Starting phenix.real_space_refine (version: 1.21rc1) on Sun May 14 02:28:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9o_8790/05_2023/5w9o_8790.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9o_8790/05_2023/5w9o_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9o_8790/05_2023/5w9o_8790.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9o_8790/05_2023/5w9o_8790.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9o_8790/05_2023/5w9o_8790.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9o_8790/05_2023/5w9o_8790.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Residue "A GLU 793": "OE1" <-> "OE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 605": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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: 16.32, per 1000 atoms: 0.50 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 - 3.50 Amino acid : False - 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: 12.64 Conformation dependent library (CDL) restraints added in 4.9 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: 2.17 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: 15.27 Time building geometry restraints manager: 13.67 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: 96.41 - 104.51: 707 104.51 - 112.61: 16249 112.61 - 120.71: 18462 120.71 - 128.81: 10284 128.81 - 136.91: 174 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 2.440 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 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: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 9.100 Check model and map are aligned: 0.490 Set scattering table: 0.250 Process input model: 82.930 Find NCS groups from input model: 1.870 Set up NCS constraints: 0.150 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: 0.000 Load rotamer database and sin/cos tables:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.370 ------------------------------------------------------------------------------- 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 : 0.013 0.100 33735 Z= 0.821 Angle : 1.659 14.227 45876 Z= 1.140 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 % 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.428 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1519 time to fit residues: 15.2517 Evaluate side-chains 25 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.427 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5598 Evaluate side-chains 35 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.112 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1526 time to fit residues: 5.7994 Evaluate side-chains 12 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.120 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1554 Evaluate side-chains 24 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.111 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: 0.2644 time to fit residues: 6.7084 Evaluate side-chains 11 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.105 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1330 Evaluate side-chains 88 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 86 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 87 average time/residue: 0.2049 time to fit residues: 22.8932 Evaluate side-chains 48 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.668 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8947 ------------------------------------------------------------------------------- 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: 9.9990 chunk 318 optimal weight: 0.3980 chunk 176 optimal weight: 0.0670 chunk 108 optimal weight: 2.9990 chunk 214 optimal weight: 0.0670 chunk 170 optimal weight: 3.9990 chunk 329 optimal weight: 0.6980 chunk 127 optimal weight: 8.9990 chunk 200 optimal weight: 0.7980 chunk 245 optimal weight: 0.9990 chunk 381 optimal weight: 4.9990 overall best weight: 0.4056 ------------------------------------------------------------------------------- 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 602 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5918 moved from start: 4.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.333 33735 Z= 0.769 Angle : 1.572 33.989 45876 Z= 0.906 Chirality : 0.088 1.925 5091 Planarity : 0.010 0.162 5961 Dihedral : 9.713 137.737 4629 Min Nonbonded Distance : 1.398 Molprobity Statistics. All-atom Clashscore : 35.74 Ramachandran Plot: Outliers : 1.92 % Allowed : 5.32 % Favored : 92.76 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.84 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.37 % Twisted Proline : 1.47 % Twisted General : 1.78 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.13), residues: 4227 helix: 0.38 (0.19), residues: 681 sheet: 0.30 (0.15), residues: 1029 loop : 0.10 (0.14), residues: 2517 *********************** 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 127 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 122 time to evaluate : 0.446 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 126 average time/residue: 0.2040 time to fit residues: 29.9000 Evaluate side-chains 51 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.412 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5363 Evaluate side-chains 24 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.109 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1094 time to fit residues: 2.9922 Evaluate side-chains 10 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.108 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1517 Evaluate side-chains 20 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.1084 time to fit residues: 2.4695 Evaluate side-chains 13 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.108 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1391 Evaluate side-chains 83 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 80 average time/residue: 0.1803 time to fit residues: 19.1681 Evaluate side-chains 43 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.634 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0748 time to fit residues: 0.9964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 211 optimal weight: 0.9980 chunk 118 optimal weight: 9.9990 chunk 317 optimal weight: 6.9990 chunk 259 optimal weight: 0.0020 chunk 105 optimal weight: 3.9990 chunk 382 optimal weight: 0.0030 chunk 412 optimal weight: 0.0970 chunk 340 optimal weight: 0.0050 chunk 378 optimal weight: 0.0070 chunk 130 optimal weight: 0.0770 chunk 306 optimal weight: 0.0870 overall best weight: 0.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 808 GLN D 812 ASN D 815 GLN ** D 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1023 GLN D1122 HIS Total number of N/Q/H flips: 5 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 41 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: C 38 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 319 GLN ** J 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 602 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5883 moved from start: 4.5348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.264 33735 Z= 0.740 Angle : 1.654 29.793 45876 Z= 0.905 Chirality : 0.083 0.950 5091 Planarity : 0.014 0.332 5961 Dihedral : 10.150 134.313 4629 Min Nonbonded Distance : 1.439 Molprobity Statistics. All-atom Clashscore : 37.13 Ramachandran Plot: Outliers : 2.13 % Allowed : 6.81 % Favored : 91.06 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.76 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 2.01 % 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: -0.93 (0.13), residues: 4227 helix: -0.75 (0.18), residues: 675 sheet: -0.16 (0.15), residues: 1083 loop : -0.73 (0.13), residues: 2469 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7294 Ramachandran restraints generated. 3647 Oldfield, 0 Emsley, 3647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7294 Ramachandran restraints generated. 3647 Oldfield, 0 Emsley, 3647 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 fitting. rotamer outliers: 17 poor density : 64 time to evaluate : 0.438 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 2 residues processed: 75 average time/residue: 0.2131 time to fit residues: 18.8504 Evaluate side-chains 37 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.416 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2440 time to fit residues: 1.1001 Evaluate side-chains 38 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 38 average time/residue: 0.1892 time to fit residues: 7.6808 Evaluate side-chains 17 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.109 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1368 Evaluate side-chains 15 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1033 time to fit residues: 1.8315 Evaluate side-chains 13 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.094 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1351 Evaluate side-chains 70 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 67 average time/residue: 0.1417 time to fit residues: 13.5801 Evaluate side-chains 42 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.639 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 377 optimal weight: 0.0070 chunk 287 optimal weight: 0.7980 chunk 198 optimal weight: 4.9990 chunk 42 optimal weight: 0.0030 chunk 182 optimal weight: 3.9990 chunk 256 optimal weight: 0.0980 chunk 383 optimal weight: 0.0270 chunk 405 optimal weight: 0.9980 chunk 200 optimal weight: 0.2980 chunk 363 optimal weight: 0.0070 chunk 109 optimal weight: 0.0060 overall best weight: 0.0100 ------------------------------------------------------------------------------- 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 808 GLN D 812 ASN ** D 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 907 GLN D 974 GLN ** D1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN ** E 41 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: ** 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 81 HIS J 319 GLN J 408 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5889 moved from start: 4.5583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.260 33735 Z= 0.719 Angle : 1.689 43.187 45876 Z= 0.901 Chirality : 0.086 1.106 5091 Planarity : 0.015 0.373 5961 Dihedral : 9.878 134.030 4629 Min Nonbonded Distance : 1.458 Molprobity Statistics. All-atom Clashscore : 41.54 Ramachandran Plot: Outliers : 1.49 % Allowed : 7.52 % Favored : 90.99 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.91 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.37 % Twisted Proline : 1.47 % Twisted General : 1.78 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.13), residues: 4227 helix: -0.89 (0.18), residues: 675 sheet: -0.39 (0.15), residues: 1110 loop : -0.89 (0.13), residues: 2442 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7294 Ramachandran restraints generated. 3647 Oldfield, 0 Emsley, 3647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7294 Ramachandran restraints generated. 3647 Oldfield, 0 Emsley, 3647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 62 time to evaluate : 0.429 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 69 average time/residue: 0.1493 time to fit residues: 12.9345 Evaluate side-chains 31 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 29 time to evaluate : 0.414 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0489 time to fit residues: 0.7070 Evaluate side-chains 25 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 22 time to evaluate : 0.108 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 25 average time/residue: 0.1971 time to fit residues: 5.3050 Evaluate side-chains 16 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.110 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1509 Evaluate side-chains 15 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.105 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0997 time to fit residues: 1.7623 Evaluate side-chains 11 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.094 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1369 Evaluate side-chains 66 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 64 average time/residue: 0.1321 time to fit residues: 12.3669 Evaluate side-chains 41 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.679 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0565 time to fit residues: 0.9907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 338 optimal weight: 0.0010 chunk 230 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 302 optimal weight: 9.9990 chunk 167 optimal weight: 5.9990 chunk 346 optimal weight: 20.0000 chunk 280 optimal weight: 2.9990 chunk 0 optimal weight: 0.8980 chunk 207 optimal weight: 4.9990 chunk 364 optimal weight: 0.0040 chunk 102 optimal weight: 0.9980 overall best weight: 0.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 766 HIS ** D 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 319 GLN J 348 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5882 moved from start: 4.5691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.262 33735 Z= 0.671 Angle : 1.659 34.263 45876 Z= 0.889 Chirality : 0.086 1.266 5091 Planarity : 0.014 0.269 5961 Dihedral : 9.879 133.862 4629 Min Nonbonded Distance : 1.523 Molprobity Statistics. All-atom Clashscore : 39.91 Ramachandran Plot: Outliers : 1.14 % Allowed : 8.16 % Favored : 90.70 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.61 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.37 % Twisted Proline : 1.47 % Twisted General : 1.86 % 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: -1.34 (0.13), residues: 4227 helix: -0.95 (0.19), residues: 678 sheet: -0.41 (0.15), residues: 1089 loop : -1.07 (0.13), residues: 2460 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7294 Ramachandran restraints generated. 3647 Oldfield, 0 Emsley, 3647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7294 Ramachandran restraints generated. 3647 Oldfield, 0 Emsley, 3647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 63 average time/residue: 0.1543 time to fit residues: 12.1515 Evaluate side-chains 34 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 0.380 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0484 time to fit residues: 0.6632 Evaluate side-chains 20 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.104 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.1222 time to fit residues: 2.7861 Evaluate side-chains 13 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.105 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1388 Evaluate side-chains 15 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.093 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1043 time to fit residues: 1.8289 Evaluate side-chains 10 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.095 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1269 Evaluate side-chains 57 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 57 average time/residue: 0.1658 time to fit residues: 13.0807 Evaluate side-chains 39 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.640 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0567 time to fit residues: 0.9735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 136 optimal weight: 9.9990 chunk 365 optimal weight: 5.9990 chunk 80 optimal weight: 9.9990 chunk 238 optimal weight: 10.0000 chunk 100 optimal weight: 0.3980 chunk 406 optimal weight: 7.9990 chunk 337 optimal weight: 0.0060 chunk 188 optimal weight: 0.0980 chunk 33 optimal weight: 20.0000 chunk 134 optimal weight: 0.6980 chunk 213 optimal weight: 0.7980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 796 GLN ** D 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1110 GLN ** D1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1217 ASN Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... 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 319 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5880 moved from start: 4.5823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.269 33735 Z= 0.644 Angle : 1.544 36.534 45876 Z= 0.826 Chirality : 0.083 1.053 5091 Planarity : 0.015 0.314 5961 Dihedral : 9.801 133.660 4629 Min Nonbonded Distance : 1.689 Molprobity Statistics. All-atom Clashscore : 37.53 Ramachandran Plot: Outliers : 0.92 % Allowed : 9.01 % Favored : 90.06 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.53 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.37 % Twisted Proline : 1.47 % Twisted General : 1.63 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.12), residues: 4227 helix: -1.07 (0.18), residues: 681 sheet: -0.60 (0.15), residues: 1059 loop : -1.17 (0.13), residues: 2487 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7294 Ramachandran restraints generated. 3647 Oldfield, 0 Emsley, 3647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7294 Ramachandran restraints generated. 3647 Oldfield, 0 Emsley, 3647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 53 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 57 average time/residue: 0.1624 time to fit residues: 11.5412 Evaluate side-chains 30 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 29 time to evaluate : 0.445 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3161 time to fit residues: 0.9299 Evaluate side-chains 22 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.121 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1715 time to fit residues: 4.1572 Evaluate side-chains 16 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.125 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1598 Evaluate side-chains 17 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.121 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1030 time to fit residues: 2.0537 Evaluate side-chains 12 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.112 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1488 Evaluate side-chains 53 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1408 time to fit residues: 10.9975 Evaluate side-chains 38 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.640 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 391 optimal weight: 0.0170 chunk 45 optimal weight: 0.8980 chunk 231 optimal weight: 4.9990 chunk 296 optimal weight: 0.0570 chunk 229 optimal weight: 0.0670 chunk 342 optimal weight: 7.9990 chunk 226 optimal weight: 20.0000 chunk 404 optimal weight: 0.0770 chunk 253 optimal weight: 0.0060 chunk 246 optimal weight: 4.9990 chunk 186 optimal weight: 0.0870 overall best weight: 0.0448 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5874 moved from start: 4.5855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.295 33735 Z= 0.715 Angle : 1.634 28.373 45876 Z= 0.863 Chirality : 0.086 1.189 5091 Planarity : 0.013 0.243 5961 Dihedral : 9.705 133.605 4629 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 40.86 Ramachandran Plot: Outliers : 0.92 % Allowed : 9.30 % Favored : 89.78 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.53 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.37 % Twisted Proline : 1.47 % Twisted General : 1.49 % 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: -1.58 (0.12), residues: 4227 helix: -0.93 (0.18), residues: 663 sheet: -0.57 (0.15), residues: 1083 loop : -1.30 (0.12), residues: 2481 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7294 Ramachandran restraints generated. 3647 Oldfield, 0 Emsley, 3647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7294 Ramachandran restraints generated. 3647 Oldfield, 0 Emsley, 3647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 45 average time/residue: 0.1260 time to fit residues: 7.5211 Evaluate side-chains 31 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 30 time to evaluate : 0.433 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0403 time to fit residues: 0.6566 Evaluate side-chains 20 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.118 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.1924 time to fit residues: 4.1986 Evaluate side-chains 14 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.115 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1508 Evaluate side-chains 14 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.103 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.1088 time to fit residues: 1.7880 Evaluate side-chains 11 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.102 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1360 Evaluate side-chains 51 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1346 time to fit residues: 10.1063 Evaluate side-chains 34 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.622 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 250 optimal weight: 1.9990 chunk 161 optimal weight: 9.9990 chunk 241 optimal weight: 2.9990 chunk 121 optimal weight: 0.4980 chunk 79 optimal weight: 0.5980 chunk 78 optimal weight: 8.9990 chunk 257 optimal weight: 8.9990 chunk 275 optimal weight: 0.7980 chunk 200 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 318 optimal weight: 0.4980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 819 GLN ** D1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 319 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5876 moved from start: 4.5899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.268 33735 Z= 0.656 Angle : 1.577 24.066 45876 Z= 0.839 Chirality : 0.083 0.989 5091 Planarity : 0.012 0.231 5961 Dihedral : 9.713 133.483 4629 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 40.05 Ramachandran Plot: Outliers : 1.21 % Allowed : 9.16 % Favored : 89.64 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.68 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.37 % Twisted Proline : 1.47 % Twisted General : 1.63 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.12), residues: 4227 helix: -1.15 (0.18), residues: 684 sheet: -0.53 (0.15), residues: 1095 loop : -1.29 (0.13), residues: 2448 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7294 Ramachandran restraints generated. 3647 Oldfield, 0 Emsley, 3647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7294 Ramachandran restraints generated. 3647 Oldfield, 0 Emsley, 3647 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 fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 41 average time/residue: 0.1373 time to fit residues: 7.4872 Evaluate side-chains 30 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 29 time to evaluate : 0.403 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0804 time to fit residues: 0.6970 Evaluate side-chains 20 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.104 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.2249 time to fit residues: 4.8673 Evaluate side-chains 13 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.113 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1490 Evaluate side-chains 14 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.110 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.1024 time to fit residues: 1.7002 Evaluate side-chains 10 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.094 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1366 Evaluate side-chains 48 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1376 time to fit residues: 9.8611 Evaluate side-chains 35 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.621 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 368 optimal weight: 0.0470 chunk 387 optimal weight: 0.8980 chunk 353 optimal weight: 0.0980 chunk 377 optimal weight: 0.0470 chunk 227 optimal weight: 9.9990 chunk 164 optimal weight: 9.9990 chunk 296 optimal weight: 0.0020 chunk 115 optimal weight: 7.9990 chunk 340 optimal weight: 0.9980 chunk 356 optimal weight: 0.0270 chunk 375 optimal weight: 0.0050 overall best weight: 0.0256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... 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 319 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5870 moved from start: 4.5946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.270 33735 Z= 0.636 Angle : 1.532 25.774 45876 Z= 0.820 Chirality : 0.080 0.995 5091 Planarity : 0.012 0.249 5961 Dihedral : 9.708 133.363 4629 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 38.70 Ramachandran Plot: Outliers : 1.06 % Allowed : 9.51 % Favored : 89.43 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.76 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.37 % Twisted Proline : 1.47 % Twisted General : 1.63 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.12), residues: 4227 helix: -1.24 (0.18), residues: 681 sheet: -0.58 (0.15), residues: 1110 loop : -1.33 (0.13), residues: 2436 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7294 Ramachandran restraints generated. 3647 Oldfield, 0 Emsley, 3647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7294 Ramachandran restraints generated. 3647 Oldfield, 0 Emsley, 3647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.423 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1444 time to fit residues: 8.4259 Evaluate side-chains 29 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.471 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7727 Evaluate side-chains 19 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.109 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1941 time to fit residues: 4.0148 Evaluate side-chains 14 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.107 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1518 Evaluate side-chains 15 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.103 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1052 time to fit residues: 1.9277 Evaluate side-chains 10 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.145 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1815 Evaluate side-chains 52 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 52 average time/residue: 0.1428 time to fit residues: 10.9342 Evaluate side-chains 37 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.654 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.0580 time to fit residues: 1.0223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 675, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 771, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.3835 > 50: distance: 1 - 2: 3.409 distance: 1 - 3: 44.722 distance: 4 - 5: 39.053 distance: 5 - 6: 44.359 distance: 5 - 8: 44.362 distance: 6 - 7: 14.766 distance: 6 - 10: 47.281 distance: 8 - 9: 42.672 distance: 11 - 12: 40.983 distance: 11 - 14: 45.334 distance: 12 - 13: 26.132 distance: 12 - 18: 49.072 distance: 14 - 15: 43.684 distance: 14 - 16: 44.465 distance: 15 - 17: 48.643 distance: 18 - 19: 31.311 distance: 19 - 20: 35.506 distance: 19 - 22: 26.110 distance: 20 - 21: 3.093 distance: 20 - 23: 48.582 distance: 23 - 24: 7.790 distance: 23 - 29: 21.174 distance: 24 - 27: 40.639 distance: 25 - 30: 45.367 distance: 28 - 29: 48.992 distance: 30 - 31: 8.682 distance: 31 - 32: 40.329 distance: 31 - 34: 29.825 distance: 32 - 33: 31.367 distance: 32 - 37: 39.189 distance: 34 - 35: 6.977 distance: 34 - 36: 55.508 distance: 37 - 38: 47.518 distance: 38 - 39: 23.642 distance: 38 - 41: 40.779 distance: 39 - 45: 52.469 distance: 41 - 42: 49.056 distance: 42 - 43: 17.713 distance: 45 - 46: 67.136 distance: 46 - 47: 40.777 distance: 47 - 48: 56.166 distance: 50 - 51: 47.359 distance: 50 - 53: 14.293 distance: 51 - 52: 26.708 distance: 51 - 61: 30.115 distance: 53 - 54: 48.248 distance: 54 - 55: 36.425 distance: 54 - 56: 9.496 distance: 55 - 57: 49.685 distance: 56 - 58: 41.538 distance: 57 - 59: 15.079 distance: 58 - 59: 22.731 distance: 59 - 60: 44.967 distance: 61 - 62: 40.879 distance: 62 - 63: 23.518 distance: 62 - 65: 4.910 distance: 63 - 64: 46.589 distance: 63 - 72: 45.914 distance: 66 - 67: 13.586 distance: 67 - 69: 12.732 distance: 68 - 70: 17.296 distance: 69 - 71: 34.430 distance: 70 - 71: 19.914 distance: 73 - 74: 38.566 distance: 74 - 75: 6.103 distance: 76 - 77: 4.370 distance: 76 - 78: 42.529 distance: 77 - 79: 22.381