Starting phenix.real_space_refine on Sat Jun 28 14:42:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5w9o_8790/06_2025/5w9o_8790.cif Found real_map, /net/cci-nas-00/data/ceres_data/5w9o_8790/06_2025/5w9o_8790.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5w9o_8790/06_2025/5w9o_8790.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5w9o_8790/06_2025/5w9o_8790.map" model { file = "/net/cci-nas-00/data/ceres_data/5w9o_8790/06_2025/5w9o_8790.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5w9o_8790/06_2025/5w9o_8790.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 180 5.16 5 C 20904 2.51 5 N 5475 2.21 5 O 6399 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 32958 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3545 Classifications: {'peptide': 463} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 437} Chain breaks: 1 Chain: "B" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "C" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 835 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3545 Classifications: {'peptide': 463} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 437} Chain breaks: 1 Chain: "E" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "F" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 835 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "G" Number of atoms: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3545 Classifications: {'peptide': 463} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 437} Chain breaks: 1 Chain: "H" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "I" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 835 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "J" Number of atoms: 5658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5658 Classifications: {'peptide': 726} Link IDs: {'CIS': 3, 'PTRANS': 36, 'TRANS': 686} Chain: "K" Number of atoms: 5658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5658 Classifications: {'peptide': 726} Link IDs: {'CIS': 5, 'PTRANS': 36, 'TRANS': 684} Chain: "L" Number of atoms: 5658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5658 Classifications: {'peptide': 726} Link IDs: {'CIS': 5, 'PTRANS': 36, 'TRANS': 684} Time building chain proxies: 18.97, per 1000 atoms: 0.58 Number of scatterers: 32958 At special positions: 0 Unit cell: (154.02, 154.02, 222.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 180 16.00 O 6399 8.00 N 5475 7.00 C 20904 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=56, symmetry=0 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS A 828 " distance=2.03 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.03 Simple disulfide: pdb=" SG CYS A 912 " - pdb=" SG CYS A 925 " distance=2.06 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.03 Simple disulfide: pdb=" SG CYS A1156 " - pdb=" SG CYS A1164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 806 " - pdb=" SG CYS D 828 " distance=2.03 Simple disulfide: pdb=" SG CYS D 811 " - pdb=" SG CYS D 817 " distance=2.02 Simple disulfide: pdb=" SG CYS D 912 " - pdb=" SG CYS D 925 " distance=2.17 Simple disulfide: pdb=" SG CYS D1156 " - pdb=" SG CYS D1164 " distance=2.39 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.02 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.15 Simple disulfide: pdb=" SG CYS G 806 " - pdb=" SG CYS G 828 " distance=2.03 Simple disulfide: pdb=" SG CYS G 811 " - pdb=" SG CYS G 817 " distance=2.03 Simple disulfide: pdb=" SG CYS G 912 " - pdb=" SG CYS G 925 " distance=2.08 Simple disulfide: pdb=" SG CYS G1106 " - pdb=" SG CYS G1117 " distance=2.03 Simple disulfide: pdb=" SG CYS G1156 " - pdb=" SG CYS G1164 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.11 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 30 " - pdb=" SG CYS J 195 " distance=2.01 Simple disulfide: pdb=" SG CYS J 176 " - pdb=" SG CYS J 214 " distance=2.60 Simple disulfide: pdb=" SG CYS J 185 " - pdb=" SG CYS J 237 " distance=2.04 Simple disulfide: pdb=" SG CYS J 339 " - pdb=" SG CYS J 349 " distance=2.03 Simple disulfide: pdb=" SG CYS J 383 " - pdb=" SG CYS J 407 " distance=1.82 Simple disulfide: pdb=" SG CYS J 425 " - pdb=" SG CYS J 478 " distance=2.02 Simple disulfide: pdb=" SG CYS J 437 " - pdb=" SG CYS J 585 " distance=2.19 Simple disulfide: pdb=" SG CYS J 503 " - pdb=" SG CYS J 526 " distance=2.02 Simple disulfide: pdb=" SG CYS J 603 " - pdb=" SG CYS J 654 " distance=2.02 Simple disulfide: pdb=" SG CYS J 620 " - pdb=" SG CYS J 650 " distance=1.94 Simple disulfide: pdb=" SG CYS J 679 " - pdb=" SG CYS J 713 " distance=2.04 Simple disulfide: pdb=" SG CYS J 727 " - pdb=" SG CYS J 736 " distance=2.02 Simple disulfide: pdb=" SG CYS K 30 " - pdb=" SG CYS K 195 " distance=2.20 Simple disulfide: pdb=" SG CYS K 176 " - pdb=" SG CYS K 214 " distance=2.40 Simple disulfide: pdb=" SG CYS K 185 " - pdb=" SG CYS K 237 " distance=2.15 Simple disulfide: pdb=" SG CYS K 339 " - pdb=" SG CYS K 349 " distance=2.04 Simple disulfide: pdb=" SG CYS K 383 " - pdb=" SG CYS K 407 " distance=2.07 Simple disulfide: pdb=" SG CYS K 425 " - pdb=" SG CYS K 478 " distance=2.14 Simple disulfide: pdb=" SG CYS K 437 " - pdb=" SG CYS K 585 " distance=2.13 Simple disulfide: pdb=" SG CYS K 503 " - pdb=" SG CYS K 526 " distance=2.02 Simple disulfide: pdb=" SG CYS K 603 " - pdb=" SG CYS K 654 " distance=2.06 Simple disulfide: pdb=" SG CYS K 620 " - pdb=" SG CYS K 650 " distance=2.01 Simple disulfide: pdb=" SG CYS K 679 " - pdb=" SG CYS K 713 " distance=2.03 Simple disulfide: pdb=" SG CYS K 727 " - pdb=" SG CYS K 736 " distance=2.02 Simple disulfide: pdb=" SG CYS L 30 " - pdb=" SG CYS L 195 " distance=2.02 Simple disulfide: pdb=" SG CYS L 176 " - pdb=" SG CYS L 214 " distance=2.55 Simple disulfide: pdb=" SG CYS L 185 " - pdb=" SG CYS L 237 " distance=2.12 Simple disulfide: pdb=" SG CYS L 339 " - pdb=" SG CYS L 349 " distance=2.03 Simple disulfide: pdb=" SG CYS L 383 " - pdb=" SG CYS L 407 " distance=2.31 Simple disulfide: pdb=" SG CYS L 425 " - pdb=" SG CYS L 478 " distance=1.99 Simple disulfide: pdb=" SG CYS L 437 " - pdb=" SG CYS L 585 " distance=2.06 Simple disulfide: pdb=" SG CYS L 503 " - pdb=" SG CYS L 526 " distance=2.02 Simple disulfide: pdb=" SG CYS L 603 " - pdb=" SG CYS L 654 " distance=2.12 Simple disulfide: pdb=" SG CYS L 620 " - pdb=" SG CYS L 650 " distance=1.66 Simple disulfide: pdb=" SG CYS L 679 " - pdb=" SG CYS L 713 " distance=2.03 Simple disulfide: pdb=" SG CYS L 727 " - pdb=" SG CYS L 736 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.37 Conformation dependent library (CDL) restraints added in 4.5 seconds 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7902 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 76 sheets defined 22.5% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.35 Creating SS restraints... Processing helix chain 'A' and resid 814 through 821 Processing helix chain 'A' and resid 824 through 854 removed outlier: 3.578A pdb=" N CYS A 828 " --> pdb=" O TYR A 824 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER A 852 " --> pdb=" O ASN A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 898 Processing helix chain 'A' and resid 907 through 912 Processing helix chain 'A' and resid 922 through 931 removed outlier: 3.586A pdb=" N ALA A 926 " --> pdb=" O ASP A 922 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TYR A 928 " --> pdb=" O ILE A 924 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL A 929 " --> pdb=" O CYS A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 953 Processing helix chain 'A' and resid 971 through 982 Processing helix chain 'A' and resid 986 through 993 Processing helix chain 'A' and resid 993 through 1007 Processing helix chain 'A' and resid 1008 through 1011 Processing helix chain 'A' and resid 1016 through 1040 removed outlier: 3.545A pdb=" N LEU A1033 " --> pdb=" O ASN A1029 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1058 Processing helix chain 'A' and resid 1059 through 1104 removed outlier: 4.694A pdb=" N ALA A1065 " --> pdb=" O PRO A1061 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN A1066 " --> pdb=" O GLU A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1200 No H-bonds generated for 'chain 'A' and resid 1198 through 1200' Processing helix chain 'B' and resid 28 through 31 Processing helix chain 'B' and resid 61 through 64 Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'D' and resid 814 through 821 Processing helix chain 'D' and resid 824 through 854 removed outlier: 3.660A pdb=" N CYS D 828 " --> pdb=" O TYR D 824 " (cutoff:3.500A) Processing helix chain 'D' and resid 888 through 898 Processing helix chain 'D' and resid 907 through 912 Processing helix chain 'D' and resid 922 through 931 removed outlier: 5.003A pdb=" N TYR D 928 " --> pdb=" O ILE D 924 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL D 929 " --> pdb=" O CYS D 925 " (cutoff:3.500A) Processing helix chain 'D' and resid 940 through 953 Processing helix chain 'D' and resid 971 through 982 Processing helix chain 'D' and resid 986 through 993 Processing helix chain 'D' and resid 993 through 1007 Processing helix chain 'D' and resid 1008 through 1010 No H-bonds generated for 'chain 'D' and resid 1008 through 1010' Processing helix chain 'D' and resid 1016 through 1039 Processing helix chain 'D' and resid 1040 through 1042 No H-bonds generated for 'chain 'D' and resid 1040 through 1042' Processing helix chain 'D' and resid 1050 through 1058 Processing helix chain 'D' and resid 1059 through 1104 removed outlier: 3.947A pdb=" N ALA D1065 " --> pdb=" O PRO D1061 " (cutoff:3.500A) Processing helix chain 'D' and resid 1198 through 1200 No H-bonds generated for 'chain 'D' and resid 1198 through 1200' Processing helix chain 'E' and resid 28 through 32 removed outlier: 4.142A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 64 Processing helix chain 'E' and resid 73 through 75 No H-bonds generated for 'chain 'E' and resid 73 through 75' Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'G' and resid 814 through 821 Processing helix chain 'G' and resid 824 through 854 removed outlier: 3.548A pdb=" N CYS G 828 " --> pdb=" O TYR G 824 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER G 852 " --> pdb=" O ASN G 848 " (cutoff:3.500A) Processing helix chain 'G' and resid 888 through 898 Processing helix chain 'G' and resid 908 through 912 Processing helix chain 'G' and resid 922 through 931 removed outlier: 3.600A pdb=" N ALA G 926 " --> pdb=" O ASP G 922 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N TYR G 928 " --> pdb=" O ILE G 924 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL G 929 " --> pdb=" O CYS G 925 " (cutoff:3.500A) Processing helix chain 'G' and resid 940 through 953 Processing helix chain 'G' and resid 971 through 982 Processing helix chain 'G' and resid 986 through 993 Processing helix chain 'G' and resid 993 through 1006 Processing helix chain 'G' and resid 1007 through 1010 Processing helix chain 'G' and resid 1016 through 1040 removed outlier: 3.717A pdb=" N LEU G1040 " --> pdb=" O LEU G1036 " (cutoff:3.500A) Processing helix chain 'G' and resid 1050 through 1058 Processing helix chain 'G' and resid 1059 through 1104 removed outlier: 3.831A pdb=" N ALA G1065 " --> pdb=" O PRO G1061 " (cutoff:3.500A) Processing helix chain 'G' and resid 1198 through 1200 No H-bonds generated for 'chain 'G' and resid 1198 through 1200' Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.988A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 73 through 76 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'J' and resid 37 through 41 Processing helix chain 'J' and resid 49 through 53 Processing helix chain 'J' and resid 104 through 108 Processing helix chain 'J' and resid 222 through 230 Processing helix chain 'J' and resid 303 through 307 Processing helix chain 'J' and resid 342 through 351 Processing helix chain 'J' and resid 385 through 390 removed outlier: 3.868A pdb=" N LEU J 388 " --> pdb=" O PHE J 385 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER J 390 " --> pdb=" O PRO J 387 " (cutoff:3.500A) Processing helix chain 'J' and resid 395 through 399 removed outlier: 3.657A pdb=" N PHE J 399 " --> pdb=" O VAL J 396 " (cutoff:3.500A) Processing helix chain 'J' and resid 410 through 415 Processing helix chain 'J' and resid 416 through 418 No H-bonds generated for 'chain 'J' and resid 416 through 418' Processing helix chain 'J' and resid 429 through 436 removed outlier: 3.897A pdb=" N ALA J 434 " --> pdb=" O PRO J 430 " (cutoff:3.500A) Processing helix chain 'J' and resid 449 through 456 removed outlier: 4.839A pdb=" N SER J 454 " --> pdb=" O SER J 451 " (cutoff:3.500A) Processing helix chain 'J' and resid 462 through 468 Processing helix chain 'J' and resid 524 through 529 Processing helix chain 'J' and resid 546 through 550 Processing helix chain 'J' and resid 694 through 702 removed outlier: 4.933A pdb=" N ARG J 700 " --> pdb=" O MET J 696 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 41 removed outlier: 4.230A pdb=" N ASP K 41 " --> pdb=" O THR K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 53 Processing helix chain 'K' and resid 104 through 108 Processing helix chain 'K' and resid 222 through 230 Processing helix chain 'K' and resid 342 through 351 Processing helix chain 'K' and resid 385 through 390 removed outlier: 3.630A pdb=" N SER K 390 " --> pdb=" O PRO K 387 " (cutoff:3.500A) Processing helix chain 'K' and resid 410 through 416 removed outlier: 3.611A pdb=" N LEU K 414 " --> pdb=" O ASN K 410 " (cutoff:3.500A) Processing helix chain 'K' and resid 431 through 436 Processing helix chain 'K' and resid 449 through 456 removed outlier: 4.898A pdb=" N SER K 454 " --> pdb=" O SER K 451 " (cutoff:3.500A) Processing helix chain 'K' and resid 462 through 468 Processing helix chain 'K' and resid 524 through 529 Processing helix chain 'K' and resid 675 through 678 removed outlier: 4.167A pdb=" N ALA K 678 " --> pdb=" O GLY K 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 675 through 678' Processing helix chain 'K' and resid 694 through 702 removed outlier: 3.576A pdb=" N LYS K 698 " --> pdb=" O ARG K 694 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ARG K 700 " --> pdb=" O MET K 696 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 41 Processing helix chain 'L' and resid 49 through 53 Processing helix chain 'L' and resid 104 through 107 Processing helix chain 'L' and resid 222 through 230 Processing helix chain 'L' and resid 268 through 273 removed outlier: 4.096A pdb=" N LEU L 273 " --> pdb=" O ARG L 269 " (cutoff:3.500A) Processing helix chain 'L' and resid 303 through 307 removed outlier: 3.770A pdb=" N ARG L 307 " --> pdb=" O GLN L 304 " (cutoff:3.500A) Processing helix chain 'L' and resid 342 through 351 Processing helix chain 'L' and resid 385 through 389 Processing helix chain 'L' and resid 410 through 416 removed outlier: 4.007A pdb=" N LEU L 414 " --> pdb=" O ASN L 410 " (cutoff:3.500A) Processing helix chain 'L' and resid 429 through 436 Processing helix chain 'L' and resid 449 through 456 removed outlier: 4.517A pdb=" N SER L 454 " --> pdb=" O SER L 451 " (cutoff:3.500A) Processing helix chain 'L' and resid 462 through 468 Processing helix chain 'L' and resid 524 through 529 Processing helix chain 'L' and resid 546 through 550 Processing helix chain 'L' and resid 694 through 702 removed outlier: 3.538A pdb=" N LYS L 698 " --> pdb=" O ARG L 694 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ARG L 700 " --> pdb=" O MET L 696 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 719 through 724 removed outlier: 7.390A pdb=" N LEU A 759 " --> pdb=" O SER J 720 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU J 722 " --> pdb=" O LEU A 759 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 768 through 769 removed outlier: 5.752A pdb=" N ILE A 768 " --> pdb=" O SER D 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 777 through 782 removed outlier: 5.872A pdb=" N VAL A1150 " --> pdb=" O LYS A1174 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N PHE A1172 " --> pdb=" O ALA A1152 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 785 through 796 Processing sheet with id=AA5, first strand: chain 'A' and resid 802 through 804 Processing sheet with id=AA6, first strand: chain 'A' and resid 857 through 858 Processing sheet with id=AA7, first strand: chain 'A' and resid 1202 through 1204 removed outlier: 6.477A pdb=" N CYS A1156 " --> pdb=" O ILE A1214 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 3 through 6 removed outlier: 5.665A pdb=" N VAL B 16 " --> pdb=" O ARG B 82B" (cutoff:3.500A) removed outlier: 4.226A pdb=" N ARG B 82B" --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA B 78 " --> pdb=" O CYS B 22 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 57 through 59 removed outlier: 6.686A pdb=" N SER B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TRP B 36 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL B 50 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE B 34 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.517A pdb=" N TYR B 98 " --> pdb=" O VAL B 100B" (cutoff:3.500A) removed outlier: 7.551A pdb=" N VAL B 100B" --> pdb=" O TYR B 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.837A pdb=" N MET C 33 " --> pdb=" O SER C 49 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N SER C 49 " --> pdb=" O MET C 33 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 719 through 724 removed outlier: 7.285A pdb=" N LEU D 759 " --> pdb=" O SER K 720 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU K 722 " --> pdb=" O LEU D 759 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 768 through 769 removed outlier: 5.675A pdb=" N ILE D 768 " --> pdb=" O SER G 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 777 through 782 removed outlier: 5.712A pdb=" N VAL D1150 " --> pdb=" O LYS D1174 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N PHE D1172 " --> pdb=" O ALA D1152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 785 through 796 Processing sheet with id=AB8, first strand: chain 'D' and resid 802 through 804 Processing sheet with id=AB9, first strand: chain 'D' and resid 1155 through 1157 removed outlier: 6.498A pdb=" N CYS D1156 " --> pdb=" O ILE D1214 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 1164 through 1167 removed outlier: 3.947A pdb=" N CYS D1164 " --> pdb=" O VAL D1205 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AC3, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.385A pdb=" N SER E 44 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N CYS E 92 " --> pdb=" O TRP E 103 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TRP E 103 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ARG E 94 " --> pdb=" O ASP E 101 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N TYR E 98 " --> pdb=" O VAL E 100B" (cutoff:3.500A) removed outlier: 7.542A pdb=" N VAL E 100B" --> pdb=" O TYR E 98 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.385A pdb=" N SER E 44 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AC6, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.210A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N MET F 33 " --> pdb=" O SER F 49 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N SER F 49 " --> pdb=" O MET F 33 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 719 through 724 removed outlier: 7.246A pdb=" N LEU G 759 " --> pdb=" O SER L 720 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU L 722 " --> pdb=" O LEU G 759 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 777 through 782 removed outlier: 5.989A pdb=" N VAL G1150 " --> pdb=" O LYS G1174 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE G1172 " --> pdb=" O ALA G1152 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 785 through 796 Processing sheet with id=AD1, first strand: chain 'G' and resid 802 through 804 Processing sheet with id=AD2, first strand: chain 'G' and resid 1165 through 1167 Processing sheet with id=AD3, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.763A pdb=" N LYS H 23 " --> pdb=" O GLN H 5 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.360A pdb=" N SER H 44 " --> pdb=" O SER H 40 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 96 through 99 removed outlier: 4.609A pdb=" N TYR H 98 " --> pdb=" O VAL H 100B" (cutoff:3.500A) removed outlier: 7.511A pdb=" N VAL H 100B" --> pdb=" O TYR H 98 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.327A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N MET I 33 " --> pdb=" O SER I 49 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER I 49 " --> pdb=" O MET I 33 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 19 through 22 Processing sheet with id=AD8, first strand: chain 'J' and resid 33 through 35 Processing sheet with id=AD9, first strand: chain 'J' and resid 68 through 76 removed outlier: 6.448A pdb=" N SER J 267 " --> pdb=" O GLN J 280 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N GLN J 280 " --> pdb=" O SER J 267 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 83 through 85 removed outlier: 3.665A pdb=" N ARG J 335 " --> pdb=" O ASP J 326 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 88 through 89 removed outlier: 7.363A pdb=" N SER J 88 " --> pdb=" O ILE J 300 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 92 through 93 Processing sheet with id=AE4, first strand: chain 'J' and resid 110 through 111 removed outlier: 4.298A pdb=" N ALA J 146 " --> pdb=" O ILE J 296 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 126 through 127 removed outlier: 4.000A pdb=" N SER J 126 " --> pdb=" O ILE J 140 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA J 309 " --> pdb=" O THR J 139 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 153 through 154 Processing sheet with id=AE7, first strand: chain 'J' and resid 187 through 189 Processing sheet with id=AE8, first strand: chain 'J' and resid 359 through 366 removed outlier: 4.193A pdb=" N VAL J 659 " --> pdb=" O VAL J 363 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N SER J 365 " --> pdb=" O VAL J 657 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL J 657 " --> pdb=" O SER J 365 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 374 through 376 Processing sheet with id=AF1, first strand: chain 'J' and resid 400 through 404 removed outlier: 6.790A pdb=" N THR J 483 " --> pdb=" O VAL J 420 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N VAL J 420 " --> pdb=" O THR J 483 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 513 through 515 removed outlier: 5.402A pdb=" N SER J 498 " --> pdb=" O VAL J 561 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL J 561 " --> pdb=" O SER J 498 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ILE J 500 " --> pdb=" O SER J 559 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N SER J 559 " --> pdb=" O ILE J 500 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 617 through 618 removed outlier: 5.218A pdb=" N VAL J 639 " --> pdb=" O LEU J 651 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL J 631 " --> pdb=" O VAL J 639 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 33 through 35 removed outlier: 6.002A pdb=" N ASP K 34 " --> pdb=" O VAL K 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'K' and resid 68 through 75 removed outlier: 3.620A pdb=" N ARG K 335 " --> pdb=" O ASP K 326 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 83 through 85 removed outlier: 6.476A pdb=" N SER K 267 " --> pdb=" O GLN K 280 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N GLN K 280 " --> pdb=" O SER K 267 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 88 through 89 removed outlier: 7.414A pdb=" N SER K 88 " --> pdb=" O ILE K 300 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR K 206 " --> pdb=" O SER K 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'K' and resid 92 through 93 Processing sheet with id=AF9, first strand: chain 'K' and resid 110 through 111 removed outlier: 4.466A pdb=" N ALA K 146 " --> pdb=" O ILE K 296 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ILE K 186 " --> pdb=" O CYS K 237 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N CYS K 237 " --> pdb=" O ILE K 186 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N GLU K 188 " --> pdb=" O ARG K 235 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ARG K 235 " --> pdb=" O GLU K 188 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 126 through 127 removed outlier: 4.325A pdb=" N SER K 126 " --> pdb=" O ILE K 140 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 153 through 154 Processing sheet with id=AG3, first strand: chain 'K' and resid 359 through 366 removed outlier: 4.083A pdb=" N VAL K 659 " --> pdb=" O VAL K 363 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N SER K 365 " --> pdb=" O VAL K 657 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL K 657 " --> pdb=" O SER K 365 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 374 through 375 Processing sheet with id=AG5, first strand: chain 'K' and resid 381 through 382 removed outlier: 6.130A pdb=" N VAL K 381 " --> pdb=" O ASN K 408 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N CYS K 407 " --> pdb=" O CYS K 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'K' and resid 400 through 404 removed outlier: 3.563A pdb=" N LYS K 400 " --> pdb=" O TYR K 445 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR K 483 " --> pdb=" O VAL K 420 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N VAL K 420 " --> pdb=" O THR K 483 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 513 through 515 removed outlier: 5.451A pdb=" N SER K 498 " --> pdb=" O VAL K 561 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL K 561 " --> pdb=" O SER K 498 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ILE K 500 " --> pdb=" O SER K 559 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N SER K 559 " --> pdb=" O ILE K 500 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 617 through 618 removed outlier: 5.500A pdb=" N VAL K 639 " --> pdb=" O LEU K 651 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL K 631 " --> pdb=" O VAL K 639 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 33 through 35 Processing sheet with id=AH1, first strand: chain 'L' and resid 68 through 75 removed outlier: 3.615A pdb=" N ARG L 335 " --> pdb=" O ASP L 326 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'L' and resid 83 through 85 removed outlier: 6.251A pdb=" N SER L 267 " --> pdb=" O GLN L 280 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N GLN L 280 " --> pdb=" O SER L 267 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 88 through 89 removed outlier: 7.366A pdb=" N SER L 88 " --> pdb=" O ILE L 300 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR L 206 " --> pdb=" O SER L 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'L' and resid 92 through 93 Processing sheet with id=AH5, first strand: chain 'L' and resid 109 through 111 removed outlier: 4.477A pdb=" N ALA L 146 " --> pdb=" O ILE L 296 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU L 180 " --> pdb=" O TYR L 241 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TYR L 241 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA L 182 " --> pdb=" O PHE L 239 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N PHE L 239 " --> pdb=" O ALA L 182 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N TYR L 184 " --> pdb=" O CYS L 237 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N CYS L 237 " --> pdb=" O TYR L 184 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'L' and resid 126 through 127 removed outlier: 4.478A pdb=" N SER L 126 " --> pdb=" O ILE L 140 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA L 309 " --> pdb=" O THR L 139 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'L' and resid 153 through 154 Processing sheet with id=AH8, first strand: chain 'L' and resid 359 through 366 removed outlier: 4.436A pdb=" N VAL L 659 " --> pdb=" O VAL L 363 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N SER L 365 " --> pdb=" O VAL L 657 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL L 657 " --> pdb=" O SER L 365 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'L' and resid 371 through 375 removed outlier: 6.409A pdb=" N GLY L 372 " --> pdb=" O GLU L 605 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N SER L 607 " --> pdb=" O GLY L 372 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL L 374 " --> pdb=" O SER L 607 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'L' and resid 381 through 382 removed outlier: 6.362A pdb=" N VAL L 381 " --> pdb=" O ASN L 408 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N CYS L 407 " --> pdb=" O CYS L 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI1 Processing sheet with id=AI2, first strand: chain 'L' and resid 400 through 404 removed outlier: 3.538A pdb=" N LYS L 400 " --> pdb=" O TYR L 445 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR L 483 " --> pdb=" O VAL L 420 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VAL L 420 " --> pdb=" O THR L 483 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'L' and resid 513 through 515 removed outlier: 5.436A pdb=" N SER L 498 " --> pdb=" O VAL L 561 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL L 561 " --> pdb=" O SER L 498 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ILE L 500 " --> pdb=" O SER L 559 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N SER L 559 " --> pdb=" O ILE L 500 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'L' and resid 617 through 618 removed outlier: 5.440A pdb=" N VAL L 639 " --> pdb=" O LEU L 651 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL L 631 " --> pdb=" O VAL L 639 " (cutoff:3.500A) 1257 hydrogen bonds defined for protein. 3231 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 16.42 Time building geometry restraints manager: 9.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 9899 1.34 - 1.48: 9621 1.48 - 1.61: 13968 1.61 - 1.75: 1 1.75 - 1.89: 246 Bond restraints: 33735 Sorted by residual: bond pdb=" N CYS L 585 " pdb=" CA CYS L 585 " ideal model delta sigma weight residual 1.456 1.372 0.083 8.70e-03 1.32e+04 9.19e+01 bond pdb=" CA VAL L 584 " pdb=" C VAL L 584 " ideal model delta sigma weight residual 1.524 1.424 0.100 1.23e-02 6.61e+03 6.61e+01 bond pdb=" CA CYS J 437 " pdb=" C CYS J 437 " ideal model delta sigma weight residual 1.523 1.619 -0.096 1.30e-02 5.92e+03 5.50e+01 bond pdb=" C CYS L 437 " pdb=" O CYS L 437 " ideal model delta sigma weight residual 1.235 1.314 -0.079 1.18e-02 7.18e+03 4.50e+01 bond pdb=" C CYS K 437 " pdb=" N TYR K 438 " ideal model delta sigma weight residual 1.331 1.400 -0.069 1.22e-02 6.72e+03 3.21e+01 ... (remaining 33730 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 42121 2.85 - 5.69: 3168 5.69 - 8.54: 502 8.54 - 11.38: 78 11.38 - 14.23: 7 Bond angle restraints: 45876 Sorted by residual: angle pdb=" C GLN I 42 " pdb=" N PRO I 43 " pdb=" CA PRO I 43 " ideal model delta sigma weight residual 119.66 127.76 -8.10 7.20e-01 1.93e+00 1.26e+02 angle pdb=" C TYR J 144 " pdb=" N PRO J 145 " pdb=" CA PRO J 145 " ideal model delta sigma weight residual 120.31 130.17 -9.86 9.80e-01 1.04e+00 1.01e+02 angle pdb=" C VAL C 58 " pdb=" N PRO C 59 " pdb=" CA PRO C 59 " ideal model delta sigma weight residual 119.92 130.59 -10.67 1.07e+00 8.73e-01 9.94e+01 angle pdb=" N GLN L 688 " pdb=" CA GLN L 688 " pdb=" C GLN L 688 " ideal model delta sigma weight residual 111.28 122.12 -10.84 1.09e+00 8.42e-01 9.88e+01 angle pdb=" O CYS L 437 " pdb=" C CYS L 437 " pdb=" N TYR L 438 " ideal model delta sigma weight residual 123.19 111.65 11.54 1.17e+00 7.31e-01 9.72e+01 ... (remaining 45871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 19360 17.70 - 35.41: 488 35.41 - 53.11: 184 53.11 - 70.81: 82 70.81 - 88.51: 22 Dihedral angle restraints: 20136 sinusoidal: 7746 harmonic: 12390 Sorted by residual: dihedral pdb=" CB CYS I 23 " pdb=" SG CYS I 23 " pdb=" SG CYS I 88 " pdb=" CB CYS I 88 " ideal model delta sinusoidal sigma weight residual 93.00 175.48 -82.48 1 1.00e+01 1.00e-02 8.34e+01 dihedral pdb=" CB CYS K 176 " pdb=" SG CYS K 176 " pdb=" SG CYS K 214 " pdb=" CB CYS K 214 " ideal model delta sinusoidal sigma weight residual 93.00 173.88 -80.88 1 1.00e+01 1.00e-02 8.08e+01 dihedral pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " pdb=" SG CYS F 88 " pdb=" CB CYS F 88 " ideal model delta sinusoidal sigma weight residual 93.00 168.92 -75.92 1 1.00e+01 1.00e-02 7.27e+01 ... (remaining 20133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 3629 0.081 - 0.161: 1255 0.161 - 0.242: 185 0.242 - 0.322: 20 0.322 - 0.403: 2 Chirality restraints: 5091 Sorted by residual: chirality pdb=" CB ILE F 2 " pdb=" CA ILE F 2 " pdb=" CG1 ILE F 2 " pdb=" CG2 ILE F 2 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" CA PHE G 850 " pdb=" N PHE G 850 " pdb=" C PHE G 850 " pdb=" CB PHE G 850 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CA GLN L 688 " pdb=" N GLN L 688 " pdb=" C GLN L 688 " pdb=" CB GLN L 688 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 5088 not shown) Planarity restraints: 5961 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 47 " -0.076 2.00e-02 2.50e+03 3.79e-02 3.58e+01 pdb=" CG TRP B 47 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP B 47 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP B 47 " 0.044 2.00e-02 2.50e+03 pdb=" NE1 TRP B 47 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP B 47 " 0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP B 47 " 0.052 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 47 " -0.034 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 47 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 47 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS K 603 " 0.028 2.00e-02 2.50e+03 5.70e-02 3.25e+01 pdb=" C CYS K 603 " -0.099 2.00e-02 2.50e+03 pdb=" O CYS K 603 " 0.038 2.00e-02 2.50e+03 pdb=" N VAL K 604 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 22 " -0.027 2.00e-02 2.50e+03 5.48e-02 3.00e+01 pdb=" C CYS B 22 " 0.095 2.00e-02 2.50e+03 pdb=" O CYS B 22 " -0.036 2.00e-02 2.50e+03 pdb=" N LYS B 23 " -0.031 2.00e-02 2.50e+03 ... (remaining 5958 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.04: 15 2.04 - 2.75: 5247 2.75 - 3.47: 45893 3.47 - 4.18: 80520 4.18 - 4.90: 136470 Nonbonded interactions: 268145 Sorted by model distance: nonbonded pdb=" OH TYR A 905 " pdb=" CA PRO A 936 " model vdw 1.325 3.470 nonbonded pdb=" OH TYR D 905 " pdb=" CA PRO D 936 " model vdw 1.497 3.470 nonbonded pdb=" OH TYR K 448 " pdb=" O MET K 452 " model vdw 1.540 3.040 nonbonded pdb=" OH TYR D 905 " pdb=" N PRO D 936 " model vdw 1.546 3.120 nonbonded pdb=" CE2 PHE K 506 " pdb=" CG2 VAL K 555 " model vdw 1.580 3.760 ... (remaining 268140 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints Number of NCS constrained groups: 4 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } pdb_interpretation.ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.430 Check model and map are aligned: 0.260 Set scattering table: 0.320 Process input model: 78.950 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.020 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.571 33791 Z= 0.881 Angle : 1.698 32.244 45988 Z= 1.152 Chirality : 0.076 0.403 5091 Planarity : 0.010 0.122 5961 Dihedral : 10.487 88.515 12066 Min Nonbonded Distance : 1.325 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.71 % Allowed : 3.88 % Favored : 95.41 % Rotamer: Outliers : 0.08 % Allowed : 0.33 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.13), residues: 4227 helix: -0.52 (0.16), residues: 670 sheet: 0.65 (0.15), residues: 1000 loop : 1.60 (0.13), residues: 2557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.005 TRP B 47 HIS 0.006 0.001 HIS G1146 PHE 0.030 0.002 PHE I 98 TYR 0.059 0.004 TYR G 909 ARG 0.006 0.000 ARG I 96 Details of bonding type rmsd hydrogen bonds : bond 0.19320 ( 1245) hydrogen bonds : angle 8.29564 ( 3231) SS BOND : bond 0.15146 ( 56) SS BOND : angle 7.48322 ( 112) covalent geometry : bond 0.01272 (33735) covalent geometry : angle 1.65911 (45876) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.397 Fit side-chains REVERT: A 928 TYR cc_start: 0.7830 (m-80) cc_final: 0.6867 (t80) REVERT: A 943 MET cc_start: 0.9187 (mtp) cc_final: 0.8551 (tpt) REVERT: A 1008 MET cc_start: 0.9130 (mmm) cc_final: 0.8579 (mmp) REVERT: A 1039 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8387 (mm-30) REVERT: A 1068 ASP cc_start: 0.9074 (m-30) cc_final: 0.8779 (p0) REVERT: A 1105 GLU cc_start: 0.8556 (tt0) cc_final: 0.8314 (tm-30) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1521 time to fit residues: 15.3229 Evaluate side-chains 25 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.425 Evaluate side-chains 35 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 100 ASP cc_start: 0.6415 (m-30) cc_final: 0.5616 (t0) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1554 time to fit residues: 5.9104 Evaluate side-chains 12 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.115 Evaluate side-chains 24 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.2538 time to fit residues: 6.4209 Evaluate side-chains 11 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.097 Evaluate side-chains 88 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 41 ASP cc_start: 0.7899 (t0) cc_final: 0.7487 (m-30) REVERT: J 172 LEU cc_start: 0.9173 (tp) cc_final: 0.8923 (pt) REVERT: J 287 TYR cc_start: 0.7595 (p90) cc_final: 0.7342 (p90) REVERT: J 338 ASP cc_start: 0.8232 (t0) cc_final: 0.7933 (t0) REVERT: J 726 ASP cc_start: 0.6209 (t0) cc_final: 0.5392 (p0) outliers start: 2 outliers final: 0 residues processed: 87 average time/residue: 0.2058 time to fit residues: 23.0444 Evaluate side-chains 50 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 354 optimal weight: 7.9990 chunk 318 optimal weight: 0.8980 chunk 176 optimal weight: 0.0040 chunk 108 optimal weight: 10.0000 chunk 214 optimal weight: 0.9990 chunk 170 optimal weight: 0.8980 chunk 329 optimal weight: 0.0040 chunk 127 optimal weight: 5.9990 chunk 200 optimal weight: 5.9990 chunk 245 optimal weight: 9.9990 chunk 381 optimal weight: 8.9990 overall best weight: 0.5606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1104 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 111 GLN J 167 HIS J 319 GLN ** J 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 636 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.085879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.073310 restraints weight = 13734.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.075026 restraints weight = 8222.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.076156 restraints weight = 5706.813| |-----------------------------------------------------------------------------| r_work (final): 0.3286 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.055306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.049162 restraints weight = 6326.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.050489 restraints weight = 3965.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.051527 restraints weight = 2744.278| |-----------------------------------------------------------------------------| r_work (final): 0.3192 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.067619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.058808 restraints weight = 5281.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.060543 restraints weight = 3635.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.061893 restraints weight = 2677.894| |-----------------------------------------------------------------------------| r_work (final): 0.3476 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.091768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.072139 restraints weight = 45954.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.073156 restraints weight = 29330.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.073820 restraints weight = 21268.732| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5708 moved from start: 4.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.263 33791 Z= 0.567 Angle : 1.490 30.768 45988 Z= 0.853 Chirality : 0.071 0.917 5091 Planarity : 0.010 0.116 5961 Dihedral : 9.521 139.493 4629 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 31.63 Ramachandran Plot: Outliers : 2.06 % Allowed : 5.11 % Favored : 92.83 % Rotamer: Outliers : 1.15 % Allowed : 2.87 % Favored : 95.98 % Cbeta Deviations : 0.53 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.37 % Twisted Proline : 1.47 % Twisted General : 1.56 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.13), residues: 4227 helix: 0.49 (0.20), residues: 678 sheet: 0.46 (0.15), residues: 972 loop : -0.02 (0.13), residues: 2577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 47 HIS 0.006 0.001 HIS K 167 PHE 0.069 0.003 PHE L 723 TYR 0.067 0.004 TYR K 361 ARG 0.018 0.001 ARG L 626 Details of bonding type rmsd hydrogen bonds : bond 0.49399 ( 1245) hydrogen bonds : angle 9.40073 ( 3231) SS BOND : bond 0.03396 ( 56) SS BOND : angle 5.80503 ( 112) covalent geometry : bond 0.00979 (33735) covalent geometry : angle 1.46447 (45876) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 126 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 756 GLU cc_start: 0.5347 (tm-30) cc_final: 0.3969 (pm20) REVERT: D 799 ILE cc_start: 0.9305 (mm) cc_final: 0.8714 (pt) REVERT: D 842 GLN cc_start: 0.8607 (mm-40) cc_final: 0.8248 (mm110) REVERT: D 905 TYR cc_start: 0.5898 (m-80) cc_final: 0.5689 (t80) REVERT: D 939 MET cc_start: 0.7204 (ptp) cc_final: 0.6936 (ptp) REVERT: D 940 ASP cc_start: 0.6447 (t0) cc_final: 0.5925 (m-30) REVERT: D 977 PHE cc_start: 0.8203 (m-10) cc_final: 0.7872 (m-80) REVERT: D 1021 LYS cc_start: 0.9040 (mtpt) cc_final: 0.8784 (tptp) REVERT: D 1039 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8202 (mm-30) REVERT: D 1127 VAL cc_start: 0.8938 (p) cc_final: 0.8594 (p) REVERT: D 1136 PHE cc_start: 0.8916 (m-80) cc_final: 0.8433 (m-10) outliers start: 5 outliers final: 0 residues processed: 131 average time/residue: 0.2150 time to fit residues: 32.7275 Evaluate side-chains 56 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.461 Evaluate side-chains 24 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.124 Fit side-chains REVERT: B 100 ASP cc_start: 0.6191 (m-30) cc_final: 0.5940 (t0) REVERT: B 100 ASP cc_start: 0.6404 (p0) cc_final: 0.6179 (p0) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1167 time to fit residues: 3.1933 Evaluate side-chains 10 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.119 Evaluate side-chains 21 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.1177 time to fit residues: 2.7918 Evaluate side-chains 13 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.103 Evaluate side-chains 86 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 171 LEU cc_start: 0.8428 (mm) cc_final: 0.8052 (tt) REVERT: J 635 TYR cc_start: 0.6983 (OUTLIER) cc_final: 0.5709 (m-80) outliers start: 9 outliers final: 0 residues processed: 82 average time/residue: 0.1708 time to fit residues: 18.7281 Evaluate side-chains 46 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 199 optimal weight: 1.9990 chunk 388 optimal weight: 6.9990 chunk 95 optimal weight: 30.0000 chunk 100 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 292 optimal weight: 8.9990 chunk 278 optimal weight: 2.9990 chunk 297 optimal weight: 0.3980 chunk 293 optimal weight: 0.3980 chunk 20 optimal weight: 20.0000 chunk 302 optimal weight: 9.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 796 GLN D 800 GLN ** D 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 907 GLN ** D 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN C 89 GLN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 81 HIS ** J 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.081841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.069351 restraints weight = 14811.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.071136 restraints weight = 8802.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.072358 restraints weight = 6015.016| |-----------------------------------------------------------------------------| r_work (final): 0.3217 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.054702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.048233 restraints weight = 6898.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.049501 restraints weight = 4590.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.050450 restraints weight = 3345.495| |-----------------------------------------------------------------------------| r_work (final): 0.3143 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.066995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.058095 restraints weight = 5687.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.059908 restraints weight = 3728.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.061295 restraints weight = 2661.932| |-----------------------------------------------------------------------------| r_work (final): 0.3454 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.091673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.074668 restraints weight = 45983.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.073935 restraints weight = 38114.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.073739 restraints weight = 36368.819| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5713 moved from start: 4.5193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.187 33791 Z= 0.525 Angle : 1.624 34.963 45988 Z= 0.884 Chirality : 0.082 1.013 5091 Planarity : 0.014 0.348 5961 Dihedral : 10.098 133.518 4629 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 33.53 Ramachandran Plot: Outliers : 1.56 % Allowed : 6.03 % Favored : 92.41 % Rotamer: Outliers : 2.13 % Allowed : 5.50 % Favored : 92.36 % Cbeta Deviations : 0.61 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.37 % Twisted Proline : 1.47 % Twisted General : 1.63 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.13), residues: 4227 helix: -0.77 (0.18), residues: 681 sheet: 0.06 (0.15), residues: 1056 loop : -0.71 (0.13), residues: 2490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP E 47 HIS 0.023 0.002 HIS A 836 PHE 0.051 0.005 PHE D 850 TYR 0.155 0.006 TYR A 809 ARG 0.058 0.002 ARG D 758 Details of bonding type rmsd hydrogen bonds : bond 0.47562 ( 1245) hydrogen bonds : angle 9.38713 ( 3231) SS BOND : bond 0.03436 ( 56) SS BOND : angle 5.17633 ( 112) covalent geometry : bond 0.00995 (33735) covalent geometry : angle 1.60524 (45876) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 842 GLN cc_start: 0.8664 (mm-40) cc_final: 0.8346 (mm-40) REVERT: D 905 TYR cc_start: 0.6053 (m-80) cc_final: 0.5819 (t80) REVERT: D 939 MET cc_start: 0.7048 (ptp) cc_final: 0.6812 (ptp) REVERT: D 940 ASP cc_start: 0.6567 (t0) cc_final: 0.6189 (m-30) REVERT: D 1036 LEU cc_start: 0.8803 (mt) cc_final: 0.8541 (mt) REVERT: D 1039 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7727 (mm-30) REVERT: D 1177 ASN cc_start: 0.8933 (t0) cc_final: 0.8478 (t0) outliers start: 19 outliers final: 5 residues processed: 80 average time/residue: 0.1707 time to fit residues: 16.5857 Evaluate side-chains 45 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.438 Evaluate side-chains 23 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.148 Fit side-chains REVERT: B 62 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8532 (mttp) REVERT: B 100 ASP cc_start: 0.6569 (p0) cc_final: 0.6206 (m-30) outliers start: 2 outliers final: 0 residues processed: 22 average time/residue: 0.1213 time to fit residues: 3.0187 Evaluate side-chains 10 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 9 time to evaluate : 0.104 Evaluate side-chains 17 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1398 time to fit residues: 2.7818 Evaluate side-chains 13 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.089 Evaluate side-chains 69 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 65 SER cc_start: 0.7321 (t) cc_final: 0.7117 (t) REVERT: J 171 LEU cc_start: 0.8473 (mm) cc_final: 0.8170 (tt) REVERT: J 290 ILE cc_start: 0.9058 (mm) cc_final: 0.8854 (mm) REVERT: J 343 ASP cc_start: 0.8025 (m-30) cc_final: 0.7661 (m-30) REVERT: J 637 ASN cc_start: 0.8078 (t0) cc_final: 0.7601 (m-40) REVERT: J 726 ASP cc_start: 0.5635 (t0) cc_final: 0.4870 (p0) outliers start: 5 outliers final: 0 residues processed: 66 average time/residue: 0.1439 time to fit residues: 13.5698 Evaluate side-chains 46 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 94 optimal weight: 0.0370 chunk 140 optimal weight: 7.9990 chunk 151 optimal weight: 0.0010 chunk 169 optimal weight: 0.7980 chunk 157 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 242 optimal weight: 0.0020 chunk 390 optimal weight: 10.0000 chunk 241 optimal weight: 0.1980 chunk 40 optimal weight: 9.9990 overall best weight: 0.2072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 406 ASN ** J 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.082188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.070174 restraints weight = 14710.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.071806 restraints weight = 9232.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.072846 restraints weight = 6567.832| |-----------------------------------------------------------------------------| r_work (final): 0.3229 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.056433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.049895 restraints weight = 6434.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.051250 restraints weight = 4061.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.052279 restraints weight = 2831.677| |-----------------------------------------------------------------------------| r_work (final): 0.3183 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.067936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.059345 restraints weight = 5302.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.061122 restraints weight = 3437.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.062378 restraints weight = 2481.978| |-----------------------------------------------------------------------------| r_work (final): 0.3519 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.091236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.073781 restraints weight = 46981.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.073705 restraints weight = 40980.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.073720 restraints weight = 32822.281| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5754 moved from start: 4.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.032 2.936 33791 Z= 1.595 Angle : 1.817 69.372 45988 Z= 0.966 Chirality : 0.082 1.014 5091 Planarity : 0.014 0.348 5961 Dihedral : 10.098 133.518 4629 Min Nonbonded Distance : 0.250 Molprobity Statistics. All-atom Clashscore : 48.73 Ramachandran Plot: Outliers : 1.56 % Allowed : 6.03 % Favored : 92.41 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.61 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.37 % Twisted Proline : 1.47 % Twisted General : 1.63 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.13), residues: 4227 helix: -0.77 (0.18), residues: 681 sheet: 0.06 (0.15), residues: 1056 loop : -0.71 (0.13), residues: 2490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP E 47 HIS 0.023 0.002 HIS A 836 PHE 0.051 0.005 PHE G 850 TYR 0.155 0.006 TYR G 809 ARG 0.058 0.002 ARG G 758 Details of bonding type rmsd hydrogen bonds : bond 0.47562 ( 1245) hydrogen bonds : angle 9.38712 ( 3231) SS BOND : bond 0.74048 ( 56) SS BOND : angle 17.33937 ( 112) covalent geometry : bond 0.00995 (33735) covalent geometry : angle 1.60504 (45876) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 842 GLN cc_start: 0.8692 (mm-40) cc_final: 0.8335 (mm-40) REVERT: D 905 TYR cc_start: 0.6030 (m-80) cc_final: 0.5791 (t80) REVERT: D 940 ASP cc_start: 0.6661 (t0) cc_final: 0.6214 (m-30) REVERT: D 1039 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7740 (mm-30) REVERT: D 1110 GLN cc_start: 0.8946 (tt0) cc_final: 0.8645 (tt0) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1506 time to fit residues: 10.4107 Evaluate side-chains 33 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.390 Evaluate side-chains 17 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.104 Fit side-chains REVERT: B 100 ASP cc_start: 0.6594 (p0) cc_final: 0.6198 (m-30) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0646 time to fit residues: 1.4067 Evaluate side-chains 9 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.138 Evaluate side-chains 17 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 LEU cc_start: 0.8900 (pt) cc_final: 0.8630 (pt) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1023 time to fit residues: 2.0348 Evaluate side-chains 12 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.105 Evaluate side-chains 51 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 171 LEU cc_start: 0.8601 (mm) cc_final: 0.8167 (tt) REVERT: J 637 ASN cc_start: 0.8344 (t0) cc_final: 0.7728 (m-40) REVERT: J 726 ASP cc_start: 0.5954 (t0) cc_final: 0.5054 (p0) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1476 time to fit residues: 11.0349 Evaluate side-chains 44 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 328 optimal weight: 6.9990 chunk 185 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 252 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 70 optimal weight: 20.0000 chunk 229 optimal weight: 0.5980 chunk 307 optimal weight: 10.0000 chunk 333 optimal weight: 0.6980 chunk 230 optimal weight: 0.0000 chunk 281 optimal weight: 0.0060 overall best weight: 1.2602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 766 HIS D 812 ASN D1023 GLN ** D1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 HIS Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.082927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.070431 restraints weight = 14237.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.072302 restraints weight = 8689.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.073372 restraints weight = 5973.990| |-----------------------------------------------------------------------------| r_work (final): 0.3244 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.055312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.049046 restraints weight = 6268.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.050367 restraints weight = 4019.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.051310 restraints weight = 2865.504| |-----------------------------------------------------------------------------| r_work (final): 0.3169 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.067443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.059148 restraints weight = 5212.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.061050 restraints weight = 3329.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.062363 restraints weight = 2308.047| |-----------------------------------------------------------------------------| r_work (final): 0.3503 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.092657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.073140 restraints weight = 46350.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.074102 restraints weight = 31246.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.074820 restraints weight = 23206.761| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5811 moved from start: 4.5525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.186 33791 Z= 0.447 Angle : 1.429 29.698 45988 Z= 0.788 Chirality : 0.075 0.949 5091 Planarity : 0.009 0.075 5961 Dihedral : 9.559 133.889 4629 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 30.49 Ramachandran Plot: Outliers : 1.28 % Allowed : 6.81 % Favored : 91.91 % Rotamer: Outliers : 0.49 % Allowed : 3.61 % Favored : 95.89 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.37 % Twisted Proline : 1.47 % Twisted General : 1.78 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.12), residues: 4227 helix: -1.01 (0.18), residues: 699 sheet: -0.26 (0.14), residues: 1122 loop : -1.19 (0.13), residues: 2406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP B 47 HIS 0.025 0.002 HIS A 836 PHE 0.058 0.004 PHE D 850 TYR 0.096 0.004 TYR J 663 ARG 0.045 0.001 ARG D 758 Details of bonding type rmsd hydrogen bonds : bond 0.45709 ( 1245) hydrogen bonds : angle 9.18195 ( 3231) SS BOND : bond 0.03453 ( 56) SS BOND : angle 4.09346 ( 112) covalent geometry : bond 0.00812 (33735) covalent geometry : angle 1.41622 (45876) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.407 Fit side-chains REVERT: D 757 MET cc_start: 0.3965 (tpt) cc_final: 0.3432 (tpt) REVERT: D 940 ASP cc_start: 0.7071 (t0) cc_final: 0.5913 (m-30) REVERT: D 1183 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7990 (mp0) REVERT: D 1184 TRP cc_start: 0.8596 (m100) cc_final: 0.8278 (m100) outliers start: 3 outliers final: 0 residues processed: 60 average time/residue: 0.1553 time to fit residues: 11.7554 Evaluate side-chains 30 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.384 Evaluate side-chains 18 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.105 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0944 time to fit residues: 2.0302 Evaluate side-chains 9 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.112 Evaluate side-chains 17 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.096 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0999 time to fit residues: 1.9747 Evaluate side-chains 10 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.101 Evaluate side-chains 57 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 171 LEU cc_start: 0.8455 (mm) cc_final: 0.8068 (tp) REVERT: J 278 MET cc_start: 0.9050 (mmm) cc_final: 0.8584 (mmm) REVERT: J 343 ASP cc_start: 0.8191 (m-30) cc_final: 0.7862 (m-30) outliers start: 3 outliers final: 0 residues processed: 55 average time/residue: 0.1356 time to fit residues: 11.0843 Evaluate side-chains 42 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 801, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.747 > 50: distance: 0 - 1: 40.423 distance: 0 - 3: 35.129 distance: 1 - 2: 38.011 distance: 1 - 7: 40.890 distance: 3 - 4: 33.941 distance: 3 - 5: 32.120 distance: 4 - 6: 6.218 distance: 7 - 8: 47.487 distance: 7 - 13: 26.107 distance: 8 - 9: 23.536 distance: 8 - 11: 32.713 distance: 9 - 10: 8.790 distance: 9 - 14: 27.885 distance: 10 - 39: 23.736 distance: 11 - 12: 11.092 distance: 12 - 13: 10.553 distance: 14 - 15: 33.109 distance: 15 - 16: 16.960 distance: 15 - 18: 14.090 distance: 16 - 17: 38.505 distance: 16 - 25: 23.530 distance: 17 - 45: 44.401 distance: 18 - 19: 23.953 distance: 19 - 20: 3.759 distance: 19 - 21: 7.409 distance: 20 - 22: 24.380 distance: 21 - 23: 21.249 distance: 22 - 24: 6.579 distance: 23 - 24: 14.573 distance: 25 - 26: 17.788 distance: 26 - 27: 17.351 distance: 26 - 29: 16.996 distance: 27 - 28: 4.653 distance: 27 - 30: 24.929 distance: 28 - 53: 48.579 distance: 30 - 31: 18.577 distance: 31 - 32: 10.960 distance: 31 - 34: 25.011 distance: 32 - 33: 21.934 distance: 32 - 39: 15.036 distance: 33 - 64: 27.581 distance: 34 - 35: 24.282 distance: 35 - 36: 29.581 distance: 36 - 37: 28.566 distance: 36 - 38: 41.395 distance: 39 - 40: 9.850 distance: 40 - 41: 32.755 distance: 40 - 43: 40.662 distance: 41 - 42: 24.219 distance: 42 - 76: 38.619 distance: 43 - 44: 32.033 distance: 45 - 46: 12.702 distance: 46 - 47: 18.838 distance: 46 - 49: 28.396 distance: 47 - 48: 50.686 distance: 47 - 53: 32.393 distance: 48 - 87: 60.365 distance: 49 - 50: 41.683 distance: 49 - 51: 43.180 distance: 50 - 52: 43.302 distance: 53 - 54: 38.761 distance: 54 - 55: 49.302 distance: 54 - 57: 27.009 distance: 55 - 56: 37.456 distance: 55 - 64: 62.425 distance: 58 - 59: 14.703 distance: 58 - 60: 47.156 distance: 59 - 61: 16.766 distance: 60 - 62: 19.236 distance: 61 - 63: 28.352 distance: 62 - 63: 35.149 distance: 64 - 65: 58.334 distance: 65 - 66: 56.156 distance: 65 - 68: 34.823 distance: 66 - 67: 23.275 distance: 66 - 76: 3.183 distance: 68 - 69: 45.435 distance: 69 - 70: 55.868 distance: 69 - 71: 29.866 distance: 70 - 72: 27.604 distance: 71 - 73: 36.161 distance: 72 - 74: 21.702 distance: 73 - 74: 45.282 distance: 74 - 75: 23.320 distance: 76 - 77: 9.165 distance: 77 - 78: 42.910 distance: 77 - 80: 40.561 distance: 78 - 79: 49.251 distance: 78 - 87: 49.912 distance: 80 - 81: 7.989 distance: 81 - 82: 11.550 distance: 82 - 83: 38.277 distance: 83 - 84: 18.263 distance: 84 - 85: 15.803 distance: 84 - 86: 21.408 distance: 87 - 88: 13.541 distance: 88 - 89: 32.050 distance: 88 - 91: 24.527 distance: 89 - 90: 21.834 distance: 91 - 92: 34.208