 407 " distance=2.34 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 478 " distance=2.02 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 585 " distance=2.19 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 526 " distance=2.02 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 654 " distance=2.13 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 650 " distance=2.01 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 713 " distance=2.04 Simple disulfide: pdb=" SG CYS B 727 " - pdb=" SG CYS B 736 " distance=2.10 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 195 " distance=2.06 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 214 " distance=2.06 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 237 " distance=2.05 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 349 " distance=2.05 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS C 407 " distance=2.20 Simple disulfide: pdb=" SG CYS C 425 " - pdb=" SG CYS C 478 " distance=2.15 Simple disulfide: pdb=" SG CYS C 437 " - pdb=" SG CYS C 585 " distance=2.14 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 526 " distance=2.02 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 654 " distance=2.12 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 650 " distance=2.04 Simple disulfide: pdb=" SG CYS C 679 " - pdb=" SG CYS C 713 " distance=2.04 Simple disulfide: pdb=" SG CYS C 727 " - pdb=" SG CYS C 736 " distance=2.02 Simple disulfide: pdb=" SG CYS J 30 " - pdb=" SG CYS J 195 " distance=2.13 Simple disulfide: pdb=" SG CYS J 176 " - pdb=" SG CYS J 214 " distance=2.08 Simple disulfide: pdb=" SG CYS J 185 " - pdb=" SG CYS J 237 " distance=2.03 Simple disulfide: pdb=" SG CYS J 339 " - pdb=" SG CYS J 349 " distance=2.05 Simple disulfide: pdb=" SG CYS J 383 " - pdb=" SG CYS J 407 " distance=1.94 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=2.06 Simple disulfide: pdb=" SG CYS J 503 " - pdb=" SG CYS J 526 " distance=2.03 Simple disulfide: pdb=" SG CYS J 603 " - pdb=" SG CYS J 654 " distance=2.20 Simple disulfide: pdb=" SG CYS J 620 " - pdb=" SG CYS J 650 " distance=2.03 Simple disulfide: pdb=" SG CYS J 679 " - pdb=" SG CYS J 713 " distance=2.05 Simple disulfide: pdb=" SG CYS J 727 " - pdb=" SG CYS J 736 " distance=1.99 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.92 Conformation dependent library (CDL) restraints added in 1.7 seconds 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7468 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 72 sheets defined 23.6% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 814 through 823 removed outlier: 3.917A pdb=" N GLU A 823 " --> pdb=" O GLN A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 854 removed outlier: 3.992A pdb=" N CYS A 828 " --> pdb=" O TYR A 824 " (cutoff:3.500A) removed outlier: 3.560A 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: 3.557A pdb=" N ALA A 926 " --> pdb=" O ASP A 922 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N TYR A 928 " --> pdb=" O ILE A 924 " (cutoff:3.500A) removed outlier: 3.956A 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 1007 through 1012 removed outlier: 3.626A pdb=" N PHE A1012 " --> pdb=" O MET A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1040 removed outlier: 3.567A 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: 4.747A pdb=" N ALA A1065 " --> pdb=" O PRO A1061 " (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 'D' and resid 814 through 821 Processing helix chain 'D' and resid 824 through 854 removed outlier: 3.599A pdb=" N CYS D 828 " --> pdb=" O TYR D 824 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER D 852 " --> pdb=" O ASN D 848 " (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: 4.972A pdb=" N TYR D 928 " --> pdb=" O ILE D 924 " (cutoff:3.500A) removed outlier: 4.507A 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 1008 removed outlier: 3.797A pdb=" N MET D1008 " --> pdb=" O ALA D1004 " (cutoff:3.500A) 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: 3.647A 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 31 Processing helix chain 'E' and resid 60 through 65 removed outlier: 4.021A pdb=" N GLY E 65 " --> pdb=" O GLN E 61 " (cutoff:3.500A) 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: 4.001A pdb=" N CYS G 828 " --> pdb=" O TYR G 824 " (cutoff:3.500A) removed outlier: 3.811A 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: 5.006A pdb=" N TYR G 928 " --> pdb=" O ILE G 924 " (cutoff:3.500A) removed outlier: 4.142A 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 1007 Processing helix chain 'G' and resid 1008 through 1010 No H-bonds generated for 'chain 'G' and resid 1008 through 1010' Processing helix chain 'G' and resid 1016 through 1040 removed outlier: 3.563A 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: 4.917A 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 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'B' and resid 37 through 41 removed outlier: 3.591A pdb=" N ASP B 41 " --> pdb=" O THR B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 133 through 137 Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 303 through 307 removed outlier: 3.780A pdb=" N ARG B 307 " --> pdb=" O GLN B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 351 Processing helix chain 'B' and resid 385 through 390 removed outlier: 3.501A pdb=" N LEU B 388 " --> pdb=" O PHE B 385 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 390 " --> pdb=" O PRO B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 399 removed outlier: 3.657A pdb=" N PHE B 399 " --> pdb=" O VAL B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 415 Processing helix chain 'B' and resid 416 through 418 No H-bonds generated for 'chain 'B' and resid 416 through 418' Processing helix chain 'B' and resid 429 through 436 removed outlier: 3.898A pdb=" N ALA B 434 " --> pdb=" O PRO B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 456 removed outlier: 4.840A pdb=" N SER B 454 " --> pdb=" O SER B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 524 through 529 Processing helix chain 'B' and resid 546 through 550 Processing helix chain 'B' and resid 676 through 678 No H-bonds generated for 'chain 'B' and resid 676 through 678' Processing helix chain 'B' and resid 694 through 702 removed outlier: 5.349A pdb=" N ARG B 700 " --> pdb=" O MET B 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 41 removed outlier: 4.076A pdb=" N ASP C 41 " --> pdb=" O THR C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 133 through 137 Processing helix chain 'C' and resid 222 through 230 Processing helix chain 'C' and resid 342 through 351 Processing helix chain 'C' and resid 385 through 390 removed outlier: 3.530A pdb=" N LEU C 388 " --> pdb=" O PHE C 385 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER C 390 " --> pdb=" O PRO C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 416 removed outlier: 3.611A pdb=" N LEU C 414 " --> pdb=" O ASN C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 436 Processing helix chain 'C' and resid 449 through 456 removed outlier: 4.898A pdb=" N SER C 454 " --> pdb=" O SER C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 524 through 529 Processing helix chain 'C' and resid 676 through 678 No H-bonds generated for 'chain 'C' and resid 676 through 678' Processing helix chain 'C' and resid 694 through 702 removed outlier: 4.914A pdb=" N ARG C 700 " --> pdb=" O MET C 696 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 41 removed outlier: 3.624A pdb=" N ASP J 41 " --> pdb=" O THR J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 53 Processing helix chain 'J' and resid 104 through 108 Processing helix chain 'J' and resid 133 through 137 Processing helix chain 'J' and resid 222 through 230 Processing helix chain 'J' and resid 303 through 307 removed outlier: 4.008A pdb=" N ARG J 307 " --> pdb=" O GLN J 304 " (cutoff:3.500A) Processing helix chain 'J' and resid 342 through 351 Processing helix chain 'J' and resid 385 through 389 removed outlier: 3.504A pdb=" N LEU J 388 " --> pdb=" O PHE J 385 " (cutoff:3.500A) Processing helix chain 'J' and resid 410 through 416 removed outlier: 4.008A pdb=" N LEU J 414 " --> pdb=" O ASN J 410 " (cutoff:3.500A) Processing helix chain 'J' and resid 429 through 436 Processing helix chain 'J' and resid 449 through 456 removed outlier: 4.518A 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 676 through 678 No H-bonds generated for 'chain 'J' and resid 676 through 678' Processing helix chain 'J' and resid 694 through 702 removed outlier: 4.936A pdb=" N ARG J 700 " --> pdb=" O MET J 696 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 719 through 724 removed outlier: 7.259A pdb=" N LEU A 759 " --> pdb=" O SER B 720 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LEU B 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: 5.684A 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 796 removed outlier: 6.931A pdb=" N TYR A 777 " --> pdb=" O ALA A1152 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ALA A1152 " --> pdb=" O TYR A 777 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LYS A 779 " --> pdb=" O VAL A1150 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL A1150 " --> pdb=" O LYS A 779 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N SER A 781 " --> pdb=" O GLU A1148 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLU A1148 " --> pdb=" O SER A 781 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N HIS A1146 " --> pdb=" O PRO A 783 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 802 through 804 Processing sheet with id=AA5, first strand: chain 'A' and resid 857 through 858 Processing sheet with id=AA6, first strand: chain 'A' and resid 1202 through 1204 removed outlier: 7.277A pdb=" N GLY A1154 " --> pdb=" O GLN A1212 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE A1214 " --> pdb=" O GLY A1154 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N CYS A1156 " --> pdb=" O ILE A1214 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1171 through 1173 Processing sheet with id=AA8, first strand: chain 'C' and resid 719 through 724 removed outlier: 6.991A pdb=" N LEU D 759 " --> pdb=" O SER C 720 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LEU C 722 " --> pdb=" O LEU D 759 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 768 through 769 removed outlier: 5.644A pdb=" N ILE D 768 " --> pdb=" O SER G 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 777 through 796 removed outlier: 6.922A pdb=" N TYR D 777 " --> pdb=" O ALA D1152 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ALA D1152 " --> pdb=" O TYR D 777 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LYS D 779 " --> pdb=" O VAL D1150 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL D1150 " --> pdb=" O LYS D 779 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N SER D 781 " --> pdb=" O GLU D1148 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLU D1148 " --> pdb=" O SER D 781 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N HIS D1146 " --> pdb=" O PRO D 783 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 777 through 796 removed outlier: 6.922A pdb=" N TYR D 777 " --> pdb=" O ALA D1152 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ALA D1152 " --> pdb=" O TYR D 777 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LYS D 779 " --> pdb=" O VAL D1150 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL D1150 " --> pdb=" O LYS D 779 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N SER D 781 " --> pdb=" O GLU D1148 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLU D1148 " --> pdb=" O SER D 781 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N HIS D1146 " --> pdb=" O PRO D 783 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N VAL D1150 " --> pdb=" O LYS D1174 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N PHE D1172 " --> pdb=" O ALA D1152 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 802 through 804 Processing sheet with id=AB4, first strand: chain 'D' and resid 1202 through 1205 removed outlier: 4.158A pdb=" N CYS D1164 " --> pdb=" O VAL D1205 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N CYS D1156 " --> pdb=" O ILE D1214 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.897A pdb=" N ALA E 78 " --> pdb=" O CYS E 22 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.289A pdb=" N SER E 44 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ALA E 33 " --> pdb=" O LYS E 95 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N CYS E 92 " --> pdb=" O TRP E 103 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N TRP E 103 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ARG E 94 " --> pdb=" O ASP E 101 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYR E 98 " --> pdb=" O VAL E 100B" (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL E 100B" --> pdb=" O TYR E 98 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.289A pdb=" N SER E 44 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ALA E 33 " --> pdb=" O LYS E 95 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.574A pdb=" N MET F 33 " --> pdb=" O SER F 49 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N SER F 49 " --> pdb=" O MET F 33 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 19 through 24 Processing sheet with id=AC1, first strand: chain 'J' and resid 719 through 724 removed outlier: 7.145A pdb=" N LEU G 759 " --> pdb=" O SER J 720 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU J 722 " --> pdb=" O LEU G 759 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 777 through 796 removed outlier: 6.923A pdb=" N TYR G 777 " --> pdb=" O ALA G1152 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ALA G1152 " --> pdb=" O TYR G 777 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LYS G 779 " --> pdb=" O VAL G1150 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL G1150 " --> pdb=" O LYS G 779 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N SER G 781 " --> pdb=" O GLU G1148 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLU G1148 " --> pdb=" O SER G 781 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N HIS G1146 " --> pdb=" O PRO G 783 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 777 through 796 removed outlier: 6.923A pdb=" N TYR G 777 " --> pdb=" O ALA G1152 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ALA G1152 " --> pdb=" O TYR G 777 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LYS G 779 " --> pdb=" O VAL G1150 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL G1150 " --> pdb=" O LYS G 779 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N SER G 781 " --> pdb=" O GLU G1148 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLU G1148 " --> pdb=" O SER G 781 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N HIS G1146 " --> pdb=" O PRO G 783 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL G1150 " --> pdb=" O LYS G1174 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N PHE G1172 " --> pdb=" O ALA G1152 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 802 through 804 Processing sheet with id=AC5, first strand: chain 'G' and resid 1155 through 1157 removed outlier: 3.839A pdb=" N ILE G1214 " --> pdb=" O CYS G1156 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 1164 through 1167 removed outlier: 3.899A pdb=" N CYS G1164 " --> pdb=" O VAL G1205 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.620A pdb=" N ALA H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.345A pdb=" N SER H 44 " --> pdb=" O SER H 40 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 96 through 99 removed outlier: 4.498A pdb=" N TYR H 98 " --> pdb=" O VAL H 100B" (cutoff:3.500A) removed outlier: 7.544A pdb=" N VAL H 100B" --> pdb=" O TYR H 98 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.186A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N MET I 33 " --> pdb=" O SER I 49 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SER I 49 " --> pdb=" O MET I 33 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 17 through 24 removed outlier: 5.663A pdb=" N GLN I 17 " --> pdb=" O PRO I 77 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 33 through 35 removed outlier: 6.118A pdb=" N ASP B 34 " --> pdb=" O VAL B 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 63 through 64 removed outlier: 6.347A pdb=" N THR B 63 " --> pdb=" O TYR J 632 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N VAL J 639 " --> pdb=" O LEU J 651 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 69 through 75 removed outlier: 3.691A pdb=" N ARG B 335 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.408A pdb=" N SER B 267 " --> pdb=" O GLN B 280 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N GLN B 280 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 88 through 89 removed outlier: 7.713A pdb=" N SER B 88 " --> pdb=" O ILE B 300 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 92 through 93 Processing sheet with id=AD9, first strand: chain 'B' and resid 110 through 111 removed outlier: 4.532A pdb=" N ALA B 146 " --> pdb=" O ILE B 296 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ILE B 186 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N CYS B 237 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLU B 188 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ARG B 235 " --> pdb=" O GLU B 188 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 126 through 127 removed outlier: 4.481A pdb=" N SER B 126 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA B 309 " --> pdb=" O THR B 139 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 153 through 154 Processing sheet with id=AE3, first strand: chain 'B' and resid 359 through 366 removed outlier: 4.442A pdb=" N VAL B 659 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N SER B 365 " --> pdb=" O VAL B 657 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N VAL B 657 " --> pdb=" O SER B 365 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N GLY B 675 " --> pdb=" O PRO B 658 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N CYS B 713 " --> pdb=" O PHE B 674 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 374 through 376 Processing sheet with id=AE5, first strand: chain 'B' and resid 400 through 404 removed outlier: 6.790A pdb=" N THR B 483 " --> pdb=" O VAL B 420 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N VAL B 420 " --> pdb=" O THR B 483 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 513 through 515 removed outlier: 5.402A pdb=" N SER B 498 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL B 561 " --> pdb=" O SER B 498 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ILE B 500 " --> pdb=" O SER B 559 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N SER B 559 " --> pdb=" O ILE B 500 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 617 through 619 removed outlier: 5.120A pdb=" N VAL B 639 " --> pdb=" O LEU B 651 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AE9, first strand: chain 'C' and resid 69 through 72 removed outlier: 3.702A pdb=" N ARG C 335 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AF2, first strand: chain 'C' and resid 75 through 76 removed outlier: 6.599A pdb=" N SER C 267 " --> pdb=" O GLN C 280 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N GLN C 280 " --> pdb=" O SER C 267 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 88 through 89 removed outlier: 7.482A pdb=" N SER C 88 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR C 206 " --> pdb=" O SER C 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'C' and resid 92 through 93 Processing sheet with id=AF5, first strand: chain 'C' and resid 110 through 111 removed outlier: 4.526A pdb=" N ALA C 146 " --> pdb=" O ILE C 296 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU C 180 " --> pdb=" O THR C 242 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N THR C 242 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ALA C 182 " --> pdb=" O MET C 240 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N MET C 240 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TYR C 184 " --> pdb=" O THR C 238 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE C 186 " --> pdb=" O ASN C 236 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ASN C 236 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLU C 188 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LEU C 234 " --> pdb=" O GLU C 188 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 126 through 127 removed outlier: 4.328A pdb=" N SER C 126 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA C 309 " --> pdb=" O THR C 139 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 153 through 154 Processing sheet with id=AF8, first strand: chain 'C' and resid 359 through 366 removed outlier: 4.230A pdb=" N VAL C 659 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N SER C 365 " --> pdb=" O VAL C 657 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N VAL C 657 " --> pdb=" O SER C 365 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N GLY C 675 " --> pdb=" O PRO C 658 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N CYS C 713 " --> pdb=" O PHE C 674 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 374 through 375 Processing sheet with id=AG1, first strand: chain 'C' and resid 381 through 382 removed outlier: 6.314A pdb=" N VAL C 381 " --> pdb=" O ASN C 408 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N CYS C 407 " --> pdb=" O CYS C 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'C' and resid 400 through 404 removed outlier: 3.563A pdb=" N LYS C 400 " --> pdb=" O TYR C 445 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR C 483 " --> pdb=" O VAL C 420 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N VAL C 420 " --> pdb=" O THR C 483 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 513 through 515 removed outlier: 5.451A pdb=" N SER C 498 " --> pdb=" O VAL C 561 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL C 561 " --> pdb=" O SER C 498 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ILE C 500 " --> pdb=" O SER C 559 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N SER C 559 " --> pdb=" O ILE C 500 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 617 through 619 removed outlier: 5.519A pdb=" N VAL C 639 " --> pdb=" O LEU C 651 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL C 631 " --> pdb=" O VAL C 639 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 33 through 35 Processing sheet with id=AG6, first strand: chain 'J' and resid 68 through 72 removed outlier: 3.633A pdb=" N ARG J 335 " --> pdb=" O ASP J 326 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'J' and resid 75 through 76 Processing sheet with id=AG8, first strand: chain 'J' and resid 75 through 76 removed outlier: 6.373A pdb=" N SER J 267 " --> pdb=" O GLN J 280 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N GLN J 280 " --> pdb=" O SER J 267 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'J' and resid 88 through 89 removed outlier: 7.462A pdb=" N SER J 88 " --> pdb=" O ILE J 300 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'J' and resid 92 through 93 Processing sheet with id=AH2, first strand: chain 'J' and resid 110 through 111 removed outlier: 4.554A pdb=" N ALA J 146 " --> pdb=" O ILE J 296 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE J 186 " --> pdb=" O CYS J 237 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N CYS J 237 " --> pdb=" O ILE J 186 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLU J 188 " --> pdb=" O ARG J 235 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ARG J 235 " --> pdb=" O GLU J 188 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 126 through 127 removed outlier: 4.355A pdb=" N SER J 126 " --> pdb=" O ILE J 140 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA J 309 " --> pdb=" O THR J 139 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'J' and resid 153 through 154 Processing sheet with id=AH5, first strand: chain 'J' and resid 359 through 366 removed outlier: 4.414A pdb=" N VAL J 659 " --> pdb=" O VAL J 363 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N SER J 365 " --> pdb=" O VAL J 657 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N VAL J 657 " --> pdb=" O SER J 365 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N GLY J 675 " --> pdb=" O PRO J 658 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N CYS J 713 " --> pdb=" O PHE J 674 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'J' and resid 371 through 375 removed outlier: 6.328A pdb=" N GLY J 372 " --> pdb=" O GLU J 605 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N SER J 607 " --> pdb=" O GLY J 372 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL J 374 " --> pdb=" O SER J 607 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'J' and resid 381 through 382 removed outlier: 6.476A pdb=" N VAL J 381 " --> pdb=" O ASN J 408 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N CYS J 407 " --> pdb=" O CYS J 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'J' and resid 400 through 404 removed outlier: 3.537A pdb=" N LYS J 400 " --> pdb=" O TYR J 445 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR J 483 " --> pdb=" O VAL J 420 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VAL J 420 " --> pdb=" O THR J 483 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 513 through 515 removed outlier: 5.437A pdb=" N SER J 498 " --> pdb=" O VAL J 561 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL J 561 " --> pdb=" O SER J 498 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ILE J 500 " --> pdb=" O SER J 559 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N SER J 559 " --> pdb=" O ILE J 500 " (cutoff:3.500A) 1208 hydrogen bonds defined for protein. 3141 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: 7.51 Time building geometry restraints manager: 3.72 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: 9457 1.34 - 1.48: 8966 1.48 - 1.61: 13197 1.61 - 1.75: 2 1.75 - 1.89: 231 Bond restraints: 31853 Sorted by residual: bond pdb=" N CYS J 585 " pdb=" CA CYS J 585 " ideal model delta sigma weight residual 1.456 1.372 0.084 8.70e-03 1.32e+04 9.25e+01 bond pdb=" CA VAL J 584 " pdb=" C VAL J 584 " ideal model delta sigma weight residual 1.524 1.424 0.099 1.23e-02 6.61e+03 6.52e+01 bond pdb=" CA CYS B 437 " pdb=" C CYS B 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 J 437 " pdb=" O CYS J 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 C 437 " pdb=" N TYR C 438 " ideal model delta sigma weight residual 1.331 1.400 -0.069 1.22e-02 6.72e+03 3.21e+01 ... (remaining 31848 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 38940 2.64 - 5.27: 3650 5.27 - 7.91: 609 7.91 - 10.55: 113 10.55 - 13.18: 13 Bond angle restraints: 43325 Sorted by residual: angle pdb=" C LEU D 935 " pdb=" N PRO D 936 " pdb=" CA PRO D 936 " ideal model delta sigma weight residual 119.66 127.46 -7.80 7.20e-01 1.93e+00 1.17e+02 angle pdb=" C GLN F 42 " pdb=" N PRO F 43 " pdb=" CA PRO F 43 " ideal model delta sigma weight residual 119.66 127.19 -7.53 7.20e-01 1.93e+00 1.09e+02 angle pdb=" C LEU A 935 " pdb=" N PRO A 936 " pdb=" CA PRO A 936 " ideal model delta sigma weight residual 119.66 127.14 -7.48 7.20e-01 1.93e+00 1.08e+02 angle pdb=" C GLY E 8 " pdb=" N PRO E 9 " pdb=" CA PRO E 9 " ideal model delta sigma weight residual 119.85 129.96 -10.11 1.01e+00 9.80e-01 1.00e+02 angle pdb=" O CYS J 437 " pdb=" C CYS J 437 " pdb=" N TYR J 438 " ideal model delta sigma weight residual 123.19 111.63 11.56 1.17e+00 7.31e-01 9.76e+01 ... (remaining 43320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 18319 17.77 - 35.54: 440 35.54 - 53.32: 163 53.32 - 71.09: 67 71.09 - 88.86: 32 Dihedral angle restraints: 19021 sinusoidal: 7315 harmonic: 11706 Sorted by residual: dihedral pdb=" CB CYS B 727 " pdb=" SG CYS B 727 " pdb=" SG CYS B 736 " pdb=" CB CYS B 736 " 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 F 23 " pdb=" SG CYS F 23 " pdb=" SG CYS F 88 " pdb=" CB CYS F 88 " ideal model delta sinusoidal sigma weight residual 93.00 172.84 -79.84 1 1.00e+01 1.00e-02 7.91e+01 dihedral pdb=" CB CYS D1106 " pdb=" SG CYS D1106 " pdb=" SG CYS D1117 " pdb=" CB CYS D1117 " ideal model delta sinusoidal sigma weight residual 93.00 165.53 -72.53 1 1.00e+01 1.00e-02 6.72e+01 ... (remaining 19018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 3021 0.069 - 0.137: 1438 0.137 - 0.206: 304 0.206 - 0.275: 42 0.275 - 0.344: 10 Chirality restraints: 4815 Sorted by residual: chirality pdb=" CA ASN J 436 " pdb=" N ASN J 436 " pdb=" C ASN J 436 " pdb=" CB ASN J 436 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CA GLN J 688 " pdb=" N GLN J 688 " pdb=" C GLN J 688 " pdb=" CB GLN J 688 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CA THR C 63 " pdb=" N THR C 63 " pdb=" C THR C 63 " pdb=" CB THR C 63 " both_signs ideal model delta sigma weight residual False 2.53 2.19 0.33 2.00e-01 2.50e+01 2.78e+00 ... (remaining 4812 not shown) Planarity restraints: 5632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D1218 " 0.106 5.00e-02 4.00e+02 1.62e-01 4.20e+01 pdb=" N PRO D1219 " -0.280 5.00e-02 4.00e+02 pdb=" CA PRO D1219 " 0.091 5.00e-02 4.00e+02 pdb=" CD PRO D1219 " 0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1218 " 0.086 5.00e-02 4.00e+02 1.31e-01 2.74e+01 pdb=" N PRO A1219 " -0.226 5.00e-02 4.00e+02 pdb=" CA PRO A1219 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO A1219 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS I 76 " 0.083 5.00e-02 4.00e+02 1.24e-01 2.46e+01 pdb=" N PRO I 77 " -0.214 5.00e-02 4.00e+02 pdb=" CA PRO I 77 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO I 77 " 0.062 5.00e-02 4.00e+02 ... (remaining 5629 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.20: 14 2.20 - 2.87: 12332 2.87 - 3.55: 43137 3.55 - 4.22: 77376 4.22 - 4.90: 125013 Nonbonded interactions: 257872 Sorted by model distance: nonbonded pdb=" OH TYR A 905 " pdb=" CA PRO A 936 " model vdw 1.520 3.470 nonbonded pdb=" CE2 PHE C 506 " pdb=" CG2 VAL C 555 " model vdw 1.574 3.760 nonbonded pdb=" O ASP B 384 " pdb=" CZ PHE B 404 " model vdw 1.808 3.340 nonbonded pdb=" CE2 PHE B 506 " pdb=" CG2 VAL B 555 " model vdw 1.965 3.760 nonbonded pdb=" CG1 VAL B 381 " pdb=" N ASN B 408 " model vdw 1.993 3.540 ... (remaining 257867 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'D' and (resid 753 through 1175 or resid 1183 through 1223)) selection = (chain 'G' and (resid 753 through 1175 or resid 1183 through 1223)) } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 30.470 Find NCS groups from input model: 0.640 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 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 0.305 31909 Z= 0.887 Angle : 1.745 38.675 43435 Z= 1.192 Chirality : 0.078 0.344 4815 Planarity : 0.011 0.162 5632 Dihedral : 10.524 88.862 11388 Min Nonbonded Distance : 1.520 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.85 % Allowed : 4.48 % Favored : 94.66 % Rotamer: Outliers : 0.06 % Allowed : 0.46 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.50 % 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: 0.78 (0.13), residues: 3992 helix: -0.20 (0.18), residues: 703 sheet: 0.25 (0.16), residues: 898 loop : 1.08 (0.13), residues: 2391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 841 TYR 0.056 0.007 TYR J 469 PHE 0.030 0.005 PHE I 32 TRP 0.054 0.009 TRP H 47 HIS 0.015 0.002 HIS C 194 Details of bonding type rmsd covalent geometry : bond 0.01355 (31853) covalent geometry : angle 1.71048 (43325) SS BOND : bond 0.07677 ( 55) SS BOND : angle 7.05107 ( 110) hydrogen bonds : bond 0.18174 ( 1167) hydrogen bonds : angle 8.64451 ( 3141) Misc. bond : bond 0.14175 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 650 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 853 VAL cc_start: 0.9175 (t) cc_final: 0.8951 (m) REVERT: A 893 LEU cc_start: 0.8522 (mt) cc_final: 0.7874 (tt) REVERT: A 1104 ASN cc_start: 0.9237 (m-40) cc_final: 0.8891 (t0) REVERT: A 1126 PHE cc_start: 0.9233 (m-80) cc_final: 0.8652 (m-80) REVERT: A 1137 MET cc_start: 0.8941 (mtm) cc_final: 0.8530 (mpp) REVERT: D 779 LYS cc_start: 0.8748 (mttt) cc_final: 0.8392 (mmmt) REVERT: D 844 ASP cc_start: 0.8751 (m-30) cc_final: 0.8509 (m-30) REVERT: D 909 TYR cc_start: 0.7866 (t80) cc_final: 0.6964 (t80) REVERT: D 980 LEU cc_start: 0.9537 (mt) cc_final: 0.9278 (mt) REVERT: D 1012 PHE cc_start: 0.7570 (m-80) cc_final: 0.7315 (m-80) REVERT: D 1201 ASN cc_start: 0.8941 (m-40) cc_final: 0.8338 (p0) REVERT: E 12 VAL cc_start: 0.7718 (t) cc_final: 0.7279 (t) REVERT: E 69 MET cc_start: 0.7013 (mtt) cc_final: 0.6503 (mtt) REVERT: F 27 GLU cc_start: 0.9112 (tp30) cc_final: 0.8859 (tp30) REVERT: F 79 GLU cc_start: 0.6572 (mt-10) cc_final: 0.6339 (tm-30) REVERT: F 81 ASP cc_start: 0.7977 (m-30) cc_final: 0.6951 (m-30) REVERT: G 913 MET cc_start: 0.3610 (mtp) cc_final: 0.3181 (ttm) REVERT: G 940 ASP cc_start: 0.8594 (t0) cc_final: 0.8031 (t0) REVERT: G 977 PHE cc_start: 0.9470 (m-80) cc_final: 0.9204 (m-80) REVERT: G 990 LEU cc_start: 0.9609 (mt) cc_final: 0.9169 (tt) REVERT: G 1024 ASP cc_start: 0.8752 (m-30) cc_final: 0.8400 (t0) REVERT: G 1086 LEU cc_start: 0.9474 (mt) cc_final: 0.8748 (mt) REVERT: G 1182 ASP cc_start: 0.8878 (m-30) cc_final: 0.8398 (t70) REVERT: G 1190 SER cc_start: 0.7808 (t) cc_final: 0.7536 (t) REVERT: G 1201 ASN cc_start: 0.9427 (m-40) cc_final: 0.9219 (t0) REVERT: H 2 VAL cc_start: 0.7734 (t) cc_final: 0.7354 (t) REVERT: H 35 HIS cc_start: 0.9226 (m-70) cc_final: 0.8853 (m-70) REVERT: I 11 LEU cc_start: 0.8435 (tp) cc_final: 0.8229 (tp) REVERT: I 27 GLU cc_start: 0.7535 (tt0) cc_final: 0.6864 (tm-30) REVERT: I 27 ASP cc_start: 0.8354 (m-30) cc_final: 0.7562 (t0) REVERT: I 27 ASN cc_start: 0.8464 (t0) cc_final: 0.7879 (t0) REVERT: I 33 MET cc_start: 0.8645 (mmm) cc_final: 0.8367 (mmm) REVERT: I 47 LEU cc_start: 0.9583 (mt) cc_final: 0.9235 (mt) REVERT: B 239 PHE cc_start: 0.8786 (m-80) cc_final: 0.8522 (m-80) REVERT: B 278 MET cc_start: 0.9079 (mtp) cc_final: 0.8108 (mmm) REVERT: B 284 LEU cc_start: 0.9258 (mt) cc_final: 0.8972 (mp) REVERT: B 332 TYR cc_start: 0.9102 (m-80) cc_final: 0.8621 (m-10) REVERT: B 541 TYR cc_start: 0.6261 (m-80) cc_final: 0.5931 (m-80) REVERT: B 587 LYS cc_start: 0.7239 (mmtt) cc_final: 0.6595 (mtpt) REVERT: B 602 ASN cc_start: 0.7684 (m-40) cc_final: 0.6924 (p0) REVERT: B 638 LEU cc_start: 0.8825 (tp) cc_final: 0.8356 (pt) REVERT: B 651 LEU cc_start: 0.8802 (tp) cc_final: 0.8515 (tp) REVERT: B 656 SER cc_start: 0.8319 (m) cc_final: 0.7413 (p) REVERT: B 686 MET cc_start: 0.6586 (mmm) cc_final: 0.6321 (mmm) REVERT: C 216 ASP cc_start: 0.8801 (m-30) cc_final: 0.8543 (m-30) REVERT: C 321 LEU cc_start: 0.8618 (mt) cc_final: 0.8068 (mt) REVERT: C 400 LYS cc_start: 0.7396 (mttt) cc_final: 0.7056 (mttt) REVERT: C 406 ASN cc_start: 0.7795 (m-40) cc_final: 0.7571 (p0) REVERT: C 589 GLU cc_start: 0.7306 (mm-30) cc_final: 0.6966 (pm20) REVERT: C 635 TYR cc_start: 0.9146 (m-80) cc_final: 0.8658 (m-80) REVERT: J 75 PHE cc_start: 0.8397 (m-80) cc_final: 0.8049 (m-80) REVERT: J 161 MET cc_start: 0.7580 (tpp) cc_final: 0.7338 (ttp) REVERT: J 171 LEU cc_start: 0.9100 (tp) cc_final: 0.8649 (pp) REVERT: J 253 TRP cc_start: 0.8076 (m100) cc_final: 0.7830 (m100) REVERT: J 497 TYR cc_start: 0.1188 (m-80) cc_final: -0.1991 (m-80) REVERT: J 642 TYR cc_start: 0.7490 (t80) cc_final: 0.7170 (t80) REVERT: J 648 TYR cc_start: 0.7474 (t80) cc_final: 0.7033 (t80) outliers start: 2 outliers final: 1 residues processed: 651 average time/residue: 0.1935 time to fit residues: 202.9720 Evaluate side-chains 310 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 309 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 197 optimal weight: 20.0000 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 0.2980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 8.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1016 ASN D 848 ASN D 927 GLN ** F 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 808 GLN G1104 ASN H 41 HIS B 521 ASN B 637 ASN ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 637 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.072554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.056838 restraints weight = 213034.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.058327 restraints weight = 128681.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.059465 restraints weight = 88151.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.060169 restraints weight = 66013.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.060730 restraints weight = 54007.269| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 31909 Z= 0.170 Angle : 0.726 11.035 43435 Z= 0.404 Chirality : 0.046 0.198 4815 Planarity : 0.007 0.107 5632 Dihedral : 5.487 25.382 4370 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.88 % Favored : 95.74 % Rotamer: Outliers : 0.03 % Allowed : 1.22 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.50 % 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: 0.60 (0.13), residues: 3992 helix: 0.72 (0.19), residues: 668 sheet: 0.31 (0.16), residues: 945 loop : 0.49 (0.13), residues: 2379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 822 TYR 0.023 0.002 TYR A 928 PHE 0.038 0.002 PHE A 850 TRP 0.022 0.002 TRP J 253 HIS 0.009 0.001 HIS B 681 Details of bonding type rmsd covalent geometry : bond 0.00356 (31853) covalent geometry : angle 0.72087 (43325) SS BOND : bond 0.00419 ( 55) SS BOND : angle 1.81794 ( 110) hydrogen bonds : bond 0.06421 ( 1167) hydrogen bonds : angle 6.69591 ( 3141) Misc. bond : bond 0.00434 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 446 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 780 LEU cc_start: 0.9568 (tt) cc_final: 0.9195 (tt) REVERT: A 827 PHE cc_start: 0.8951 (m-10) cc_final: 0.8707 (m-80) REVERT: A 893 LEU cc_start: 0.8474 (mt) cc_final: 0.7894 (tp) REVERT: A 906 MET cc_start: 0.6888 (mmp) cc_final: 0.6374 (mpp) REVERT: A 933 LYS cc_start: 0.8393 (mttt) cc_final: 0.7877 (mmtt) REVERT: A 977 PHE cc_start: 0.8894 (m-10) cc_final: 0.8668 (m-80) REVERT: A 1038 SER cc_start: 0.9087 (p) cc_final: 0.8254 (p) REVERT: A 1104 ASN cc_start: 0.9180 (m-40) cc_final: 0.8803 (t0) REVERT: A 1126 PHE cc_start: 0.9083 (m-80) cc_final: 0.8555 (m-80) REVERT: D 779 LYS cc_start: 0.8708 (mttt) cc_final: 0.8161 (mmmt) REVERT: D 1141 TYR cc_start: 0.8599 (t80) cc_final: 0.8308 (t80) REVERT: D 1180 ILE cc_start: 0.8648 (mp) cc_final: 0.8391 (mt) REVERT: D 1201 ASN cc_start: 0.8729 (m-40) cc_final: 0.8346 (p0) REVERT: F 2 ILE cc_start: 0.8376 (mm) cc_final: 0.7855 (tp) REVERT: F 33 MET cc_start: 0.8179 (mmp) cc_final: 0.7935 (mmm) REVERT: F 81 ASP cc_start: 0.7306 (m-30) cc_final: 0.6716 (m-30) REVERT: F 104 LEU cc_start: 0.8751 (tp) cc_final: 0.8534 (tp) REVERT: G 844 ASP cc_start: 0.9320 (m-30) cc_final: 0.8838 (m-30) REVERT: G 913 MET cc_start: 0.3825 (mtp) cc_final: 0.3317 (ttm) REVERT: G 938 LEU cc_start: 0.9083 (tt) cc_final: 0.8765 (tt) REVERT: G 940 ASP cc_start: 0.8450 (t0) cc_final: 0.7630 (t0) REVERT: G 943 MET cc_start: 0.8487 (tpp) cc_final: 0.7961 (mmt) REVERT: G 977 PHE cc_start: 0.9285 (m-80) cc_final: 0.8966 (m-80) REVERT: G 990 LEU cc_start: 0.9546 (mt) cc_final: 0.9173 (tt) REVERT: G 1024 ASP cc_start: 0.8613 (m-30) cc_final: 0.8389 (t0) REVERT: G 1039 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7911 (mt-10) REVERT: G 1040 LEU cc_start: 0.8746 (mm) cc_final: 0.8208 (tp) REVERT: G 1201 ASN cc_start: 0.9398 (m-40) cc_final: 0.9084 (m-40) REVERT: H 20 ILE cc_start: 0.8366 (mt) cc_final: 0.8157 (tp) REVERT: H 35 HIS cc_start: 0.8980 (m-70) cc_final: 0.8452 (m-70) REVERT: H 80 MET cc_start: 0.8460 (tmm) cc_final: 0.7826 (tmm) REVERT: I 27 GLU cc_start: 0.7428 (tt0) cc_final: 0.7039 (tm-30) REVERT: I 27 ASP cc_start: 0.8115 (m-30) cc_final: 0.7676 (t70) REVERT: I 27 ASN cc_start: 0.8218 (t0) cc_final: 0.5981 (m-40) REVERT: I 33 MET cc_start: 0.7965 (mmm) cc_final: 0.7390 (mmm) REVERT: I 49 SER cc_start: 0.7763 (m) cc_final: 0.7416 (p) REVERT: B 49 ASP cc_start: 0.8688 (t0) cc_final: 0.6286 (t0) REVERT: B 230 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8499 (tp30) REVERT: B 278 MET cc_start: 0.8586 (mtp) cc_final: 0.7994 (mmm) REVERT: B 284 LEU cc_start: 0.9369 (mt) cc_final: 0.9103 (mp) REVERT: B 287 TYR cc_start: 0.6498 (p90) cc_final: 0.6075 (p90) REVERT: B 313 PHE cc_start: 0.5825 (t80) cc_final: 0.5570 (t80) REVERT: B 332 TYR cc_start: 0.8456 (m-80) cc_final: 0.7798 (m-80) REVERT: B 343 ASP cc_start: 0.8934 (m-30) cc_final: 0.8516 (p0) REVERT: B 346 GLN cc_start: 0.8748 (tm-30) cc_final: 0.8363 (tm-30) REVERT: B 541 TYR cc_start: 0.6936 (m-80) cc_final: 0.6559 (m-10) REVERT: B 602 ASN cc_start: 0.7673 (m-40) cc_final: 0.6921 (p0) REVERT: C 49 ASP cc_start: 0.8018 (t0) cc_final: 0.7170 (m-30) REVERT: C 148 MET cc_start: 0.8739 (ttt) cc_final: 0.8490 (ttt) REVERT: C 288 ASP cc_start: 0.8788 (m-30) cc_final: 0.8275 (t0) REVERT: C 400 LYS cc_start: 0.7301 (mttt) cc_final: 0.6727 (mttt) REVERT: C 406 ASN cc_start: 0.8236 (m-40) cc_final: 0.7897 (p0) REVERT: C 589 GLU cc_start: 0.6862 (mm-30) cc_final: 0.6611 (pm20) REVERT: C 635 TYR cc_start: 0.8938 (m-80) cc_final: 0.8447 (m-80) REVERT: C 659 VAL cc_start: 0.9358 (m) cc_final: 0.9093 (p) REVERT: J 75 PHE cc_start: 0.8223 (m-80) cc_final: 0.7164 (m-80) REVERT: J 80 ASP cc_start: 0.8491 (t0) cc_final: 0.8262 (t0) REVERT: J 161 MET cc_start: 0.7174 (tpp) cc_final: 0.6832 (ttp) REVERT: J 240 MET cc_start: 0.8278 (ttt) cc_final: 0.7945 (tpt) REVERT: J 278 MET cc_start: 0.9499 (mmp) cc_final: 0.9221 (mmp) REVERT: J 321 LEU cc_start: 0.8130 (mt) cc_final: 0.7883 (mp) REVERT: J 377 GLN cc_start: 0.8771 (mt0) cc_final: 0.8497 (pm20) REVERT: J 415 LEU cc_start: 0.8392 (tp) cc_final: 0.8181 (tp) REVERT: J 689 TYR cc_start: 0.8102 (p90) cc_final: 0.7778 (p90) outliers start: 1 outliers final: 0 residues processed: 447 average time/residue: 0.1872 time to fit residues: 138.3491 Evaluate side-chains 284 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 234 optimal weight: 30.0000 chunk 202 optimal weight: 20.0000 chunk 301 optimal weight: 40.0000 chunk 89 optimal weight: 7.9990 chunk 203 optimal weight: 6.9990 chunk 134 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 277 optimal weight: 6.9990 chunk 2 optimal weight: 20.0000 chunk 317 optimal weight: 1.9990 chunk 358 optimal weight: 0.6980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1146 HIS D 848 ASN ** D1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1056 GLN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1104 ASN G1163 ASN H 41 HIS B 125 ASN ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 167 HIS J 377 GLN J 421 ASN ** J 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.071788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.056067 restraints weight = 215146.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.057593 restraints weight = 130436.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.058649 restraints weight = 89302.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.059224 restraints weight = 66940.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.059799 restraints weight = 56027.203| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 31909 Z= 0.146 Angle : 0.641 9.377 43435 Z= 0.352 Chirality : 0.043 0.170 4815 Planarity : 0.006 0.098 5632 Dihedral : 5.134 28.331 4370 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.21 % Favored : 95.47 % Rotamer: Outliers : 0.06 % Allowed : 1.62 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.50 % 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: 0.49 (0.13), residues: 3992 helix: 0.68 (0.19), residues: 711 sheet: 0.34 (0.16), residues: 966 loop : 0.34 (0.13), residues: 2315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 62 TYR 0.028 0.001 TYR A 909 PHE 0.039 0.002 PHE A 850 TRP 0.015 0.001 TRP J 553 HIS 0.008 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00308 (31853) covalent geometry : angle 0.63721 (43325) SS BOND : bond 0.00684 ( 55) SS BOND : angle 1.55264 ( 110) hydrogen bonds : bond 0.05342 ( 1167) hydrogen bonds : angle 6.16308 ( 3141) Misc. bond : bond 0.00249 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 392 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 803 THR cc_start: 0.9057 (p) cc_final: 0.7951 (p) REVERT: A 893 LEU cc_start: 0.8633 (mt) cc_final: 0.8003 (tp) REVERT: A 906 MET cc_start: 0.6935 (mmp) cc_final: 0.6352 (mpp) REVERT: A 924 ILE cc_start: 0.7345 (pt) cc_final: 0.6896 (pt) REVERT: A 933 LYS cc_start: 0.8380 (mttt) cc_final: 0.8003 (mttp) REVERT: A 1038 SER cc_start: 0.8774 (p) cc_final: 0.7969 (p) REVERT: A 1104 ASN cc_start: 0.9181 (m-40) cc_final: 0.8891 (t0) REVERT: A 1126 PHE cc_start: 0.8983 (m-80) cc_final: 0.8606 (m-80) REVERT: D 779 LYS cc_start: 0.8587 (mttt) cc_final: 0.8154 (mmmt) REVERT: D 913 MET cc_start: 0.7235 (mmt) cc_final: 0.7026 (tpp) REVERT: D 939 MET cc_start: 0.8534 (tpp) cc_final: 0.8300 (tpp) REVERT: D 1201 ASN cc_start: 0.8895 (m-40) cc_final: 0.8421 (p0) REVERT: F 33 MET cc_start: 0.8280 (mmp) cc_final: 0.8074 (mmm) REVERT: F 38 GLN cc_start: 0.8010 (tm-30) cc_final: 0.7660 (tm-30) REVERT: F 85 MET cc_start: 0.8898 (tpt) cc_final: 0.8037 (tpp) REVERT: G 940 ASP cc_start: 0.8402 (t0) cc_final: 0.7719 (t0) REVERT: G 954 SER cc_start: 0.8423 (t) cc_final: 0.7943 (m) REVERT: G 977 PHE cc_start: 0.9320 (m-10) cc_final: 0.9071 (m-80) REVERT: G 990 LEU cc_start: 0.9515 (mt) cc_final: 0.9131 (tt) REVERT: G 1024 ASP cc_start: 0.8629 (m-30) cc_final: 0.8239 (t0) REVERT: G 1040 LEU cc_start: 0.8848 (mm) cc_final: 0.8256 (tp) REVERT: G 1138 HIS cc_start: 0.8188 (m-70) cc_final: 0.7635 (m170) REVERT: G 1201 ASN cc_start: 0.9370 (m-40) cc_final: 0.9147 (m-40) REVERT: H 35 HIS cc_start: 0.9040 (m-70) cc_final: 0.8569 (m-70) REVERT: H 82 LEU cc_start: 0.8355 (tp) cc_final: 0.8116 (tp) REVERT: I 27 GLU cc_start: 0.7874 (tt0) cc_final: 0.7197 (tm-30) REVERT: I 27 VAL cc_start: 0.6703 (p) cc_final: 0.5508 (p) REVERT: I 33 MET cc_start: 0.8427 (mmm) cc_final: 0.7483 (mmm) REVERT: I 37 GLN cc_start: 0.8417 (tt0) cc_final: 0.8212 (pt0) REVERT: I 42 GLN cc_start: 0.9275 (mt0) cc_final: 0.8695 (mp-120) REVERT: I 47 LEU cc_start: 0.9543 (mt) cc_final: 0.8853 (mt) REVERT: I 49 SER cc_start: 0.7893 (m) cc_final: 0.7597 (p) REVERT: B 148 MET cc_start: 0.8979 (ttp) cc_final: 0.8593 (ttp) REVERT: B 278 MET cc_start: 0.8664 (mtp) cc_final: 0.8099 (mmm) REVERT: B 287 TYR cc_start: 0.6462 (p90) cc_final: 0.6028 (p90) REVERT: B 313 PHE cc_start: 0.6169 (t80) cc_final: 0.5575 (t80) REVERT: B 332 TYR cc_start: 0.8389 (m-80) cc_final: 0.7836 (m-80) REVERT: C 49 ASP cc_start: 0.8232 (t0) cc_final: 0.7825 (t0) REVERT: C 148 MET cc_start: 0.8693 (ttt) cc_final: 0.8249 (ttt) REVERT: C 161 MET cc_start: 0.8415 (tpt) cc_final: 0.7812 (tpp) REVERT: C 388 LEU cc_start: 0.5851 (tp) cc_final: 0.5532 (tp) REVERT: C 406 ASN cc_start: 0.8234 (m-40) cc_final: 0.7807 (p0) REVERT: C 415 LEU cc_start: 0.8025 (tp) cc_final: 0.7435 (mt) REVERT: C 507 LEU cc_start: 0.8096 (tp) cc_final: 0.7838 (mp) REVERT: C 635 TYR cc_start: 0.8891 (m-80) cc_final: 0.8459 (m-80) REVERT: J 149 LEU cc_start: 0.8896 (mp) cc_final: 0.8624 (mp) REVERT: J 161 MET cc_start: 0.7293 (tpp) cc_final: 0.6978 (ttp) REVERT: J 169 LEU cc_start: 0.9643 (tt) cc_final: 0.9385 (tp) REVERT: J 171 LEU cc_start: 0.9197 (tp) cc_final: 0.8599 (pp) REVERT: J 321 LEU cc_start: 0.8612 (mt) cc_final: 0.8295 (mp) outliers start: 2 outliers final: 0 residues processed: 393 average time/residue: 0.1774 time to fit residues: 117.2741 Evaluate side-chains 254 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 381 optimal weight: 20.0000 chunk 221 optimal weight: 20.0000 chunk 177 optimal weight: 20.0000 chunk 176 optimal weight: 8.9990 chunk 105 optimal weight: 7.9990 chunk 205 optimal weight: 0.8980 chunk 230 optimal weight: 2.9990 chunk 284 optimal weight: 0.7980 chunk 337 optimal weight: 10.0000 chunk 225 optimal weight: 30.0000 chunk 257 optimal weight: 9.9990 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 772 GLN D 848 ASN D 915 GLN ** D1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 993 ASN ** G1028 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 HIS ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 599 GLN ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 708 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.069708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.053832 restraints weight = 215661.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.055255 restraints weight = 144549.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.056325 restraints weight = 98775.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.056601 restraints weight = 71236.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.057015 restraints weight = 64412.641| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 31909 Z= 0.176 Angle : 0.648 9.747 43435 Z= 0.352 Chirality : 0.043 0.179 4815 Planarity : 0.005 0.086 5632 Dihedral : 5.076 28.980 4370 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.43 % Favored : 95.27 % Rotamer: Outliers : 0.03 % Allowed : 2.03 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.50 % 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: 0.21 (0.13), residues: 3992 helix: 0.82 (0.19), residues: 712 sheet: 0.28 (0.16), residues: 973 loop : -0.04 (0.13), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 691 TYR 0.023 0.002 TYR J 648 PHE 0.029 0.002 PHE A 850 TRP 0.013 0.001 TRP J 310 HIS 0.009 0.001 HIS B 681 Details of bonding type rmsd covalent geometry : bond 0.00372 (31853) covalent geometry : angle 0.64563 (43325) SS BOND : bond 0.00603 ( 55) SS BOND : angle 1.28067 ( 110) hydrogen bonds : bond 0.04912 ( 1167) hydrogen bonds : angle 5.99707 ( 3141) Misc. bond : bond 0.00092 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 334 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 840 LEU cc_start: 0.9498 (mm) cc_final: 0.9296 (mm) REVERT: A 893 LEU cc_start: 0.8785 (mt) cc_final: 0.8028 (tt) REVERT: A 906 MET cc_start: 0.7112 (mmp) cc_final: 0.6522 (mpp) REVERT: A 933 LYS cc_start: 0.8544 (mttt) cc_final: 0.8102 (mttp) REVERT: A 1126 PHE cc_start: 0.8974 (m-80) cc_final: 0.8451 (m-80) REVERT: D 757 MET cc_start: 0.8206 (tmm) cc_final: 0.7679 (tmm) REVERT: D 779 LYS cc_start: 0.8677 (mttt) cc_final: 0.8250 (mmmt) REVERT: D 1172 PHE cc_start: 0.8533 (m-10) cc_final: 0.8112 (m-10) REVERT: D 1201 ASN cc_start: 0.9070 (m-40) cc_final: 0.8525 (p0) REVERT: E 56 ASN cc_start: 0.8445 (m-40) cc_final: 0.7722 (p0) REVERT: E 63 PHE cc_start: 0.8740 (m-80) cc_final: 0.8327 (m-10) REVERT: E 72 ASP cc_start: 0.8970 (t70) cc_final: 0.8671 (t0) REVERT: F 33 MET cc_start: 0.8365 (mmp) cc_final: 0.8151 (mmm) REVERT: F 38 GLN cc_start: 0.8006 (tm-30) cc_final: 0.7745 (tm-30) REVERT: F 85 MET cc_start: 0.8882 (tpt) cc_final: 0.8145 (tpt) REVERT: G 844 ASP cc_start: 0.9170 (m-30) cc_final: 0.8892 (m-30) REVERT: G 940 ASP cc_start: 0.8684 (t0) cc_final: 0.8008 (t0) REVERT: G 954 SER cc_start: 0.8713 (t) cc_final: 0.8240 (m) REVERT: G 978 TYR cc_start: 0.9040 (t80) cc_final: 0.8563 (t80) REVERT: G 1024 ASP cc_start: 0.8773 (m-30) cc_final: 0.8554 (t0) REVERT: G 1040 LEU cc_start: 0.8837 (mm) cc_final: 0.8206 (tp) REVERT: G 1138 HIS cc_start: 0.8244 (m-70) cc_final: 0.7737 (m170) REVERT: H 35 HIS cc_start: 0.9020 (m-70) cc_final: 0.8566 (m-70) REVERT: H 100 MET cc_start: 0.5467 (mmm) cc_final: 0.5121 (mmm) REVERT: I 27 GLU cc_start: 0.7923 (tt0) cc_final: 0.7171 (tm-30) REVERT: I 27 VAL cc_start: 0.6583 (p) cc_final: 0.5261 (p) REVERT: I 33 MET cc_start: 0.8464 (mmm) cc_final: 0.7453 (mmm) REVERT: I 42 GLN cc_start: 0.9370 (mt0) cc_final: 0.8760 (mp-120) REVERT: I 47 LEU cc_start: 0.9523 (mt) cc_final: 0.9178 (mt) REVERT: I 49 SER cc_start: 0.7872 (m) cc_final: 0.7622 (p) REVERT: I 63 ILE cc_start: 0.8964 (pt) cc_final: 0.8742 (mp) REVERT: B 148 MET cc_start: 0.9033 (ttp) cc_final: 0.8774 (ttp) REVERT: B 239 PHE cc_start: 0.8246 (m-10) cc_final: 0.8016 (m-80) REVERT: B 278 MET cc_start: 0.8652 (mtp) cc_final: 0.8060 (mmm) REVERT: B 287 TYR cc_start: 0.6621 (p90) cc_final: 0.6152 (p90) REVERT: B 293 TYR cc_start: 0.5464 (t80) cc_final: 0.5183 (t80) REVERT: B 332 TYR cc_start: 0.8369 (m-80) cc_final: 0.8012 (m-10) REVERT: B 343 ASP cc_start: 0.9002 (m-30) cc_final: 0.8772 (m-30) REVERT: B 541 TYR cc_start: 0.6515 (t80) cc_final: 0.6244 (t80) REVERT: B 569 MET cc_start: 0.6107 (mpp) cc_final: 0.5895 (mpp) REVERT: C 49 ASP cc_start: 0.8164 (t0) cc_final: 0.7835 (m-30) REVERT: C 148 MET cc_start: 0.8626 (ttt) cc_final: 0.8197 (ttt) REVERT: C 265 LEU cc_start: 0.9504 (mt) cc_final: 0.9296 (pp) REVERT: C 400 LYS cc_start: 0.8178 (mttt) cc_final: 0.7917 (ttpt) REVERT: C 415 LEU cc_start: 0.8025 (tp) cc_final: 0.7395 (mt) REVERT: C 635 TYR cc_start: 0.8894 (m-80) cc_final: 0.8505 (m-80) REVERT: J 75 PHE cc_start: 0.8576 (m-80) cc_final: 0.8305 (m-80) REVERT: J 149 LEU cc_start: 0.9051 (mp) cc_final: 0.8752 (mp) REVERT: J 161 MET cc_start: 0.7363 (tpp) cc_final: 0.7048 (ttm) REVERT: J 321 LEU cc_start: 0.8732 (mt) cc_final: 0.8307 (mp) outliers start: 1 outliers final: 0 residues processed: 334 average time/residue: 0.1823 time to fit residues: 102.7430 Evaluate side-chains 239 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 265 optimal weight: 20.0000 chunk 379 optimal weight: 50.0000 chunk 315 optimal weight: 10.0000 chunk 56 optimal weight: 0.0270 chunk 64 optimal weight: 9.9990 chunk 73 optimal weight: 0.9980 chunk 122 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 386 optimal weight: 20.0000 chunk 346 optimal weight: 20.0000 chunk 88 optimal weight: 4.9990 overall best weight: 5.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1208 GLN D 848 ASN ** D 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 987 GLN ** D1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 GLN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1129 ASN H 41 HIS ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 408 ASN ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 627 GLN J 348 HIS J 627 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.068769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.053124 restraints weight = 217517.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.054563 restraints weight = 132039.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.055542 restraints weight = 90987.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.056271 restraints weight = 69049.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.056694 restraints weight = 56656.759| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 31909 Z= 0.189 Angle : 0.647 9.785 43435 Z= 0.350 Chirality : 0.043 0.171 4815 Planarity : 0.005 0.071 5632 Dihedral : 5.073 29.533 4370 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.06 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.50 % 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: 0.06 (0.13), residues: 3992 helix: 0.92 (0.20), residues: 695 sheet: 0.22 (0.16), residues: 943 loop : -0.24 (0.13), residues: 2354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 62 TYR 0.035 0.002 TYR A 928 PHE 0.032 0.002 PHE A 977 TRP 0.012 0.001 TRP J 553 HIS 0.009 0.001 HIS G1122 Details of bonding type rmsd covalent geometry : bond 0.00402 (31853) covalent geometry : angle 0.64431 (43325) SS BOND : bond 0.00439 ( 55) SS BOND : angle 1.41979 ( 110) hydrogen bonds : bond 0.04817 ( 1167) hydrogen bonds : angle 5.98473 ( 3141) Misc. bond : bond 0.00064 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 840 LEU cc_start: 0.9509 (mm) cc_final: 0.9057 (mm) REVERT: A 842 GLN cc_start: 0.9207 (mp10) cc_final: 0.8945 (mp10) REVERT: A 893 LEU cc_start: 0.8898 (mt) cc_final: 0.8294 (tp) REVERT: A 906 MET cc_start: 0.6943 (mmp) cc_final: 0.6225 (mpp) REVERT: A 924 ILE cc_start: 0.7461 (pt) cc_final: 0.6838 (pt) REVERT: A 933 LYS cc_start: 0.8562 (mttt) cc_final: 0.8125 (mttp) REVERT: A 1008 MET cc_start: 0.7763 (tpt) cc_final: 0.7505 (tpt) REVERT: A 1126 PHE cc_start: 0.8798 (m-80) cc_final: 0.8343 (m-80) REVERT: D 779 LYS cc_start: 0.8568 (mttt) cc_final: 0.8171 (mmmt) REVERT: D 972 PHE cc_start: 0.8198 (t80) cc_final: 0.7985 (t80) REVERT: D 1172 PHE cc_start: 0.8491 (m-10) cc_final: 0.8127 (m-10) REVERT: D 1180 ILE cc_start: 0.8669 (mp) cc_final: 0.8412 (mt) REVERT: E 56 ASN cc_start: 0.8542 (m-40) cc_final: 0.8071 (p0) REVERT: E 63 PHE cc_start: 0.8711 (m-80) cc_final: 0.8326 (m-10) REVERT: E 69 MET cc_start: 0.7128 (mmt) cc_final: 0.6734 (mmm) REVERT: E 72 ASP cc_start: 0.8814 (t70) cc_final: 0.8583 (t0) REVERT: F 85 MET cc_start: 0.8869 (tpt) cc_final: 0.8635 (tpp) REVERT: G 854 LYS cc_start: 0.8561 (tmtt) cc_final: 0.8176 (tmtt) REVERT: G 913 MET cc_start: 0.3735 (mtp) cc_final: 0.3417 (ptp) REVERT: G 940 ASP cc_start: 0.8635 (t0) cc_final: 0.8098 (t0) REVERT: G 954 SER cc_start: 0.8853 (t) cc_final: 0.8348 (m) REVERT: G 978 TYR cc_start: 0.8899 (t80) cc_final: 0.8469 (t80) REVERT: G 990 LEU cc_start: 0.9459 (mt) cc_final: 0.9258 (mt) REVERT: H 35 HIS cc_start: 0.8905 (m-70) cc_final: 0.8427 (m170) REVERT: I 27 GLU cc_start: 0.8063 (tt0) cc_final: 0.7316 (tm-30) REVERT: I 27 VAL cc_start: 0.6589 (p) cc_final: 0.5211 (p) REVERT: I 33 MET cc_start: 0.8381 (mmm) cc_final: 0.7541 (mmm) REVERT: I 42 GLN cc_start: 0.9247 (mt0) cc_final: 0.8687 (mp-120) REVERT: B 148 MET cc_start: 0.8978 (ttp) cc_final: 0.8540 (ttp) REVERT: B 278 MET cc_start: 0.8700 (mtp) cc_final: 0.8237 (mmm) REVERT: B 287 TYR cc_start: 0.6545 (p90) cc_final: 0.6156 (p90) REVERT: B 332 TYR cc_start: 0.8091 (m-80) cc_final: 0.7850 (m-10) REVERT: B 343 ASP cc_start: 0.8845 (m-30) cc_final: 0.8612 (m-30) REVERT: C 148 MET cc_start: 0.8503 (ttt) cc_final: 0.8080 (ttt) REVERT: C 149 LEU cc_start: 0.9458 (mm) cc_final: 0.9196 (mm) REVERT: C 400 LYS cc_start: 0.8239 (mttt) cc_final: 0.7857 (ttpt) REVERT: C 406 ASN cc_start: 0.8077 (m-40) cc_final: 0.7665 (m-40) REVERT: C 415 LEU cc_start: 0.8137 (tp) cc_final: 0.7501 (mt) REVERT: C 436 ASN cc_start: 0.7658 (m110) cc_final: 0.7373 (m110) REVERT: C 466 GLN cc_start: 0.6689 (mm-40) cc_final: 0.6190 (mm-40) REVERT: C 635 TYR cc_start: 0.8795 (m-80) cc_final: 0.8395 (m-80) REVERT: J 75 PHE cc_start: 0.8766 (m-80) cc_final: 0.8536 (m-80) REVERT: J 148 MET cc_start: 0.8422 (tpt) cc_final: 0.8189 (tpp) REVERT: J 149 LEU cc_start: 0.8875 (mp) cc_final: 0.8588 (mp) REVERT: J 171 LEU cc_start: 0.9218 (tp) cc_final: 0.8748 (pp) REVERT: J 321 LEU cc_start: 0.8761 (mt) cc_final: 0.8467 (mp) REVERT: J 415 LEU cc_start: 0.8555 (tp) cc_final: 0.8348 (tp) REVERT: J 522 GLN cc_start: 0.8650 (tt0) cc_final: 0.8325 (tm-30) outliers start: 0 outliers final: 0 residues processed: 313 average time/residue: 0.1706 time to fit residues: 90.1073 Evaluate side-chains 231 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 367 optimal weight: 8.9990 chunk 167 optimal weight: 5.9990 chunk 107 optimal weight: 40.0000 chunk 81 optimal weight: 4.9990 chunk 353 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 298 optimal weight: 40.0000 chunk 85 optimal weight: 0.0000 chunk 315 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 993 ASN ** D1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 800 GLN ** G1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1132 ASN H 41 HIS ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN J 681 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.069434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.053828 restraints weight = 217005.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.055219 restraints weight = 131879.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.056247 restraints weight = 91320.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.056940 restraints weight = 68945.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.057457 restraints weight = 56837.831| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 31909 Z= 0.134 Angle : 0.598 9.996 43435 Z= 0.323 Chirality : 0.042 0.167 4815 Planarity : 0.005 0.103 5632 Dihedral : 4.904 29.349 4370 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.63 % Favored : 95.04 % Rotamer: Outliers : 0.03 % Allowed : 1.01 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.50 % 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: 0.05 (0.13), residues: 3992 helix: 0.99 (0.20), residues: 723 sheet: 0.20 (0.16), residues: 955 loop : -0.29 (0.13), residues: 2314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 629 TYR 0.019 0.001 TYR J 497 PHE 0.027 0.001 PHE D 977 TRP 0.010 0.001 TRP G 960 HIS 0.009 0.001 HIS J 681 Details of bonding type rmsd covalent geometry : bond 0.00282 (31853) covalent geometry : angle 0.59409 (43325) SS BOND : bond 0.00321 ( 55) SS BOND : angle 1.44362 ( 110) hydrogen bonds : bond 0.04538 ( 1167) hydrogen bonds : angle 5.74292 ( 3141) Misc. bond : bond 0.00263 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 312 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 840 LEU cc_start: 0.9571 (mm) cc_final: 0.9055 (mm) REVERT: A 893 LEU cc_start: 0.8946 (mt) cc_final: 0.8329 (tp) REVERT: A 906 MET cc_start: 0.7124 (mmp) cc_final: 0.6542 (mpp) REVERT: A 933 LYS cc_start: 0.8532 (mttt) cc_final: 0.8036 (mttp) REVERT: A 1126 PHE cc_start: 0.8912 (m-80) cc_final: 0.8428 (m-80) REVERT: A 1137 MET cc_start: 0.8592 (mpp) cc_final: 0.8331 (mpp) REVERT: D 779 LYS cc_start: 0.8659 (mttt) cc_final: 0.8120 (mmmt) REVERT: D 801 LYS cc_start: 0.9388 (mttt) cc_final: 0.8940 (mtmt) REVERT: D 943 MET cc_start: 0.8791 (tpp) cc_final: 0.8296 (tpp) REVERT: D 1172 PHE cc_start: 0.8596 (m-10) cc_final: 0.8171 (m-80) REVERT: D 1180 ILE cc_start: 0.8688 (mp) cc_final: 0.8427 (mt) REVERT: E 56 ASN cc_start: 0.8412 (m-40) cc_final: 0.7848 (p0) REVERT: E 63 PHE cc_start: 0.8752 (m-80) cc_final: 0.8364 (m-10) REVERT: E 69 MET cc_start: 0.7176 (mmt) cc_final: 0.6764 (mmm) REVERT: E 72 ASP cc_start: 0.8838 (t70) cc_final: 0.8554 (t0) REVERT: F 85 MET cc_start: 0.8925 (tpt) cc_final: 0.8587 (tpp) REVERT: G 854 LYS cc_start: 0.8475 (tmtt) cc_final: 0.8182 (tmtt) REVERT: G 913 MET cc_start: 0.3872 (mtp) cc_final: 0.3577 (ptp) REVERT: G 940 ASP cc_start: 0.8753 (t0) cc_final: 0.8048 (t0) REVERT: G 954 SER cc_start: 0.8884 (t) cc_final: 0.8394 (m) REVERT: G 1040 LEU cc_start: 0.8726 (mm) cc_final: 0.7883 (tp) REVERT: H 35 HIS cc_start: 0.8947 (m-70) cc_final: 0.8602 (m-70) REVERT: I 27 GLU cc_start: 0.8057 (tt0) cc_final: 0.7287 (tm-30) REVERT: I 27 VAL cc_start: 0.6559 (p) cc_final: 0.5212 (p) REVERT: I 33 MET cc_start: 0.8402 (mmm) cc_final: 0.7521 (mmm) REVERT: I 42 GLN cc_start: 0.9403 (mt0) cc_final: 0.8765 (mp-120) REVERT: B 49 ASP cc_start: 0.8755 (t70) cc_final: 0.7291 (t0) REVERT: B 52 LYS cc_start: 0.9149 (mptt) cc_final: 0.8727 (mmtp) REVERT: B 148 MET cc_start: 0.9013 (ttp) cc_final: 0.8801 (ttp) REVERT: B 278 MET cc_start: 0.8769 (mtp) cc_final: 0.8157 (mmm) REVERT: B 287 TYR cc_start: 0.6572 (p90) cc_final: 0.6109 (p90) REVERT: B 332 TYR cc_start: 0.8332 (m-80) cc_final: 0.8039 (m-10) REVERT: C 148 MET cc_start: 0.8475 (ttt) cc_final: 0.7970 (ttt) REVERT: C 149 LEU cc_start: 0.9438 (mm) cc_final: 0.9143 (mm) REVERT: C 180 LEU cc_start: 0.9496 (tp) cc_final: 0.9159 (pp) REVERT: C 400 LYS cc_start: 0.8231 (mttt) cc_final: 0.7923 (ttpt) REVERT: C 406 ASN cc_start: 0.8154 (m-40) cc_final: 0.7720 (m-40) REVERT: C 415 LEU cc_start: 0.8095 (tp) cc_final: 0.7514 (mt) REVERT: C 507 LEU cc_start: 0.7973 (tp) cc_final: 0.7684 (mp) REVERT: C 635 TYR cc_start: 0.8810 (m-80) cc_final: 0.8473 (m-80) REVERT: J 75 PHE cc_start: 0.8778 (m-80) cc_final: 0.8465 (m-80) REVERT: J 148 MET cc_start: 0.8526 (tpt) cc_final: 0.8280 (tpp) REVERT: J 149 LEU cc_start: 0.8904 (mp) cc_final: 0.8537 (mp) REVERT: J 240 MET cc_start: 0.8642 (tpt) cc_final: 0.8410 (tpt) REVERT: J 321 LEU cc_start: 0.8720 (mt) cc_final: 0.8407 (mp) REVERT: J 521 ASN cc_start: 0.7343 (p0) cc_final: 0.7065 (m-40) REVERT: J 563 MET cc_start: 0.5235 (mmp) cc_final: 0.4887 (tpp) outliers start: 1 outliers final: 1 residues processed: 313 average time/residue: 0.1717 time to fit residues: 90.9637 Evaluate side-chains 227 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 226 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 366 optimal weight: 9.9990 chunk 256 optimal weight: 2.9990 chunk 351 optimal weight: 7.9990 chunk 279 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 341 optimal weight: 5.9990 chunk 237 optimal weight: 30.0000 chunk 391 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1119 GLN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 1 GLN H 41 HIS ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 HIS B 421 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.067809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.052664 restraints weight = 222053.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.054721 restraints weight = 143949.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.054921 restraints weight = 94134.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.055390 restraints weight = 68299.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.055505 restraints weight = 62759.828| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.4980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 31909 Z= 0.203 Angle : 0.669 10.304 43435 Z= 0.359 Chirality : 0.043 0.164 4815 Planarity : 0.005 0.095 5632 Dihedral : 5.083 29.958 4370 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.86 % Favored : 93.84 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.50 % 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: -0.28 (0.13), residues: 3992 helix: 0.79 (0.19), residues: 714 sheet: 0.01 (0.16), residues: 947 loop : -0.54 (0.13), residues: 2331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 62 TYR 0.017 0.002 TYR C 292 PHE 0.027 0.002 PHE D 977 TRP 0.015 0.002 TRP J 310 HIS 0.009 0.001 HIS B 681 Details of bonding type rmsd covalent geometry : bond 0.00434 (31853) covalent geometry : angle 0.66601 (43325) SS BOND : bond 0.00389 ( 55) SS BOND : angle 1.44797 ( 110) hydrogen bonds : bond 0.04701 ( 1167) hydrogen bonds : angle 5.96178 ( 3141) Misc. bond : bond 0.00124 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 840 LEU cc_start: 0.9607 (mm) cc_final: 0.9164 (mm) REVERT: A 906 MET cc_start: 0.7277 (mmp) cc_final: 0.6551 (mpp) REVERT: A 933 LYS cc_start: 0.8740 (mttt) cc_final: 0.8076 (mmtt) REVERT: A 1108 LYS cc_start: 0.9160 (mttt) cc_final: 0.8925 (mtmt) REVERT: A 1126 PHE cc_start: 0.8933 (m-80) cc_final: 0.8383 (m-80) REVERT: D 757 MET cc_start: 0.8537 (tmm) cc_final: 0.8243 (ppp) REVERT: D 779 LYS cc_start: 0.8715 (mttt) cc_final: 0.8115 (mmmt) REVERT: D 827 PHE cc_start: 0.9432 (m-80) cc_final: 0.9212 (m-80) REVERT: D 943 MET cc_start: 0.8839 (tpp) cc_final: 0.8430 (tpp) REVERT: D 1008 MET cc_start: 0.8577 (tpt) cc_final: 0.8185 (tpp) REVERT: D 1141 TYR cc_start: 0.8912 (t80) cc_final: 0.8691 (t80) REVERT: D 1172 PHE cc_start: 0.8671 (m-10) cc_final: 0.8247 (m-10) REVERT: E 56 ASN cc_start: 0.8586 (m-40) cc_final: 0.8048 (p0) REVERT: E 63 PHE cc_start: 0.8833 (m-80) cc_final: 0.8412 (m-10) REVERT: E 69 MET cc_start: 0.7248 (mmt) cc_final: 0.6891 (mmt) REVERT: E 72 ASP cc_start: 0.8834 (t70) cc_final: 0.8568 (t0) REVERT: E 100 MET cc_start: 0.5939 (tpp) cc_final: 0.5530 (tpp) REVERT: F 85 MET cc_start: 0.9030 (tpt) cc_final: 0.8727 (tpp) REVERT: F 104 LEU cc_start: 0.9038 (tp) cc_final: 0.8838 (tp) REVERT: G 940 ASP cc_start: 0.8754 (t0) cc_final: 0.8053 (t0) REVERT: G 954 SER cc_start: 0.9011 (t) cc_final: 0.8575 (m) REVERT: H 35 HIS cc_start: 0.9087 (m-70) cc_final: 0.8723 (m-70) REVERT: I 27 GLU cc_start: 0.8068 (tt0) cc_final: 0.7277 (tm-30) REVERT: I 27 VAL cc_start: 0.6419 (p) cc_final: 0.4976 (p) REVERT: I 33 MET cc_start: 0.8477 (mmm) cc_final: 0.7608 (mmm) REVERT: I 42 GLN cc_start: 0.9401 (mt0) cc_final: 0.8716 (mp10) REVERT: I 87 PHE cc_start: 0.9062 (m-10) cc_final: 0.8843 (m-80) REVERT: B 49 ASP cc_start: 0.8776 (t70) cc_final: 0.7037 (t0) REVERT: B 52 LYS cc_start: 0.9176 (mptt) cc_final: 0.8771 (mmtp) REVERT: B 239 PHE cc_start: 0.8313 (m-10) cc_final: 0.8062 (m-80) REVERT: B 278 MET cc_start: 0.8888 (mtp) cc_final: 0.8392 (mmm) REVERT: B 287 TYR cc_start: 0.6525 (p90) cc_final: 0.6125 (p90) REVERT: B 293 TYR cc_start: 0.5192 (t80) cc_final: 0.4629 (t80) REVERT: B 332 TYR cc_start: 0.8335 (m-80) cc_final: 0.7896 (m-80) REVERT: B 343 ASP cc_start: 0.8870 (m-30) cc_final: 0.8664 (m-30) REVERT: C 148 MET cc_start: 0.8569 (ttt) cc_final: 0.7967 (ttt) REVERT: C 149 LEU cc_start: 0.9461 (mm) cc_final: 0.9144 (mm) REVERT: C 180 LEU cc_start: 0.9482 (tp) cc_final: 0.9182 (pp) REVERT: C 388 LEU cc_start: 0.5388 (tp) cc_final: 0.4815 (tp) REVERT: C 406 ASN cc_start: 0.7981 (m-40) cc_final: 0.7534 (m-40) REVERT: C 436 ASN cc_start: 0.7343 (m-40) cc_final: 0.7138 (m-40) REVERT: C 466 GLN cc_start: 0.6795 (mm-40) cc_final: 0.6375 (mm-40) REVERT: C 635 TYR cc_start: 0.8791 (m-80) cc_final: 0.8485 (m-80) REVERT: J 148 MET cc_start: 0.8241 (tpt) cc_final: 0.7987 (tpp) REVERT: J 149 LEU cc_start: 0.8919 (mp) cc_final: 0.8617 (mp) REVERT: J 240 MET cc_start: 0.8703 (tpt) cc_final: 0.8447 (tpt) REVERT: J 399 PHE cc_start: 0.8136 (m-10) cc_final: 0.6700 (m-10) REVERT: J 469 TYR cc_start: 0.2942 (t80) cc_final: 0.2633 (t80) REVERT: J 521 ASN cc_start: 0.7007 (p0) cc_final: 0.6650 (m-40) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.1734 time to fit residues: 86.3793 Evaluate side-chains 219 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 320 optimal weight: 9.9990 chunk 329 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 349 optimal weight: 8.9990 chunk 323 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 77 optimal weight: 0.9980 chunk 367 optimal weight: 10.0000 chunk 309 optimal weight: 7.9990 chunk 339 optimal weight: 30.0000 chunk 275 optimal weight: 10.0000 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 HIS ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN C 280 GLN ** J 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.067060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.051637 restraints weight = 222533.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.052948 restraints weight = 135723.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.053923 restraints weight = 94465.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.054585 restraints weight = 72121.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.054986 restraints weight = 59580.122| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.5435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 31909 Z= 0.211 Angle : 0.682 10.768 43435 Z= 0.366 Chirality : 0.044 0.282 4815 Planarity : 0.005 0.082 5632 Dihedral : 5.310 30.334 4370 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.96 % Favored : 93.74 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.56 (0.13), residues: 3992 helix: 0.61 (0.19), residues: 715 sheet: -0.03 (0.16), residues: 941 loop : -0.81 (0.13), residues: 2336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 847 TYR 0.030 0.002 TYR A 928 PHE 0.039 0.002 PHE D 977 TRP 0.016 0.002 TRP J 310 HIS 0.008 0.001 HIS H 41 Details of bonding type rmsd covalent geometry : bond 0.00449 (31853) covalent geometry : angle 0.67912 (43325) SS BOND : bond 0.00484 ( 55) SS BOND : angle 1.40677 ( 110) hydrogen bonds : bond 0.04780 ( 1167) hydrogen bonds : angle 6.03938 ( 3141) Misc. bond : bond 0.00118 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 840 LEU cc_start: 0.9618 (mm) cc_final: 0.9186 (mm) REVERT: A 906 MET cc_start: 0.7047 (mmp) cc_final: 0.6385 (mpp) REVERT: A 933 LYS cc_start: 0.8708 (mttt) cc_final: 0.8105 (mmtt) REVERT: A 1126 PHE cc_start: 0.8853 (m-80) cc_final: 0.8399 (m-80) REVERT: A 1137 MET cc_start: 0.8687 (mpp) cc_final: 0.8275 (mpp) REVERT: D 1172 PHE cc_start: 0.8733 (m-10) cc_final: 0.8314 (m-10) REVERT: D 1180 ILE cc_start: 0.8629 (mp) cc_final: 0.8325 (mt) REVERT: E 63 PHE cc_start: 0.8761 (m-80) cc_final: 0.8354 (m-10) REVERT: E 69 MET cc_start: 0.6875 (mmt) cc_final: 0.6572 (mmm) REVERT: E 72 ASP cc_start: 0.8891 (t70) cc_final: 0.8597 (t0) REVERT: E 100 MET cc_start: 0.6271 (tpp) cc_final: 0.5761 (tpp) REVERT: F 2 ILE cc_start: 0.8592 (mm) cc_final: 0.8352 (mm) REVERT: F 27 GLU cc_start: 0.8912 (pm20) cc_final: 0.8602 (pm20) REVERT: F 33 MET cc_start: 0.8054 (mmp) cc_final: 0.7847 (mmm) REVERT: F 85 MET cc_start: 0.9062 (tpt) cc_final: 0.8627 (tpp) REVERT: F 104 LEU cc_start: 0.9080 (tp) cc_final: 0.8873 (tp) REVERT: G 943 MET cc_start: 0.8327 (tpp) cc_final: 0.7992 (mmt) REVERT: G 954 SER cc_start: 0.9125 (t) cc_final: 0.8692 (m) REVERT: H 35 HIS cc_start: 0.9161 (m-70) cc_final: 0.8797 (m-70) REVERT: I 33 MET cc_start: 0.8452 (mmm) cc_final: 0.7683 (mmm) REVERT: I 42 GLN cc_start: 0.9374 (mt0) cc_final: 0.8612 (mp10) REVERT: I 87 PHE cc_start: 0.9083 (m-10) cc_final: 0.8724 (m-80) REVERT: B 49 ASP cc_start: 0.8745 (t70) cc_final: 0.6912 (t0) REVERT: B 52 LYS cc_start: 0.9169 (mptt) cc_final: 0.8785 (mmtp) REVERT: B 239 PHE cc_start: 0.8337 (m-80) cc_final: 0.8098 (m-80) REVERT: B 287 TYR cc_start: 0.6592 (p90) cc_final: 0.6288 (p90) REVERT: B 638 LEU cc_start: 0.9082 (tp) cc_final: 0.8048 (pt) REVERT: B 651 LEU cc_start: 0.8649 (tp) cc_final: 0.8082 (tp) REVERT: C 148 MET cc_start: 0.8550 (ttt) cc_final: 0.7953 (ttt) REVERT: C 149 LEU cc_start: 0.9495 (mm) cc_final: 0.9216 (mm) REVERT: C 180 LEU cc_start: 0.9508 (tp) cc_final: 0.9226 (pp) REVERT: C 406 ASN cc_start: 0.7996 (m-40) cc_final: 0.7279 (p0) REVERT: C 466 GLN cc_start: 0.6807 (mm-40) cc_final: 0.6313 (mm-40) REVERT: C 635 TYR cc_start: 0.8771 (m-80) cc_final: 0.8120 (m-10) REVERT: C 717 LEU cc_start: 0.9012 (mt) cc_final: 0.8495 (mt) REVERT: J 149 LEU cc_start: 0.8850 (mp) cc_final: 0.8526 (mp) REVERT: J 171 LEU cc_start: 0.9291 (tp) cc_final: 0.8937 (pp) REVERT: J 240 MET cc_start: 0.8664 (tpt) cc_final: 0.8383 (tpt) REVERT: J 399 PHE cc_start: 0.8076 (m-10) cc_final: 0.7219 (m-10) REVERT: J 521 ASN cc_start: 0.7232 (p0) cc_final: 0.6787 (m-40) REVERT: J 648 TYR cc_start: 0.8371 (t80) cc_final: 0.8112 (t80) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.1819 time to fit residues: 84.6728 Evaluate side-chains 208 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 375 optimal weight: 0.1980 chunk 339 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 390 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 225 optimal weight: 20.0000 chunk 130 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 227 optimal weight: 9.9990 chunk 218 optimal weight: 0.0570 overall best weight: 1.2300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1063 GLN A1163 ASN ** D1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 772 GLN ** G1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 HIS ** C 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.069108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.053503 restraints weight = 213606.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.054937 restraints weight = 129413.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.055926 restraints weight = 89082.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.056635 restraints weight = 67647.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.057006 restraints weight = 55219.711| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.5511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 31909 Z= 0.116 Angle : 0.599 10.944 43435 Z= 0.319 Chirality : 0.043 0.297 4815 Planarity : 0.005 0.075 5632 Dihedral : 4.857 28.125 4370 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.88 % Favored : 94.81 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.50 % 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: -0.20 (0.13), residues: 3992 helix: 1.13 (0.20), residues: 712 sheet: 0.20 (0.16), residues: 914 loop : -0.64 (0.13), residues: 2366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 181 TYR 0.021 0.001 TYR D1141 PHE 0.022 0.001 PHE C 183 TRP 0.034 0.002 TRP B 253 HIS 0.007 0.001 HIS H 41 Details of bonding type rmsd covalent geometry : bond 0.00242 (31853) covalent geometry : angle 0.59504 (43325) SS BOND : bond 0.00274 ( 55) SS BOND : angle 1.42359 ( 110) hydrogen bonds : bond 0.04349 ( 1167) hydrogen bonds : angle 5.59200 ( 3141) Misc. bond : bond 0.00082 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 840 LEU cc_start: 0.9475 (mm) cc_final: 0.9226 (pp) REVERT: A 906 MET cc_start: 0.7148 (mmp) cc_final: 0.6299 (mpp) REVERT: A 933 LYS cc_start: 0.8605 (mttt) cc_final: 0.7968 (mmtt) REVERT: A 1126 PHE cc_start: 0.8869 (m-80) cc_final: 0.8410 (m-80) REVERT: D 939 MET cc_start: 0.8742 (ttt) cc_final: 0.8029 (ttm) REVERT: D 1008 MET cc_start: 0.8479 (tpt) cc_final: 0.8193 (tpp) REVERT: D 1012 PHE cc_start: 0.8188 (m-80) cc_final: 0.7847 (m-80) REVERT: D 1172 PHE cc_start: 0.8638 (m-10) cc_final: 0.8294 (m-80) REVERT: E 63 PHE cc_start: 0.8830 (m-80) cc_final: 0.8493 (m-10) REVERT: E 69 MET cc_start: 0.6999 (mmt) cc_final: 0.6466 (mmm) REVERT: E 72 ASP cc_start: 0.8869 (t70) cc_final: 0.8502 (t0) REVERT: E 100 MET cc_start: 0.5880 (tpp) cc_final: 0.5465 (tpp) REVERT: F 2 ILE cc_start: 0.8465 (mm) cc_final: 0.8186 (mm) REVERT: F 27 GLU cc_start: 0.8877 (pm20) cc_final: 0.8554 (pm20) REVERT: F 85 MET cc_start: 0.9015 (tpt) cc_final: 0.8517 (tpp) REVERT: G 786 PHE cc_start: 0.8927 (p90) cc_final: 0.8720 (p90) REVERT: G 854 LYS cc_start: 0.8570 (tmtt) cc_final: 0.8320 (tmtt) REVERT: G 913 MET cc_start: 0.4159 (mtp) cc_final: 0.3910 (ptp) REVERT: G 940 ASP cc_start: 0.8678 (t0) cc_final: 0.7329 (t0) REVERT: G 954 SER cc_start: 0.9033 (t) cc_final: 0.8535 (m) REVERT: G 1040 LEU cc_start: 0.8619 (mm) cc_final: 0.7783 (tp) REVERT: H 35 HIS cc_start: 0.9125 (m-70) cc_final: 0.8702 (m-70) REVERT: I 27 VAL cc_start: 0.6887 (p) cc_final: 0.5970 (p) REVERT: I 33 MET cc_start: 0.8339 (mmm) cc_final: 0.7564 (mmm) REVERT: I 42 GLN cc_start: 0.9369 (mt0) cc_final: 0.8642 (mp10) REVERT: I 87 PHE cc_start: 0.9025 (m-10) cc_final: 0.8774 (m-80) REVERT: B 49 ASP cc_start: 0.8729 (t70) cc_final: 0.7084 (t0) REVERT: B 52 LYS cc_start: 0.9170 (mptt) cc_final: 0.8801 (mmtp) REVERT: B 239 PHE cc_start: 0.8354 (m-80) cc_final: 0.7888 (m-80) REVERT: B 278 MET cc_start: 0.8609 (mmp) cc_final: 0.8202 (mmm) REVERT: B 287 TYR cc_start: 0.6394 (p90) cc_final: 0.6109 (p90) REVERT: B 343 ASP cc_start: 0.8772 (m-30) cc_final: 0.8570 (m-30) REVERT: B 638 LEU cc_start: 0.9004 (tp) cc_final: 0.8062 (pt) REVERT: B 651 LEU cc_start: 0.8524 (tp) cc_final: 0.7849 (tp) REVERT: C 148 MET cc_start: 0.8651 (ttt) cc_final: 0.8412 (ttt) REVERT: C 180 LEU cc_start: 0.9592 (tp) cc_final: 0.9238 (pp) REVERT: C 269 ARG cc_start: 0.9035 (tpt-90) cc_final: 0.7844 (tpt90) REVERT: C 400 LYS cc_start: 0.8145 (mttt) cc_final: 0.7919 (ttpt) REVERT: C 406 ASN cc_start: 0.8230 (m-40) cc_final: 0.7510 (p0) REVERT: C 466 GLN cc_start: 0.6959 (mm-40) cc_final: 0.6473 (mm-40) REVERT: C 497 TYR cc_start: 0.5450 (m-80) cc_final: 0.4740 (m-80) REVERT: C 507 LEU cc_start: 0.7926 (tp) cc_final: 0.7637 (mp) REVERT: C 635 TYR cc_start: 0.8665 (m-80) cc_final: 0.8419 (m-80) REVERT: C 717 LEU cc_start: 0.8975 (mt) cc_final: 0.8563 (mt) REVERT: J 149 LEU cc_start: 0.8841 (mp) cc_final: 0.8594 (mp) REVERT: J 399 PHE cc_start: 0.7877 (m-10) cc_final: 0.7180 (m-10) REVERT: J 521 ASN cc_start: 0.7331 (p0) cc_final: 0.6945 (m-40) REVERT: J 569 MET cc_start: 0.7592 (mmt) cc_final: 0.7344 (mmm) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.1774 time to fit residues: 90.4321 Evaluate side-chains 223 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 22 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 95 optimal weight: 20.0000 chunk 198 optimal weight: 9.9990 chunk 206 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 301 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 268 optimal weight: 30.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1163 ASN ** D1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 842 GLN G1063 GLN G1104 ASN H 41 HIS ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.067981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.052237 restraints weight = 216197.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.053680 restraints weight = 130685.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.054649 restraints weight = 89555.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.055353 restraints weight = 67984.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.055764 restraints weight = 55694.976| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.5715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 31909 Z= 0.157 Angle : 0.636 13.138 43435 Z= 0.338 Chirality : 0.043 0.242 4815 Planarity : 0.005 0.076 5632 Dihedral : 4.923 28.062 4370 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.91 % Favored : 93.81 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.50 % 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: -0.31 (0.13), residues: 3992 helix: 1.08 (0.20), residues: 715 sheet: 0.07 (0.16), residues: 928 loop : -0.72 (0.13), residues: 2349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 181 TYR 0.025 0.002 TYR D 947 PHE 0.043 0.002 PHE D 977 TRP 0.029 0.002 TRP B 253 HIS 0.007 0.001 HIS B 681 Details of bonding type rmsd covalent geometry : bond 0.00337 (31853) covalent geometry : angle 0.63281 (43325) SS BOND : bond 0.00310 ( 55) SS BOND : angle 1.47211 ( 110) hydrogen bonds : bond 0.04405 ( 1167) hydrogen bonds : angle 5.69447 ( 3141) Misc. bond : bond 0.00092 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 840 LEU cc_start: 0.9486 (mm) cc_final: 0.9232 (pp) REVERT: A 906 MET cc_start: 0.7030 (mmp) cc_final: 0.6166 (mpp) REVERT: A 933 LYS cc_start: 0.8670 (mttt) cc_final: 0.8077 (mmtt) REVERT: A 1126 PHE cc_start: 0.8837 (m-80) cc_final: 0.8389 (m-80) REVERT: D 1008 MET cc_start: 0.8474 (tpt) cc_final: 0.8234 (tpp) REVERT: D 1012 PHE cc_start: 0.8117 (m-80) cc_final: 0.7813 (m-80) REVERT: D 1172 PHE cc_start: 0.8595 (m-10) cc_final: 0.8200 (m-80) REVERT: E 63 PHE cc_start: 0.8842 (m-80) cc_final: 0.8504 (m-10) REVERT: E 72 ASP cc_start: 0.8870 (t70) cc_final: 0.8561 (t0) REVERT: E 80 MET cc_start: 0.8347 (tpt) cc_final: 0.8128 (tpt) REVERT: E 100 MET cc_start: 0.5973 (tpp) cc_final: 0.5487 (tpp) REVERT: F 2 ILE cc_start: 0.8575 (mm) cc_final: 0.8369 (mm) REVERT: F 27 GLU cc_start: 0.8934 (pm20) cc_final: 0.8632 (pm20) REVERT: F 85 MET cc_start: 0.9039 (tpt) cc_final: 0.8542 (tpp) REVERT: G 854 LYS cc_start: 0.8608 (tmtt) cc_final: 0.8349 (tmtt) REVERT: G 940 ASP cc_start: 0.8422 (t0) cc_final: 0.7902 (t70) REVERT: G 954 SER cc_start: 0.9073 (t) cc_final: 0.8608 (m) REVERT: I 33 MET cc_start: 0.8403 (mmm) cc_final: 0.7641 (mmm) REVERT: I 42 GLN cc_start: 0.9329 (mt0) cc_final: 0.8577 (mp10) REVERT: I 87 PHE cc_start: 0.9066 (m-10) cc_final: 0.8818 (m-80) REVERT: B 49 ASP cc_start: 0.8682 (t70) cc_final: 0.7029 (t0) REVERT: B 52 LYS cc_start: 0.9155 (mptt) cc_final: 0.8796 (mmtp) REVERT: B 147 PHE cc_start: 0.8291 (m-10) cc_final: 0.8031 (m-10) REVERT: B 239 PHE cc_start: 0.8306 (m-80) cc_final: 0.7886 (m-80) REVERT: B 278 MET cc_start: 0.8745 (mmp) cc_final: 0.8432 (mmm) REVERT: B 287 TYR cc_start: 0.6522 (p90) cc_final: 0.6242 (p90) REVERT: B 638 LEU cc_start: 0.9059 (tp) cc_final: 0.8170 (pt) REVERT: B 651 LEU cc_start: 0.8629 (tp) cc_final: 0.8130 (tp) REVERT: C 148 MET cc_start: 0.8587 (ttt) cc_final: 0.8287 (ttt) REVERT: C 406 ASN cc_start: 0.8031 (m-40) cc_final: 0.7245 (p0) REVERT: C 436 ASN cc_start: 0.7792 (m-40) cc_final: 0.7590 (m-40) REVERT: C 466 GLN cc_start: 0.6891 (mm-40) cc_final: 0.6380 (mm-40) REVERT: C 497 TYR cc_start: 0.5568 (m-80) cc_final: 0.4816 (m-80) REVERT: C 635 TYR cc_start: 0.8745 (m-80) cc_final: 0.8104 (m-80) REVERT: C 717 LEU cc_start: 0.9014 (mt) cc_final: 0.8639 (mt) REVERT: J 148 MET cc_start: 0.8344 (tpt) cc_final: 0.8060 (tpt) REVERT: J 149 LEU cc_start: 0.8853 (mp) cc_final: 0.8468 (mp) REVERT: J 399 PHE cc_start: 0.8047 (m-10) cc_final: 0.7077 (m-10) REVERT: J 521 ASN cc_start: 0.7299 (p0) cc_final: 0.6854 (m-40) REVERT: J 569 MET cc_start: 0.7542 (mmt) cc_final: 0.7301 (mmm) outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.1695 time to fit residues: 81.5525 Evaluate side-chains 212 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 343 optimal weight: 20.0000 chunk 303 optimal weight: 30.0000 chunk 6 optimal weight: 5.9990 chunk 164 optimal weight: 20.0000 chunk 297 optimal weight: 20.0000 chunk 147 optimal weight: 3.9990 chunk 348 optimal weight: 8.9990 chunk 161 optimal weight: 10.0000 chunk 162 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 148 optimal weight: 0.0670 overall best weight: 5.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 769 GLN ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1163 ASN ** D1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1104 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 HIS ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 516 GLN ** J 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.067154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.051694 restraints weight = 217872.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.053058 restraints weight = 133588.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.054006 restraints weight = 92316.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.054672 restraints weight = 70150.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.055058 restraints weight = 57642.370| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.5974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 31909 Z= 0.186 Angle : 0.663 11.584 43435 Z= 0.354 Chirality : 0.044 0.195 4815 Planarity : 0.005 0.075 5632 Dihedral : 5.136 27.834 4370 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.46 % Favored : 93.24 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.50 % 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: -0.51 (0.13), residues: 3992 helix: 0.78 (0.19), residues: 718 sheet: 0.01 (0.17), residues: 926 loop : -0.83 (0.13), residues: 2348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1057 TYR 0.025 0.002 TYR A 928 PHE 0.017 0.002 PHE G1116 TRP 0.024 0.002 TRP B 253 HIS 0.012 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00398 (31853) covalent geometry : angle 0.65958 (43325) SS BOND : bond 0.00334 ( 55) SS BOND : angle 1.54851 ( 110) hydrogen bonds : bond 0.04569 ( 1167) hydrogen bonds : angle 5.85521 ( 3141) Misc. bond : bond 0.00104 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4843.82 seconds wall clock time: 85 minutes 15.60 seconds (5115.60 seconds total)