Starting phenix.real_space_refine on Fri May 30 06:09:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5w9o_8790/05_2025/5w9o_8790.cif Found real_map, /net/cci-nas-00/data/ceres_data/5w9o_8790/05_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_8790/05_2025/5w9o_8790.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5w9o_8790/05_2025/5w9o_8790.map" model { file = "/net/cci-nas-00/data/ceres_data/5w9o_8790/05_2025/5w9o_8790.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5w9o_8790/05_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 17.25, per 1000 atoms: 0.52 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: 7.57 Conformation dependent library (CDL) restraints added in 4.4 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: 4.98 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: 14.54 Time building geometry restraints manager: 8.83 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: 1.870 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: 1.250 Check model and map are aligned: 0.230 Set scattering table: 0.300 Process input model: 70.950 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.430 ------------------------------------------------------------------------------- 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 : 0.410 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: 0.1502 time to fit residues: 15.1463 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 : 0.382 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 : 0.101 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: 0.1449 time to fit residues: 5.4956 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 : 0.098 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 : 0.087 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: 0.2464 time to fit residues: 6.2351 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 : 0.105 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 : 0.642 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: 0.2055 time to fit residues: 23.0182 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 : 0.650 ------------------------------------------------------------------------------- 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 = 36)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.073269 restraints weight = 13734.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.075021 restraints weight = 8281.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.076260 restraints weight = 5705.425| |-----------------------------------------------------------------------------| r_work (final): 0.3291 |-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 = 39)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.049159 restraints weight = 6326.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.050488 restraints weight = 3965.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.051525 restraints weight = 2744.312| |-----------------------------------------------------------------------------| r_work (final): 0.3191 |-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 = 31)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.058807 restraints weight = 5281.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.060540 restraints weight = 3639.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.061899 restraints weight = 2679.622| |-----------------------------------------------------------------------------| 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 = 57)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.072124 restraints weight = 45954.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.073151 restraints weight = 29365.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.073726 restraints weight = 21030.938| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5704 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 J 723 TYR 0.067 0.004 TYR K 361 ARG 0.018 0.001 ARG K 626 Details of bonding type rmsd hydrogen bonds : bond 0.49399 ( 1245) hydrogen bonds : angle 9.40072 ( 3231) SS BOND : bond 0.03396 ( 56) SS BOND : angle 5.80499 ( 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 : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 756 GLU cc_start: 0.5353 (tm-30) cc_final: 0.3969 (pm20) REVERT: D 799 ILE cc_start: 0.9306 (mm) cc_final: 0.8716 (pt) REVERT: D 842 GLN cc_start: 0.8592 (mm-40) cc_final: 0.8233 (mm110) REVERT: D 905 TYR cc_start: 0.5885 (m-80) cc_final: 0.5681 (t80) REVERT: D 939 MET cc_start: 0.7221 (ptp) cc_final: 0.6961 (ptp) REVERT: D 940 ASP cc_start: 0.6443 (t0) cc_final: 0.5955 (m-30) REVERT: D 977 PHE cc_start: 0.8221 (m-10) cc_final: 0.7882 (m-80) REVERT: D 1021 LYS cc_start: 0.9048 (mtpt) cc_final: 0.8782 (tptp) REVERT: D 1039 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8205 (mm-30) REVERT: D 1127 VAL cc_start: 0.8929 (p) cc_final: 0.8573 (p) REVERT: D 1136 PHE cc_start: 0.8903 (m-80) cc_final: 0.8430 (m-10) outliers start: 5 outliers final: 0 residues processed: 131 average time/residue: 0.2057 time to fit residues: 31.4938 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 : 0.401 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 : 0.109 Fit side-chains REVERT: B 100 ASP cc_start: 0.6190 (m-30) cc_final: 0.5940 (t0) REVERT: B 100 ASP cc_start: 0.6405 (p0) cc_final: 0.6180 (p0) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1050 time to fit residues: 2.8801 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 : 0.108 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 : 0.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.1066 time to fit residues: 2.5394 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 : 0.099 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 : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 171 LEU cc_start: 0.8467 (mm) cc_final: 0.8072 (tt) REVERT: J 635 TYR cc_start: 0.7014 (OUTLIER) cc_final: 0.5731 (m-80) outliers start: 9 outliers final: 0 residues processed: 82 average time/residue: 0.1741 time to fit residues: 19.1010 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 : 0.560 ------------------------------------------------------------------------------- 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: 0.3980 chunk 388 optimal weight: 10.0000 chunk 95 optimal weight: 30.0000 chunk 100 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 292 optimal weight: 6.9990 chunk 278 optimal weight: 2.9990 chunk 297 optimal weight: 0.6980 chunk 293 optimal weight: 0.0000 chunk 20 optimal weight: 20.0000 chunk 302 optimal weight: 10.0000 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 815 GLN D 907 GLN ** D 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 981 ASN D1023 GLN ** D1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1122 HIS D1217 ASN Total number of N/Q/H flips: 6 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 81 HIS ** J 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 319 GLN ** 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: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.082661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.070155 restraints weight = 14571.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.071979 restraints weight = 8642.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.073279 restraints weight = 5855.414| |-----------------------------------------------------------------------------| r_work (final): 0.3231 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.055366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.049511 restraints weight = 7432.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.050726 restraints weight = 4827.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.051635 restraints weight = 3440.698| |-----------------------------------------------------------------------------| r_work (final): 0.3153 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.066912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.058802 restraints weight = 5906.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.060451 restraints weight = 3850.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.061742 restraints weight = 2754.781| |-----------------------------------------------------------------------------| r_work (final): 0.3479 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.090596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.070692 restraints weight = 44312.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.071005 restraints weight = 30073.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.070687 restraints weight = 26489.629| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5709 moved from start: 4.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.249 33791 Z= 0.664 Angle : 1.784 44.236 45988 Z= 0.980 Chirality : 0.076 0.810 5091 Planarity : 0.013 0.232 5961 Dihedral : 9.858 134.913 4629 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 40.26 Ramachandran Plot: Outliers : 1.85 % Allowed : 5.89 % Favored : 92.26 % Rotamer: Outliers : 1.89 % Allowed : 3.78 % Favored : 94.33 % Cbeta Deviations : 0.53 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 1.41 % 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: -0.56 (0.13), residues: 4227 helix: -0.46 (0.18), residues: 660 sheet: 0.06 (0.15), residues: 1053 loop : -0.48 (0.13), residues: 2514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP E 47 HIS 0.025 0.003 HIS A 836 PHE 0.053 0.005 PHE D 850 TYR 0.154 0.008 TYR A 928 ARG 0.013 0.001 ARG F 61 Details of bonding type rmsd hydrogen bonds : bond 0.48856 ( 1245) hydrogen bonds : angle 9.39516 ( 3231) SS BOND : bond 0.03361 ( 56) SS BOND : angle 5.68295 ( 112) covalent geometry : bond 0.01322 (33735) covalent geometry : angle 1.76447 (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 89 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 799 ILE cc_start: 0.8889 (mm) cc_final: 0.8421 (pt) REVERT: D 841 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8060 (mmp80) REVERT: D 842 GLN cc_start: 0.8653 (mm-40) cc_final: 0.8064 (mm110) REVERT: D 905 TYR cc_start: 0.6188 (m-80) cc_final: 0.5784 (t80) REVERT: D 909 TYR cc_start: 0.1092 (OUTLIER) cc_final: 0.0319 (m-80) REVERT: D 939 MET cc_start: 0.7028 (ptp) cc_final: 0.6821 (ptp) REVERT: D 940 ASP cc_start: 0.6530 (t0) cc_final: 0.6269 (m-30) REVERT: D 1039 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8092 (mm-30) REVERT: D 1127 VAL cc_start: 0.8988 (p) cc_final: 0.8781 (p) REVERT: D 1136 PHE cc_start: 0.8909 (m-80) cc_final: 0.8645 (m-10) REVERT: D 1177 ASN cc_start: 0.8930 (t0) cc_final: 0.8065 (p0) outliers start: 16 outliers final: 3 residues processed: 83 average time/residue: 0.1564 time to fit residues: 15.8109 Evaluate side-chains 47 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.439 Evaluate side-chains 18 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.117 Fit side-chains REVERT: B 100 ASP cc_start: 0.6203 (p0) cc_final: 0.5996 (p0) outliers start: 1 outliers final: 0 residues processed: 18 average time/residue: 0.1348 time to fit residues: 2.7455 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 : 0.116 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 : 0.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 LEU cc_start: 0.9010 (pt) cc_final: 0.8793 (pt) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0936 time to fit residues: 1.8704 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 : 0.101 Evaluate side-chains 66 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.604 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: 0.8417 (mm) cc_final: 0.8077 (tt) REVERT: J 343 ASP cc_start: 0.7954 (m-30) cc_final: 0.7627 (m-30) outliers start: 6 outliers final: 1 residues processed: 63 average time/residue: 0.1425 time to fit residues: 12.7920 Evaluate side-chains 45 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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: 7.9990 chunk 140 optimal weight: 1.9990 chunk 151 optimal weight: 0.3980 chunk 169 optimal weight: 10.0000 chunk 157 optimal weight: 5.9990 chunk 248 optimal weight: 3.9990 chunk 44 optimal weight: 0.1980 chunk 242 optimal weight: 0.0060 chunk 390 optimal weight: 8.9990 chunk 241 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 796 GLN D 812 ASN ** D1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1122 HIS ** D1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1146 HIS Total number of N/Q/H flips: 4 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 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 319 GLN ** 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 = 0.3445 r_free = 0.3445 target = 0.083223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.071012 restraints weight = 14620.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.072701 restraints weight = 8929.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.073873 restraints weight = 6270.041| |-----------------------------------------------------------------------------| r_work (final): 0.3250 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.055472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.049192 restraints weight = 6547.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.050484 restraints weight = 4149.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.051385 restraints weight = 2908.421| |-----------------------------------------------------------------------------| r_work (final): 0.3123 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.068308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.060762 restraints weight = 5237.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.062587 restraints weight = 3358.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.063937 restraints weight = 2312.398| |-----------------------------------------------------------------------------| r_work (final): 0.3537 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.091601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.072085 restraints weight = 46876.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.073018 restraints weight = 31749.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.073807 restraints weight = 23244.921| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5826 moved from start: 4.5318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.178 33791 Z= 0.526 Angle : 1.567 42.032 45988 Z= 0.856 Chirality : 0.079 1.182 5091 Planarity : 0.012 0.236 5961 Dihedral : 9.711 134.322 4629 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 33.44 Ramachandran Plot: Outliers : 1.28 % Allowed : 6.88 % Favored : 91.84 % Rotamer: Outliers : 0.99 % Allowed : 4.84 % Favored : 94.17 % Cbeta Deviations : 0.46 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.37 % Twisted Proline : 1.47 % Twisted General : 1.41 % 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: -1.03 (0.12), residues: 4227 helix: -0.71 (0.19), residues: 681 sheet: -0.11 (0.14), residues: 1089 loop : -0.91 (0.13), residues: 2457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP E 47 HIS 0.025 0.002 HIS D 836 PHE 0.061 0.004 PHE G 850 TYR 0.152 0.006 TYR G 809 ARG 0.056 0.001 ARG D 758 Details of bonding type rmsd hydrogen bonds : bond 0.47118 ( 1245) hydrogen bonds : angle 9.19663 ( 3231) SS BOND : bond 0.03532 ( 56) SS BOND : angle 5.29922 ( 112) covalent geometry : bond 0.00993 (33735) covalent geometry : angle 1.54731 (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 63 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: D 842 GLN cc_start: 0.8495 (mm-40) cc_final: 0.8195 (mm-40) REVERT: D 905 TYR cc_start: 0.5936 (m-80) cc_final: 0.5696 (t80) REVERT: D 939 MET cc_start: 0.6942 (ptp) cc_final: 0.6620 (ptp) REVERT: D 940 ASP cc_start: 0.6773 (t0) cc_final: 0.5934 (m-30) REVERT: D 977 PHE cc_start: 0.7716 (m-80) cc_final: 0.7485 (m-80) REVERT: D 1127 VAL cc_start: 0.9000 (p) cc_final: 0.8764 (p) REVERT: D 1136 PHE cc_start: 0.9094 (m-80) cc_final: 0.8699 (m-10) REVERT: D 1177 ASN cc_start: 0.8894 (t0) cc_final: 0.8480 (t0) outliers start: 8 outliers final: 3 residues processed: 61 average time/residue: 0.1480 time to fit residues: 11.4131 Evaluate side-chains 41 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.398 Evaluate side-chains 19 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.116 Fit side-chains REVERT: B 100 ASP cc_start: 0.6513 (p0) cc_final: 0.6047 (m-30) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0894 time to fit residues: 2.0430 Evaluate side-chains 11 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.119 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 : 0.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1005 time to fit residues: 1.9975 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 : 0.100 Evaluate side-chains 67 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 171 LEU cc_start: 0.8442 (mm) cc_final: 0.8055 (tp) REVERT: J 278 MET cc_start: 0.9016 (mmm) cc_final: 0.8153 (mmm) REVERT: J 293 TYR cc_start: 0.5938 (t80) cc_final: 0.5537 (t80) REVERT: J 343 ASP cc_start: 0.8198 (m-30) cc_final: 0.7840 (m-30) REVERT: J 637 ASN cc_start: 0.8125 (t0) cc_final: 0.7350 (m-40) REVERT: J 726 ASP cc_start: 0.5681 (t0) cc_final: 0.4937 (p0) outliers start: 4 outliers final: 0 residues processed: 66 average time/residue: 0.1514 time to fit residues: 13.8285 Evaluate side-chains 45 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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: 1.9990 chunk 185 optimal weight: 4.9990 chunk 11 optimal weight: 30.0000 chunk 252 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 chunk 229 optimal weight: 7.9990 chunk 307 optimal weight: 9.9990 chunk 333 optimal weight: 6.9990 chunk 230 optimal weight: 0.9980 chunk 281 optimal weight: 7.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1122 HIS 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 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 319 GLN ** 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 = 0.3425 r_free = 0.3425 target = 0.081861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.069091 restraints weight = 14671.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.070886 restraints weight = 8835.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.072119 restraints weight = 6073.303| |-----------------------------------------------------------------------------| r_work (final): 0.3217 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.054934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.049127 restraints weight = 6373.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.050393 restraints weight = 4102.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.051388 restraints weight = 2856.612| |-----------------------------------------------------------------------------| r_work (final): 0.3166 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.067404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.058778 restraints weight = 5505.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.060780 restraints weight = 3250.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.062215 restraints weight = 2201.925| |-----------------------------------------------------------------------------| r_work (final): 0.3479 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.091871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.074284 restraints weight = 46670.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.073793 restraints weight = 37111.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.074286 restraints weight = 30953.305| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5838 moved from start: 4.5446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.236 33791 Z= 0.578 Angle : 1.671 34.620 45988 Z= 0.901 Chirality : 0.084 1.165 5091 Planarity : 0.014 0.309 5961 Dihedral : 9.765 133.624 4629 Min Nonbonded Distance : 1.696 Molprobity Statistics. All-atom Clashscore : 36.11 Ramachandran Plot: Outliers : 1.28 % Allowed : 7.24 % Favored : 91.48 % Rotamer: Outliers : 0.57 % Allowed : 2.96 % Favored : 96.47 % Cbeta Deviations : 0.76 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.37 % Twisted Proline : 0.00 % 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: -1.26 (0.12), residues: 4227 helix: -0.78 (0.19), residues: 666 sheet: -0.25 (0.14), residues: 1086 loop : -1.12 (0.13), residues: 2475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP E 47 HIS 0.025 0.003 HIS D 836 PHE 0.153 0.006 PHE I 62 TYR 0.075 0.005 TYR D 809 ARG 0.078 0.003 ARG J 652 Details of bonding type rmsd hydrogen bonds : bond 0.46654 ( 1245) hydrogen bonds : angle 9.17484 ( 3231) SS BOND : bond 0.03719 ( 56) SS BOND : angle 6.72679 ( 112) covalent geometry : bond 0.01103 (33735) covalent geometry : angle 1.64008 (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 50 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.401 Fit side-chains REVERT: D 842 GLN cc_start: 0.8652 (mm-40) cc_final: 0.8424 (mm-40) REVERT: D 905 TYR cc_start: 0.6273 (m-80) cc_final: 0.5734 (t80) REVERT: D 977 PHE cc_start: 0.7735 (m-80) cc_final: 0.7466 (m-80) REVERT: D 1036 LEU cc_start: 0.9003 (mt) cc_final: 0.8463 (mt) REVERT: D 1039 GLU cc_start: 0.8387 (mm-30) cc_final: 0.7883 (mm-30) REVERT: D 1127 VAL cc_start: 0.9074 (p) cc_final: 0.8822 (p) REVERT: D 1136 PHE cc_start: 0.8994 (m-80) cc_final: 0.8653 (m-10) outliers start: 3 outliers final: 0 residues processed: 50 average time/residue: 0.1680 time to fit residues: 10.4718 Evaluate side-chains 29 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.391 Evaluate side-chains 16 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.112 Fit side-chains REVERT: B 100 TYR cc_start: 0.7344 (m-80) cc_final: 0.7125 (m-80) REVERT: B 100 ASP cc_start: 0.6488 (p0) cc_final: 0.6134 (m-30) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0635 time to fit residues: 1.3094 Evaluate side-chains 11 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.107 Evaluate side-chains 19 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.105 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 18 average time/residue: 0.0982 time to fit residues: 2.0552 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 : 0.097 Evaluate side-chains 55 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 148 MET cc_start: 0.7666 (tpt) cc_final: 0.7390 (tpp) REVERT: J 171 LEU cc_start: 0.8516 (mm) cc_final: 0.8062 (tp) REVERT: J 278 MET cc_start: 0.8997 (mmm) cc_final: 0.7938 (mmm) REVERT: J 293 TYR cc_start: 0.6106 (t80) cc_final: 0.5676 (t80) REVERT: J 361 TYR cc_start: 0.7698 (m-10) cc_final: 0.7300 (m-10) REVERT: J 637 ASN cc_start: 0.8058 (t0) cc_final: 0.7144 (m-40) REVERT: J 726 ASP cc_start: 0.6222 (t0) cc_final: 0.5347 (p0) outliers start: 2 outliers final: 0 residues processed: 54 average time/residue: 0.1562 time to fit residues: 11.9030 Evaluate side-chains 45 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 76 optimal weight: 8.9990 chunk 373 optimal weight: 0.0270 chunk 225 optimal weight: 0.0870 chunk 227 optimal weight: 10.0000 chunk 375 optimal weight: 0.1980 chunk 132 optimal weight: 7.9990 chunk 308 optimal weight: 0.0070 chunk 185 optimal weight: 0.0770 chunk 206 optimal weight: 7.9990 chunk 134 optimal weight: 0.0770 chunk 250 optimal weight: 3.9990 overall best weight: 0.0550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1119 GLN ** D1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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... Flipped N/Q/H residues before XYZ refinement: ** C 38 GLN ** 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: ** J 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 406 ASN ** J 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 637 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.082450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.069886 restraints weight = 14893.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.071587 restraints weight = 9204.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.072775 restraints weight = 6462.729| |-----------------------------------------------------------------------------| r_work (final): 0.3230 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.053452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.048000 restraints weight = 6725.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.049245 restraints weight = 4267.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.050148 restraints weight = 2954.842| |-----------------------------------------------------------------------------| r_work (final): 0.3137 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.066717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.057134 restraints weight = 5460.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.058961 restraints weight = 3581.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.060318 restraints weight = 2597.448| |-----------------------------------------------------------------------------| r_work (final): 0.3465 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.091471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.073024 restraints weight = 47660.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.073669 restraints weight = 32945.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.073785 restraints weight = 24318.593| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5744 moved from start: 4.5520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.395 33791 Z= 0.650 Angle : 1.717 34.620 45988 Z= 0.920 Chirality : 0.084 1.165 5091 Planarity : 0.015 0.309 5961 Dihedral : 9.765 133.624 4629 Min Nonbonded Distance : 0.444 Molprobity Statistics. All-atom Clashscore : 43.20 Ramachandran Plot: Outliers : 1.28 % Allowed : 7.24 % Favored : 91.48 % Rotamer: Outliers : 0.16 % Allowed : 0.00 % Favored : 99.84 % Cbeta Deviations : 0.76 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.37 % Twisted Proline : 0.00 % 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: -1.26 (0.12), residues: 4227 helix: -0.78 (0.19), residues: 666 sheet: -0.25 (0.14), residues: 1086 loop : -1.12 (0.13), residues: 2475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP E 47 HIS 0.025 0.003 HIS D 836 PHE 0.153 0.006 PHE C 62 TYR 0.075 0.005 TYR D 809 ARG 0.078 0.003 ARG L 652 Details of bonding type rmsd hydrogen bonds : bond 0.46654 ( 1245) hydrogen bonds : angle 9.17484 ( 3231) SS BOND : bond 0.14572 ( 56) SS BOND : angle 10.45088 ( 112) covalent geometry : bond 0.01108 (33735) covalent geometry : angle 1.63961 (45876) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.408 Fit side-chains REVERT: D 757 MET cc_start: 0.2570 (ttm) cc_final: 0.2363 (ttm) REVERT: D 842 GLN cc_start: 0.8655 (mm-40) cc_final: 0.8440 (mm-40) REVERT: D 905 TYR cc_start: 0.6287 (m-80) cc_final: 0.5733 (t80) REVERT: D 977 PHE cc_start: 0.7715 (m-80) cc_final: 0.7435 (m-80) REVERT: D 1035 LYS cc_start: 0.8792 (mttp) cc_final: 0.8561 (mttp) REVERT: D 1036 LEU cc_start: 0.8908 (mt) cc_final: 0.8443 (mt) REVERT: D 1039 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7880 (mm-30) REVERT: D 1127 VAL cc_start: 0.9094 (p) cc_final: 0.8861 (p) REVERT: D 1136 PHE cc_start: 0.9103 (m-80) cc_final: 0.8648 (m-10) outliers start: 1 outliers final: 0 residues processed: 41 average time/residue: 0.1106 time to fit residues: 6.3051 Evaluate side-chains 29 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.365 Evaluate side-chains 16 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.099 Fit side-chains REVERT: B 100 ASP cc_start: 0.6643 (p0) cc_final: 0.6153 (m-30) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0597 time to fit residues: 1.2378 Evaluate side-chains 11 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.101 Evaluate side-chains 16 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.101 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 46 LEU cc_start: 0.8941 (pt) cc_final: 0.8685 (pt) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0990 time to fit residues: 1.8531 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 : 0.104 Evaluate side-chains 52 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 171 LEU cc_start: 0.8363 (mm) cc_final: 0.8001 (tp) REVERT: J 278 MET cc_start: 0.9044 (mmm) cc_final: 0.7953 (mmm) REVERT: J 293 TYR cc_start: 0.5866 (t80) cc_final: 0.5452 (t80) REVERT: J 343 ASP cc_start: 0.8163 (m-30) cc_final: 0.7841 (m-30) REVERT: J 360 VAL cc_start: 0.7380 (t) cc_final: 0.7173 (t) REVERT: J 361 TYR cc_start: 0.7755 (m-10) cc_final: 0.7365 (m-10) REVERT: J 637 ASN cc_start: 0.7740 (OUTLIER) cc_final: 0.7040 (m-40) REVERT: J 726 ASP cc_start: 0.5992 (t0) cc_final: 0.5164 (p0) outliers start: 1 outliers final: 0 residues processed: 51 average time/residue: 0.1540 time to fit residues: 11.1806 Evaluate side-chains 45 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 258 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 144 optimal weight: 4.9990 chunk 47 optimal weight: 0.0970 chunk 251 optimal weight: 4.9990 chunk 335 optimal weight: 10.0000 chunk 244 optimal weight: 30.0000 chunk 370 optimal weight: 2.9990 chunk 343 optimal weight: 8.9990 chunk 204 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1119 GLN ** D1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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... Flipped N/Q/H residues before XYZ refinement: ** C 38 GLN ** 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: ** J 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 406 ASN ** J 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 627 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 = 0.3440 r_free = 0.3440 target = 0.082684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.070222 restraints weight = 15115.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.071855 restraints weight = 9254.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.073035 restraints weight = 6545.900| |-----------------------------------------------------------------------------| r_work (final): 0.3229 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.053528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.047747 restraints weight = 7282.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.049139 restraints weight = 4404.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.050130 restraints weight = 2972.963| |-----------------------------------------------------------------------------| r_work (final): 0.3145 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.067255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.057805 restraints weight = 5467.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.059753 restraints weight = 3498.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.061154 restraints weight = 2496.241| |-----------------------------------------------------------------------------| r_work (final): 0.3483 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.091489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.073042 restraints weight = 47668.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.074109 restraints weight = 33527.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.074359 restraints weight = 22169.753| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5731 moved from start: 4.5524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.448 33791 Z= 0.658 Angle : 1.759 53.549 45988 Z= 0.938 Chirality : 0.084 1.165 5091 Planarity : 0.015 0.309 5961 Dihedral : 9.765 133.624 4629 Min Nonbonded Distance : 0.444 Molprobity Statistics. All-atom Clashscore : 43.39 Ramachandran Plot: Outliers : 1.28 % Allowed : 7.24 % Favored : 91.48 % Rotamer: Outliers : 0.08 % Allowed : 0.00 % Favored : 99.92 % Cbeta Deviations : 0.76 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.37 % Twisted Proline : 0.00 % 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: -1.26 (0.12), residues: 4227 helix: -0.78 (0.19), residues: 666 sheet: -0.25 (0.14), residues: 1086 loop : -1.12 (0.13), residues: 2475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP E 47 HIS 0.025 0.003 HIS D 836 PHE 0.153 0.006 PHE F 62 TYR 0.075 0.005 TYR A 809 ARG 0.078 0.003 ARG L 652 Details of bonding type rmsd hydrogen bonds : bond 0.46654 ( 1245) hydrogen bonds : angle 9.17484 ( 3231) SS BOND : bond 0.15385 ( 56) SS BOND : angle 13.03582 ( 112) covalent geometry : bond 0.01108 (33735) covalent geometry : angle 1.63961 (45876) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.371 Fit side-chains REVERT: D 757 MET cc_start: 0.2569 (ttm) cc_final: 0.2362 (ttm) REVERT: D 842 GLN cc_start: 0.8657 (mm-40) cc_final: 0.8441 (mm-40) REVERT: D 905 TYR cc_start: 0.6319 (m-80) cc_final: 0.5746 (t80) REVERT: D 977 PHE cc_start: 0.7718 (m-80) cc_final: 0.7430 (m-80) REVERT: D 1035 LYS cc_start: 0.8789 (mttp) cc_final: 0.8562 (mttp) REVERT: D 1036 LEU cc_start: 0.8912 (mt) cc_final: 0.8448 (mt) REVERT: D 1039 GLU cc_start: 0.8417 (mm-30) cc_final: 0.7889 (mm-30) REVERT: D 1127 VAL cc_start: 0.9097 (p) cc_final: 0.8865 (p) REVERT: D 1136 PHE cc_start: 0.9098 (m-80) cc_final: 0.8647 (m-10) outliers start: 1 outliers final: 0 residues processed: 42 average time/residue: 0.1162 time to fit residues: 6.7075 Evaluate side-chains 32 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.410 Evaluate side-chains 16 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.101 Fit side-chains REVERT: B 100 ASP cc_start: 0.6598 (p0) cc_final: 0.6140 (m-30) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0631 time to fit residues: 1.3056 Evaluate side-chains 11 residues out of total 102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.102 Evaluate side-chains 16 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 46 LEU cc_start: 0.8955 (pt) cc_final: 0.8704 (pt) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1004 time to fit residues: 1.8764 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 : 0.094 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 : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 171 LEU cc_start: 0.8292 (mm) cc_final: 0.7958 (tp) REVERT: J 278 MET cc_start: 0.9042 (mmm) cc_final: 0.8006 (mmm) REVERT: J 293 TYR cc_start: 0.5741 (t80) cc_final: 0.5334 (t80) REVERT: J 343 ASP cc_start: 0.8158 (m-30) cc_final: 0.7840 (m-30) REVERT: J 360 VAL cc_start: 0.7400 (t) cc_final: 0.7197 (t) REVERT: J 361 TYR cc_start: 0.7766 (m-10) cc_final: 0.7378 (m-10) REVERT: J 637 ASN cc_start: 0.7589 (t0) cc_final: 0.7093 (m-40) REVERT: J 726 ASP cc_start: 0.5834 (t0) cc_final: 0.5053 (p0) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1566 time to fit residues: 11.2923 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 : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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: 54.7417 > 50: distance: 1 - 2: 17.598 distance: 1 - 3: 4.147 distance: 4 - 5: 9.318 distance: 5 - 6: 22.337 distance: 5 - 8: 18.222 distance: 6 - 7: 16.511 distance: 6 - 11: 29.917 distance: 8 - 9: 21.775 distance: 8 - 10: 28.480 distance: 11 - 12: 11.682 distance: 12 - 13: 29.101 distance: 12 - 15: 15.339 distance: 13 - 14: 20.720 distance: 13 - 19: 22.334 distance: 14 - 44: 28.012 distance: 15 - 16: 25.684 distance: 16 - 17: 20.253 distance: 16 - 18: 25.276 distance: 19 - 20: 24.939 distance: 20 - 21: 14.633 distance: 20 - 23: 26.352 distance: 21 - 22: 22.174 distance: 21 - 28: 14.946 distance: 22 - 54: 39.300 distance: 23 - 24: 8.335 distance: 24 - 25: 25.228 distance: 25 - 26: 7.737 distance: 25 - 27: 8.118 distance: 28 - 29: 13.211 distance: 29 - 30: 31.716 distance: 29 - 32: 16.401 distance: 30 - 31: 35.293 distance: 30 - 33: 28.542 distance: 31 - 63: 10.259 distance: 33 - 34: 52.642 distance: 34 - 35: 50.623 distance: 34 - 37: 54.742 distance: 35 - 36: 24.958 distance: 35 - 44: 45.871 distance: 36 - 70: 44.025 distance: 37 - 38: 9.141 distance: 38 - 39: 9.673 distance: 38 - 40: 16.004 distance: 39 - 41: 11.714 distance: 40 - 42: 18.846 distance: 41 - 43: 3.901 distance: 42 - 43: 14.417 distance: 44 - 45: 39.944 distance: 45 - 46: 36.658 distance: 45 - 48: 23.277 distance: 46 - 47: 39.655 distance: 46 - 54: 28.544 distance: 48 - 49: 16.334 distance: 49 - 50: 12.540 distance: 49 - 51: 13.498 distance: 50 - 52: 24.210 distance: 51 - 53: 14.843 distance: 52 - 53: 8.689 distance: 54 - 55: 13.682 distance: 55 - 56: 31.841 distance: 55 - 58: 30.806 distance: 56 - 57: 18.969 distance: 56 - 63: 22.100 distance: 58 - 59: 18.268 distance: 59 - 60: 28.184 distance: 60 - 61: 21.643 distance: 61 - 62: 21.877 distance: 63 - 64: 15.618 distance: 64 - 65: 22.814 distance: 64 - 67: 31.875 distance: 65 - 66: 37.903 distance: 65 - 70: 22.380 distance: 67 - 68: 13.823 distance: 67 - 69: 17.909 distance: 70 - 71: 20.966 distance: 71 - 72: 24.245 distance: 71 - 74: 15.779 distance: 72 - 73: 20.644 distance: 74 - 75: 8.001 distance: 75 - 76: 11.536 distance: 76 - 77: 6.118