Starting phenix.real_space_refine on Sun Mar 24 04:02:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbw_6489/03_2024/3jbw_6489_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbw_6489/03_2024/3jbw_6489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbw_6489/03_2024/3jbw_6489.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbw_6489/03_2024/3jbw_6489.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbw_6489/03_2024/3jbw_6489_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbw_6489/03_2024/3jbw_6489_neut.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 19997 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 222 5.49 5 S 112 5.16 5 C 11864 2.51 5 N 3575 2.21 5 O 4222 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 477": "NH1" <-> "NH2" Residue "A ARG 490": "NH1" <-> "NH2" Residue "A TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 505": "NH1" <-> "NH2" Residue "A ARG 513": "NH1" <-> "NH2" Residue "A ARG 641": "NH1" <-> "NH2" Residue "A GLU 741": "OE1" <-> "OE2" Residue "A ARG 756": "NH1" <-> "NH2" Residue "A ARG 795": "NH1" <-> "NH2" Residue "A GLU 846": "OE1" <-> "OE2" Residue "A ARG 870": "NH1" <-> "NH2" Residue "A ARG 971": "NH1" <-> "NH2" Residue "A ARG 991": "NH1" <-> "NH2" Residue "A ARG 999": "NH1" <-> "NH2" Residue "B ARG 49": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 114": "NH1" <-> "NH2" Residue "B ARG 123": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 167": "NH1" <-> "NH2" Residue "B ARG 232": "NH1" <-> "NH2" Residue "B ARG 235": "NH1" <-> "NH2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B ARG 315": "NH1" <-> "NH2" Residue "C ARG 505": "NH1" <-> "NH2" Residue "C ARG 513": "NH1" <-> "NH2" Residue "C TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 641": "NH1" <-> "NH2" Residue "C PHE 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 708": "NH1" <-> "NH2" Residue "C GLU 731": "OE1" <-> "OE2" Residue "C ARG 795": "NH1" <-> "NH2" Residue "C ARG 848": "NH1" <-> "NH2" Residue "C ARG 870": "NH1" <-> "NH2" Residue "C ARG 971": "NH1" <-> "NH2" Residue "C ARG 999": "NH1" <-> "NH2" Residue "C GLU 1005": "OE1" <-> "OE2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D ARG 58": "NH1" <-> "NH2" Residue "D ARG 96": "NH1" <-> "NH2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D ARG 118": "NH1" <-> "NH2" Residue "D ARG 123": "NH1" <-> "NH2" Residue "D GLU 125": "OE1" <-> "OE2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D ARG 167": "NH1" <-> "NH2" Residue "D ARG 232": "NH1" <-> "NH2" Residue "D ARG 235": "NH1" <-> "NH2" Residue "D GLU 280": "OE1" <-> "OE2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D ARG 315": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19997 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 5008 Classifications: {'peptide': 622} Link IDs: {'CIS': 6, 'PCIS': 2, 'PTRANS': 20, 'TRANS': 593} Chain: "B" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2714 Classifications: {'peptide': 351} Link IDs: {'CIS': 9, 'PCIS': 2, 'PTRANS': 22, 'TRANS': 317} Chain: "C" Number of atoms: 5008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 5008 Classifications: {'peptide': 622} Link IDs: {'CIS': 6, 'PCIS': 2, 'PTRANS': 20, 'TRANS': 593} Chain: "D" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2714 Classifications: {'peptide': 351} Link IDs: {'CIS': 9, 'PCIS': 2, 'PTRANS': 22, 'TRANS': 317} Chain: "E" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 697 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "F" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1027 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "G" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1256 Classifications: {'DNA': 61} Link IDs: {'rna3p': 60} Chain: "H" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 919 Classifications: {'DNA': 45} Link IDs: {'rna3p': 44} Chain: "I" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 326 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "J" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 326 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2680 SG CYS A 749 81.650 59.752 105.359 1.00130.76 S ATOM 10402 SG CYS C 749 23.075 92.261 100.786 1.00110.57 S Residues with excluded nonbonded symmetry interactions: 29 residue: pdb=" P DA E 22 " occ=0.96 ... (19 atoms not shown) pdb=" C4 DA E 22 " occ=0.96 residue: pdb=" P DA E 23 " occ=0.75 ... (19 atoms not shown) pdb=" C4 DA E 23 " occ=0.75 residue: pdb=" P DA E 24 " occ=0.71 ... (19 atoms not shown) pdb=" C4 DA E 24 " occ=0.71 residue: pdb=" P DA E 25 " occ=0.93 ... (19 atoms not shown) pdb=" C4 DA E 25 " occ=0.93 residue: pdb=" P DA E 26 " occ=0.90 ... (19 atoms not shown) pdb=" C4 DA E 26 " occ=0.90 residue: pdb=" P DC E 28 " occ=0.84 ... (17 atoms not shown) pdb=" C6 DC E 28 " occ=0.84 residue: pdb=" P DG F 7 " occ=0.69 ... (20 atoms not shown) pdb=" C4 DG F 7 " occ=0.69 residue: pdb=" P DG F 8 " occ=0.61 ... (20 atoms not shown) pdb=" C4 DG F 8 " occ=0.61 residue: pdb=" P DT F 9 " occ=0.71 ... (18 atoms not shown) pdb=" C6 DT F 9 " occ=0.71 residue: pdb=" P DT F 10 " occ=0.72 ... (18 atoms not shown) pdb=" C6 DT F 10 " occ=0.72 residue: pdb=" P DT F 11 " occ=0.80 ... (18 atoms not shown) pdb=" C6 DT F 11 " occ=0.80 residue: pdb=" P DT F 12 " occ=0.75 ... (18 atoms not shown) pdb=" C6 DT F 12 " occ=0.75 ... (remaining 17 not shown) Time building chain proxies: 10.16, per 1000 atoms: 0.51 Number of scatterers: 19997 At special positions: 0 Unit cell: (108.24, 153.75, 161.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 112 16.00 P 222 15.00 O 4222 8.00 N 3575 7.00 C 11864 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 8.82 Conformation dependent library (CDL) restraints added in 2.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 749 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 964 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 959 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 964 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 749 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 959 " 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3612 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 19 sheets defined 37.0% alpha, 21.5% beta 59 base pairs and 164 stacking pairs defined. Time for finding SS restraints: 7.06 Creating SS restraints... Processing helix chain 'A' and resid 414 through 418 Processing helix chain 'A' and resid 420 through 426 removed outlier: 4.253A pdb=" N HIS A 425 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 442 removed outlier: 3.924A pdb=" N GLU A 439 " --> pdb=" O LYS A 435 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LYS A 440 " --> pdb=" O THR A 436 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU A 441 " --> pdb=" O PHE A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 459 removed outlier: 4.565A pdb=" N VAL A 449 " --> pdb=" O ASP A 445 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N CYS A 450 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU A 456 " --> pdb=" O THR A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 473 removed outlier: 4.173A pdb=" N GLU A 469 " --> pdb=" O LYS A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 492 Processing helix chain 'A' and resid 496 through 510 Processing helix chain 'A' and resid 518 through 524 Processing helix chain 'A' and resid 577 through 588 Processing helix chain 'A' and resid 589 through 600 Processing helix chain 'A' and resid 686 through 707 removed outlier: 3.948A pdb=" N LEU A 690 " --> pdb=" O ASP A 686 " (cutoff:3.500A) Proline residue: A 696 - end of helix removed outlier: 4.594A pdb=" N GLU A 706 " --> pdb=" O LYS A 702 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N SER A 707 " --> pdb=" O ALA A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 738 Processing helix chain 'A' and resid 755 through 762 Processing helix chain 'A' and resid 771 through 785 Processing helix chain 'A' and resid 790 through 799 removed outlier: 3.778A pdb=" N ASP A 796 " --> pdb=" O ASP A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 835 removed outlier: 4.163A pdb=" N GLY A 835 " --> pdb=" O GLN A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 862 Processing helix chain 'A' and resid 872 through 880 removed outlier: 3.712A pdb=" N MET A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 889 Processing helix chain 'A' and resid 894 through 917 removed outlier: 3.798A pdb=" N GLU A 899 " --> pdb=" O GLU A 895 " (cutoff:3.500A) Proline residue: A 913 - end of helix Processing helix chain 'A' and resid 919 through 924 Processing helix chain 'A' and resid 924 through 930 Processing helix chain 'A' and resid 930 through 946 Processing helix chain 'A' and resid 946 through 951 removed outlier: 3.785A pdb=" N TYR A 950 " --> pdb=" O PHE A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 964 Processing helix chain 'A' and resid 964 through 972 Processing helix chain 'A' and resid 975 through 979 Processing helix chain 'A' and resid 980 through 985 Processing helix chain 'A' and resid 986 through 996 Processing helix chain 'A' and resid 1004 through 1017 removed outlier: 3.560A pdb=" N ASP A1008 " --> pdb=" O PHE A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1023 removed outlier: 3.826A pdb=" N GLN A1022 " --> pdb=" O SER A1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 314 Processing helix chain 'C' and resid 419 through 443 removed outlier: 4.334A pdb=" N GLN C 423 " --> pdb=" O THR C 419 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N HIS C 425 " --> pdb=" O ARG C 421 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ASP C 429 " --> pdb=" O HIS C 425 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU C 430 " --> pdb=" O ARG C 426 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY C 443 " --> pdb=" O GLU C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 460 removed outlier: 3.609A pdb=" N THR C 452 " --> pdb=" O SER C 448 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N PHE C 454 " --> pdb=" O CYS C 450 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LEU C 455 " --> pdb=" O LEU C 451 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU C 456 " --> pdb=" O THR C 452 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA C 457 " --> pdb=" O LEU C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 473 removed outlier: 4.161A pdb=" N MET C 473 " --> pdb=" O GLU C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 494 Processing helix chain 'C' and resid 496 through 510 Processing helix chain 'C' and resid 518 through 524 removed outlier: 3.529A pdb=" N LEU C 522 " --> pdb=" O PRO C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 589 Processing helix chain 'C' and resid 589 through 601 Processing helix chain 'C' and resid 686 through 705 removed outlier: 3.821A pdb=" N LEU C 690 " --> pdb=" O ASP C 686 " (cutoff:3.500A) Proline residue: C 696 - end of helix Processing helix chain 'C' and resid 730 through 738 Processing helix chain 'C' and resid 757 through 762 Processing helix chain 'C' and resid 771 through 785 Processing helix chain 'C' and resid 790 through 798 Processing helix chain 'C' and resid 814 through 835 removed outlier: 3.684A pdb=" N CYS C 818 " --> pdb=" O ASP C 814 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY C 835 " --> pdb=" O GLN C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 862 Processing helix chain 'C' and resid 872 through 881 removed outlier: 3.960A pdb=" N THR C 881 " --> pdb=" O ARG C 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 881 through 890 removed outlier: 3.737A pdb=" N ALA C 887 " --> pdb=" O GLU C 883 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL C 888 " --> pdb=" O ALA C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 917 removed outlier: 3.668A pdb=" N LEU C 902 " --> pdb=" O ARG C 898 " (cutoff:3.500A) Proline residue: C 913 - end of helix Processing helix chain 'C' and resid 919 through 924 Processing helix chain 'C' and resid 924 through 930 removed outlier: 3.571A pdb=" N LEU C 928 " --> pdb=" O CYS C 924 " (cutoff:3.500A) Processing helix chain 'C' and resid 930 through 946 Processing helix chain 'C' and resid 946 through 951 removed outlier: 3.684A pdb=" N TYR C 950 " --> pdb=" O PHE C 946 " (cutoff:3.500A) Processing helix chain 'C' and resid 955 through 964 Processing helix chain 'C' and resid 964 through 973 Processing helix chain 'C' and resid 980 through 985 Processing helix chain 'C' and resid 986 through 993 Processing helix chain 'C' and resid 1001 through 1018 removed outlier: 4.729A pdb=" N LEU C1006 " --> pdb=" O LYS C1002 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N GLU C1007 " --> pdb=" O THR C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1018 through 1027 removed outlier: 3.786A pdb=" N GLN C1022 " --> pdb=" O SER C1018 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE C1024 " --> pdb=" O TYR C1020 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA C1027 " --> pdb=" O LYS C1023 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 314 Processing sheet with id= A, first strand: chain 'A' and resid 536 through 539 removed outlier: 6.657A pdb=" N THR A 612 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE A 649 " --> pdb=" O THR A 612 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL A 614 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL A 640 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU A 679 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N PHE A 642 " --> pdb=" O LEU A 677 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 536 through 539 removed outlier: 6.657A pdb=" N THR A 612 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE A 649 " --> pdb=" O THR A 612 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL A 614 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N MET A 647 " --> pdb=" O GLN A 664 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLN A 664 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE A 649 " --> pdb=" O ILE A 662 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 2 through 6 removed outlier: 3.739A pdb=" N PHE B 345 " --> pdb=" O LEU B 6 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N THR B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 20 through 23 removed outlier: 4.471A pdb=" N VAL B 28 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 61 through 62 removed outlier: 6.742A pdb=" N SER B 61 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N CYS B 124 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N THR B 121 " --> pdb=" O ASP B 112 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 141 through 147 Processing sheet with id= G, first strand: chain 'B' and resid 159 through 161 Processing sheet with id= H, first strand: chain 'B' and resid 209 through 212 Processing sheet with id= I, first strand: chain 'B' and resid 263 through 265 Processing sheet with id= J, first strand: chain 'C' and resid 536 through 539 removed outlier: 6.494A pdb=" N THR C 612 " --> pdb=" O ILE C 649 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE C 649 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL C 614 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL C 640 " --> pdb=" O LEU C 679 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LEU C 679 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE C 642 " --> pdb=" O LEU C 677 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 536 through 539 removed outlier: 6.494A pdb=" N THR C 612 " --> pdb=" O ILE C 649 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE C 649 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL C 614 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N MET C 647 " --> pdb=" O GLN C 664 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLN C 664 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE C 649 " --> pdb=" O ILE C 662 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 2 through 6 removed outlier: 3.770A pdb=" N PHE D 345 " --> pdb=" O LEU D 6 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N THR D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE D 318 " --> pdb=" O ALA D 330 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 20 through 23 removed outlier: 4.559A pdb=" N VAL D 28 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 76 through 80 removed outlier: 4.480A pdb=" N LEU D 106 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR D 121 " --> pdb=" O ASP D 112 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 96 through 97 removed outlier: 3.669A pdb=" N GLU D 101 " --> pdb=" O THR D 97 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 141 through 147 Processing sheet with id= Q, first strand: chain 'D' and resid 159 through 161 Processing sheet with id= R, first strand: chain 'D' and resid 209 through 212 removed outlier: 3.628A pdb=" N LEU D 233 " --> pdb=" O LEU D 252 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 263 through 265 removed outlier: 4.195A pdb=" N CYS D 287 " --> pdb=" O ARG D 302 " (cutoff:3.500A) 721 hydrogen bonds defined for protein. 2004 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 141 hydrogen bonds 262 hydrogen bond angles 0 basepair planarities 59 basepair parallelities 164 stacking parallelities Total time for adding SS restraints: 10.50 Time building geometry restraints manager: 9.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2914 1.32 - 1.45: 6824 1.45 - 1.58: 10519 1.58 - 1.71: 452 1.71 - 1.84: 171 Bond restraints: 20880 Sorted by residual: bond pdb=" O3' DA H 2 " pdb=" P DC H 3 " ideal model delta sigma weight residual 1.607 1.767 -0.160 1.50e-02 4.44e+03 1.14e+02 bond pdb=" P DT G 42 " pdb=" O5' DT G 42 " ideal model delta sigma weight residual 1.600 1.395 0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" O3' DC G 41 " pdb=" P DT G 42 " ideal model delta sigma weight residual 1.607 1.742 -0.135 1.50e-02 4.44e+03 8.08e+01 bond pdb=" C3' DA H 2 " pdb=" O3' DA H 2 " ideal model delta sigma weight residual 1.422 1.684 -0.262 3.00e-02 1.11e+03 7.64e+01 bond pdb=" C3' DG G 45 " pdb=" O3' DG G 45 " ideal model delta sigma weight residual 1.422 1.659 -0.237 3.00e-02 1.11e+03 6.24e+01 ... (remaining 20875 not shown) Histogram of bond angle deviations from ideal: 85.67 - 96.00: 2 96.00 - 106.33: 2087 106.33 - 116.66: 13682 116.66 - 126.99: 12674 126.99 - 137.32: 714 Bond angle restraints: 29159 Sorted by residual: angle pdb=" N ARG C 420 " pdb=" CA ARG C 420 " pdb=" C ARG C 420 " ideal model delta sigma weight residual 111.33 131.50 -20.17 1.21e+00 6.83e-01 2.78e+02 angle pdb=" N ALA C 422 " pdb=" CA ALA C 422 " pdb=" C ALA C 422 " ideal model delta sigma weight residual 113.43 92.89 20.54 1.26e+00 6.30e-01 2.66e+02 angle pdb=" N ARG C 999 " pdb=" CA ARG C 999 " pdb=" C ARG C 999 " ideal model delta sigma weight residual 111.07 124.38 -13.31 1.07e+00 8.73e-01 1.55e+02 angle pdb=" N ASP C 468 " pdb=" CA ASP C 468 " pdb=" C ASP C 468 " ideal model delta sigma weight residual 111.14 123.22 -12.08 1.08e+00 8.57e-01 1.25e+02 angle pdb=" N ARG A 426 " pdb=" CA ARG A 426 " pdb=" C ARG A 426 " ideal model delta sigma weight residual 111.69 124.20 -12.51 1.23e+00 6.61e-01 1.03e+02 ... (remaining 29154 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 10922 35.99 - 71.98: 1038 71.98 - 107.96: 33 107.96 - 143.95: 3 143.95 - 179.94: 4 Dihedral angle restraints: 12000 sinusoidal: 6384 harmonic: 5616 Sorted by residual: dihedral pdb=" CA ASN A 462 " pdb=" C ASN A 462 " pdb=" N GLU A 463 " pdb=" CA GLU A 463 " ideal model delta harmonic sigma weight residual 180.00 139.75 40.25 0 5.00e+00 4.00e-02 6.48e+01 dihedral pdb=" CA ARG C 477 " pdb=" C ARG C 477 " pdb=" N GLY C 478 " pdb=" CA GLY C 478 " ideal model delta harmonic sigma weight residual -180.00 -146.07 -33.93 0 5.00e+00 4.00e-02 4.60e+01 dihedral pdb=" C ARG C 421 " pdb=" N ARG C 421 " pdb=" CA ARG C 421 " pdb=" CB ARG C 421 " ideal model delta harmonic sigma weight residual -122.60 -138.36 15.76 0 2.50e+00 1.60e-01 3.98e+01 ... (remaining 11997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.152: 3042 0.152 - 0.304: 131 0.304 - 0.456: 12 0.456 - 0.608: 5 0.608 - 0.760: 2 Chirality restraints: 3192 Sorted by residual: chirality pdb=" CA ARG C 421 " pdb=" N ARG C 421 " pdb=" C ARG C 421 " pdb=" CB ARG C 421 " both_signs ideal model delta sigma weight residual False 2.51 1.75 0.76 2.00e-01 2.50e+01 1.44e+01 chirality pdb=" P DC H 3 " pdb=" OP1 DC H 3 " pdb=" OP2 DC H 3 " pdb=" O5' DC H 3 " both_signs ideal model delta sigma weight residual True 2.35 -3.00 -0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CG LEU A 451 " pdb=" CB LEU A 451 " pdb=" CD1 LEU A 451 " pdb=" CD2 LEU A 451 " both_signs ideal model delta sigma weight residual False -2.59 -3.16 0.57 2.00e-01 2.50e+01 8.19e+00 ... (remaining 3189 not shown) Planarity restraints: 2994 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA H 2 " -0.069 2.00e-02 2.50e+03 3.17e-02 2.77e+01 pdb=" N9 DA H 2 " -0.004 2.00e-02 2.50e+03 pdb=" C8 DA H 2 " 0.049 2.00e-02 2.50e+03 pdb=" N7 DA H 2 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DA H 2 " 0.018 2.00e-02 2.50e+03 pdb=" C6 DA H 2 " -0.002 2.00e-02 2.50e+03 pdb=" N6 DA H 2 " -0.037 2.00e-02 2.50e+03 pdb=" N1 DA H 2 " -0.018 2.00e-02 2.50e+03 pdb=" C2 DA H 2 " 0.008 2.00e-02 2.50e+03 pdb=" N3 DA H 2 " 0.030 2.00e-02 2.50e+03 pdb=" C4 DA H 2 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 450 " -0.026 2.00e-02 2.50e+03 5.25e-02 2.76e+01 pdb=" C CYS A 450 " 0.091 2.00e-02 2.50e+03 pdb=" O CYS A 450 " -0.034 2.00e-02 2.50e+03 pdb=" N LEU A 451 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 480 " 0.024 2.00e-02 2.50e+03 4.68e-02 2.19e+01 pdb=" C GLY A 480 " -0.081 2.00e-02 2.50e+03 pdb=" O GLY A 480 " 0.030 2.00e-02 2.50e+03 pdb=" N LEU A 481 " 0.027 2.00e-02 2.50e+03 ... (remaining 2991 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 221 2.56 - 3.15: 16056 3.15 - 3.73: 32711 3.73 - 4.32: 45489 4.32 - 4.90: 70294 Nonbonded interactions: 164771 Sorted by model distance: nonbonded pdb=" NZ LYS B 119 " pdb=" OP1 DG J 6 " model vdw 1.977 2.520 nonbonded pdb=" C3' DT G 12 " pdb=" OP2 DT G 13 " model vdw 2.058 2.776 nonbonded pdb=" OP1 DT G 42 " pdb=" C5' DT G 42 " model vdw 2.060 2.752 nonbonded pdb=" O2 DC E 15 " pdb=" N2 DG F 20 " model vdw 2.066 2.496 nonbonded pdb=" NE2 GLN A 858 " pdb=" O ALA A 887 " model vdw 2.101 2.520 ... (remaining 164766 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 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.07 max=1.00 mean=0.99 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: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.250 Construct map_model_manager: 0.010 Extract box with map and model: 2.570 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 63.820 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 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 0.262 20880 Z= 0.748 Angle : 1.698 29.321 29159 Z= 1.029 Chirality : 0.076 0.760 3192 Planarity : 0.007 0.053 2994 Dihedral : 21.901 179.939 8388 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 22.69 Ramachandran Plot: Outliers : 0.88 % Allowed : 5.57 % Favored : 93.55 % Rotamer: Outliers : 4.88 % Allowed : 12.04 % Favored : 83.08 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 1.57 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.37 (0.14), residues: 1938 helix: -2.83 (0.15), residues: 613 sheet: -0.91 (0.25), residues: 326 loop : -2.29 (0.14), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP C 978 HIS 0.022 0.003 HIS A 414 PHE 0.042 0.004 PHE C 454 TYR 0.025 0.003 TYR A 908 ARG 0.068 0.002 ARG C 459 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 629 time to evaluate : 1.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 ARG cc_start: 0.4529 (ptt-90) cc_final: 0.3231 (tpm170) REVERT: A 425 HIS cc_start: 0.8275 (t-90) cc_final: 0.7510 (m170) REVERT: A 430 LEU cc_start: 0.8658 (mt) cc_final: 0.8179 (mt) REVERT: A 432 ASN cc_start: 0.9136 (t0) cc_final: 0.8661 (t0) REVERT: A 456 LEU cc_start: 0.6555 (OUTLIER) cc_final: 0.5831 (tt) REVERT: A 524 ASN cc_start: 0.8994 (t0) cc_final: 0.8502 (t0) REVERT: A 527 LYS cc_start: 0.9006 (mttm) cc_final: 0.7966 (tptt) REVERT: A 572 ILE cc_start: 0.9567 (mt) cc_final: 0.9094 (tt) REVERT: A 599 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7588 (tp30) REVERT: A 664 GLN cc_start: 0.8135 (tt0) cc_final: 0.7834 (tp40) REVERT: A 671 GLU cc_start: 0.8495 (mm-30) cc_final: 0.7733 (pm20) REVERT: A 672 LEU cc_start: 0.9190 (mt) cc_final: 0.8828 (mt) REVERT: A 690 LEU cc_start: 0.9605 (tp) cc_final: 0.9269 (tp) REVERT: A 704 MET cc_start: 0.9277 (ttm) cc_final: 0.8919 (mtp) REVERT: A 801 VAL cc_start: 0.8965 (t) cc_final: 0.8652 (t) REVERT: A 820 ILE cc_start: 0.9336 (mt) cc_final: 0.9098 (pt) REVERT: A 905 MET cc_start: 0.8292 (tpp) cc_final: 0.7931 (tmm) REVERT: A 911 MET cc_start: 0.9619 (ptm) cc_final: 0.8662 (mtm) REVERT: A 947 LYS cc_start: 0.8857 (tttt) cc_final: 0.8481 (tppt) REVERT: A 956 ASN cc_start: 0.9269 (m-40) cc_final: 0.8434 (m-40) REVERT: A 960 LYS cc_start: 0.9231 (mttt) cc_final: 0.8340 (mmtm) REVERT: A 1005 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8271 (pp20) REVERT: A 1023 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8682 (tmtt) REVERT: B 19 PHE cc_start: 0.9178 (p90) cc_final: 0.8865 (p90) REVERT: B 64 ASN cc_start: 0.9280 (m-40) cc_final: 0.8971 (m-40) REVERT: B 109 LEU cc_start: 0.9210 (tt) cc_final: 0.8921 (mm) REVERT: B 146 ASN cc_start: 0.7170 (m-40) cc_final: 0.6838 (t0) REVERT: B 162 MET cc_start: 0.8905 (mtt) cc_final: 0.8527 (ptp) REVERT: B 173 ASN cc_start: 0.8850 (t0) cc_final: 0.8527 (t0) REVERT: B 199 GLU cc_start: 0.8795 (mm-30) cc_final: 0.7553 (tt0) REVERT: B 213 GLN cc_start: 0.8153 (tp-100) cc_final: 0.7827 (pp30) REVERT: B 214 ASP cc_start: 0.7607 (p0) cc_final: 0.6463 (p0) REVERT: B 266 ILE cc_start: 0.5853 (OUTLIER) cc_final: 0.5410 (mt) REVERT: B 273 ILE cc_start: 0.8697 (mm) cc_final: 0.8273 (tp) REVERT: B 289 TYR cc_start: 0.7972 (t80) cc_final: 0.7762 (t80) REVERT: B 317 TRP cc_start: 0.7954 (p-90) cc_final: 0.7651 (p-90) REVERT: B 334 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7681 (tp30) REVERT: B 347 GLN cc_start: 0.8390 (tt0) cc_final: 0.8139 (tm-30) REVERT: C 421 ARG cc_start: 0.3170 (OUTLIER) cc_final: 0.1670 (tmm-80) REVERT: C 455 LEU cc_start: 0.7973 (mp) cc_final: 0.7466 (tp) REVERT: C 464 HIS cc_start: 0.6222 (OUTLIER) cc_final: 0.5991 (p-80) REVERT: C 489 ILE cc_start: 0.9018 (mt) cc_final: 0.8788 (mm) REVERT: C 543 LYS cc_start: 0.8785 (mttt) cc_final: 0.8532 (mmmm) REVERT: C 545 VAL cc_start: 0.9249 (t) cc_final: 0.8785 (t) REVERT: C 578 TYR cc_start: 0.8483 (t80) cc_final: 0.8056 (t80) REVERT: C 594 MET cc_start: 0.8643 (mmm) cc_final: 0.8014 (mtp) REVERT: C 620 ASP cc_start: 0.9059 (t0) cc_final: 0.8056 (p0) REVERT: C 622 MET cc_start: 0.7819 (ttp) cc_final: 0.7451 (ttm) REVERT: C 649 ILE cc_start: 0.9328 (OUTLIER) cc_final: 0.9078 (tt) REVERT: C 669 ASN cc_start: 0.8759 (m-40) cc_final: 0.7985 (m-40) REVERT: C 677 LEU cc_start: 0.9420 (tt) cc_final: 0.9127 (tp) REVERT: C 679 LEU cc_start: 0.9318 (mp) cc_final: 0.8881 (mp) REVERT: C 686 ASP cc_start: 0.8338 (p0) cc_final: 0.7672 (p0) REVERT: C 698 VAL cc_start: 0.9260 (t) cc_final: 0.8940 (p) REVERT: C 712 SER cc_start: 0.8996 (p) cc_final: 0.8758 (m) REVERT: C 730 ASP cc_start: 0.8992 (p0) cc_final: 0.8272 (m-30) REVERT: C 732 LYS cc_start: 0.9008 (tttt) cc_final: 0.8675 (ttmm) REVERT: C 831 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.8704 (tp40) REVERT: C 868 VAL cc_start: 0.8399 (m) cc_final: 0.8063 (m) REVERT: C 871 MET cc_start: 0.8124 (ttp) cc_final: 0.7737 (ttp) REVERT: C 896 GLU cc_start: 0.8473 (mp0) cc_final: 0.7933 (pm20) REVERT: C 905 MET cc_start: 0.8214 (tpp) cc_final: 0.7788 (tmm) REVERT: C 909 LEU cc_start: 0.8684 (mt) cc_final: 0.8333 (mt) REVERT: C 915 TRP cc_start: 0.9156 (p-90) cc_final: 0.7849 (p-90) REVERT: C 926 ASP cc_start: 0.9123 (p0) cc_final: 0.8860 (p0) REVERT: C 983 ASN cc_start: 0.8914 (t0) cc_final: 0.8570 (t0) REVERT: C 985 SER cc_start: 0.9500 (m) cc_final: 0.9205 (p) REVERT: C 989 LEU cc_start: 0.9329 (mt) cc_final: 0.9062 (mt) REVERT: C 995 LYS cc_start: 0.9442 (mtmm) cc_final: 0.9126 (mmtm) REVERT: C 1005 GLU cc_start: 0.8769 (tt0) cc_final: 0.8471 (mt-10) REVERT: C 1006 LEU cc_start: 0.8596 (mt) cc_final: 0.8206 (mp) REVERT: C 1020 TYR cc_start: 0.8976 (t80) cc_final: 0.8763 (t80) REVERT: D 1 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.8177 (mtt) REVERT: D 16 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7777 (pt0) REVERT: D 29 TYR cc_start: 0.8493 (m-80) cc_final: 0.8216 (m-80) REVERT: D 39 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7405 (tpt-90) REVERT: D 55 LEU cc_start: 0.9151 (tp) cc_final: 0.8914 (tt) REVERT: D 60 ILE cc_start: 0.9276 (mm) cc_final: 0.8934 (mt) REVERT: D 69 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.7771 (mt) REVERT: D 117 ASN cc_start: 0.7866 (t0) cc_final: 0.7043 (p0) REVERT: D 148 ARG cc_start: 0.8173 (ttm110) cc_final: 0.7322 (ptt90) REVERT: D 162 MET cc_start: 0.8847 (tpt) cc_final: 0.8554 (tpp) REVERT: D 188 GLU cc_start: 0.7841 (tp30) cc_final: 0.7586 (mm-30) REVERT: D 217 TYR cc_start: 0.8478 (m-80) cc_final: 0.8222 (m-10) REVERT: D 293 ASP cc_start: 0.9193 (t0) cc_final: 0.8916 (t70) REVERT: D 303 GLU cc_start: 0.8551 (tt0) cc_final: 0.8300 (tm-30) REVERT: D 310 GLU cc_start: 0.8474 (tt0) cc_final: 0.8224 (tp30) outliers start: 83 outliers final: 11 residues processed: 679 average time/residue: 0.3976 time to fit residues: 394.2535 Evaluate side-chains 360 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 336 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 8.9990 chunk 162 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 167 optimal weight: 0.0470 chunk 64 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 chunk 194 optimal weight: 6.9990 overall best weight: 3.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 629 HIS A 766 HIS A 822 ASN ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 ASN ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 831 GLN ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 937 GLN ** C1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 170 GLN D 278 GLN ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 20880 Z= 0.297 Angle : 0.849 12.627 29159 Z= 0.467 Chirality : 0.046 0.217 3192 Planarity : 0.007 0.107 2994 Dihedral : 24.814 177.505 4568 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 22.61 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.72 % Favored : 96.03 % Rotamer: Outliers : 0.35 % Allowed : 4.11 % Favored : 95.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 1.62 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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 (0.17), residues: 1938 helix: -0.73 (0.19), residues: 616 sheet: -0.15 (0.27), residues: 307 loop : -1.53 (0.17), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 560 HIS 0.010 0.002 HIS B 79 PHE 0.027 0.002 PHE B 189 TYR 0.018 0.002 TYR C 908 ARG 0.029 0.001 ARG C 421 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 425 time to evaluate : 3.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 ARG cc_start: 0.3916 (ptt-90) cc_final: 0.3251 (tpp-160) REVERT: A 418 LEU cc_start: 0.7264 (mm) cc_final: 0.6992 (mm) REVERT: A 430 LEU cc_start: 0.8560 (mt) cc_final: 0.8218 (mt) REVERT: A 473 MET cc_start: 0.8763 (ptm) cc_final: 0.8554 (ptm) REVERT: A 524 ASN cc_start: 0.9144 (t0) cc_final: 0.8914 (m110) REVERT: A 527 LYS cc_start: 0.8659 (mttm) cc_final: 0.8000 (tptt) REVERT: A 572 ILE cc_start: 0.9695 (mt) cc_final: 0.9296 (tt) REVERT: A 575 ARG cc_start: 0.7941 (ptt90) cc_final: 0.7717 (ptm-80) REVERT: A 671 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7683 (pm20) REVERT: A 698 VAL cc_start: 0.9357 (t) cc_final: 0.9111 (t) REVERT: A 704 MET cc_start: 0.9096 (ttm) cc_final: 0.8851 (ttm) REVERT: A 705 MET cc_start: 0.8699 (mmm) cc_final: 0.7866 (mmm) REVERT: A 730 ASP cc_start: 0.7258 (p0) cc_final: 0.6478 (p0) REVERT: A 774 GLU cc_start: 0.9242 (tt0) cc_final: 0.9015 (pp20) REVERT: A 851 TRP cc_start: 0.8739 (m-10) cc_final: 0.8209 (m-10) REVERT: A 911 MET cc_start: 0.9565 (ptm) cc_final: 0.9270 (ptt) REVERT: A 945 MET cc_start: 0.8579 (mtp) cc_final: 0.8323 (mmt) REVERT: A 947 LYS cc_start: 0.8872 (tttt) cc_final: 0.8434 (tppt) REVERT: A 955 THR cc_start: 0.8370 (t) cc_final: 0.7763 (m) REVERT: A 957 TYR cc_start: 0.9347 (m-80) cc_final: 0.8935 (m-80) REVERT: A 960 LYS cc_start: 0.9483 (mttt) cc_final: 0.8650 (mmtm) REVERT: A 1005 GLU cc_start: 0.8985 (pt0) cc_final: 0.8785 (pt0) REVERT: B 19 PHE cc_start: 0.9279 (p90) cc_final: 0.8741 (p90) REVERT: B 46 PHE cc_start: 0.8348 (m-80) cc_final: 0.8143 (m-80) REVERT: B 64 ASN cc_start: 0.9401 (m-40) cc_final: 0.8956 (m-40) REVERT: B 81 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7603 (mm-30) REVERT: B 92 ILE cc_start: 0.9245 (mp) cc_final: 0.9008 (mp) REVERT: B 119 LYS cc_start: 0.7668 (ttmt) cc_final: 0.6934 (mmmt) REVERT: B 124 CYS cc_start: 0.8443 (t) cc_final: 0.8142 (t) REVERT: B 146 ASN cc_start: 0.7068 (m-40) cc_final: 0.6697 (t0) REVERT: B 150 LYS cc_start: 0.9029 (mptt) cc_final: 0.8783 (mppt) REVERT: B 198 PRO cc_start: 0.8896 (Cg_exo) cc_final: 0.8337 (Cg_endo) REVERT: B 199 GLU cc_start: 0.8633 (mm-30) cc_final: 0.7659 (tt0) REVERT: B 271 TYR cc_start: 0.8704 (m-80) cc_final: 0.8450 (m-10) REVERT: B 285 MET cc_start: 0.8143 (ttm) cc_final: 0.7744 (tpp) REVERT: B 317 TRP cc_start: 0.7895 (p-90) cc_final: 0.7548 (p-90) REVERT: C 424 LYS cc_start: 0.8063 (mttt) cc_final: 0.7337 (pttt) REVERT: C 455 LEU cc_start: 0.8327 (mp) cc_final: 0.7974 (tp) REVERT: C 537 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7797 (tm-30) REVERT: C 594 MET cc_start: 0.8376 (mmm) cc_final: 0.8122 (mtp) REVERT: C 619 CYS cc_start: 0.9244 (t) cc_final: 0.8984 (p) REVERT: C 753 ASP cc_start: 0.9042 (m-30) cc_final: 0.8410 (m-30) REVERT: C 812 THR cc_start: 0.8728 (t) cc_final: 0.8379 (t) REVERT: C 872 ASN cc_start: 0.9509 (p0) cc_final: 0.9113 (p0) REVERT: C 903 LYS cc_start: 0.9241 (tptt) cc_final: 0.8860 (tptt) REVERT: C 915 TRP cc_start: 0.9069 (p-90) cc_final: 0.8045 (p-90) REVERT: C 916 ARG cc_start: 0.9208 (tpt170) cc_final: 0.8973 (tpp-160) REVERT: C 926 ASP cc_start: 0.9088 (p0) cc_final: 0.8865 (p0) REVERT: C 938 PHE cc_start: 0.9314 (t80) cc_final: 0.8888 (t80) REVERT: C 983 ASN cc_start: 0.8616 (t0) cc_final: 0.8116 (t0) REVERT: C 995 LYS cc_start: 0.9290 (mttp) cc_final: 0.9041 (mmtm) REVERT: C 1005 GLU cc_start: 0.8567 (tt0) cc_final: 0.8202 (tp30) REVERT: D 7 THR cc_start: 0.8369 (p) cc_final: 0.7802 (t) REVERT: D 60 ILE cc_start: 0.9093 (mm) cc_final: 0.8774 (mt) REVERT: D 109 LEU cc_start: 0.9372 (tt) cc_final: 0.9165 (tt) REVERT: D 117 ASN cc_start: 0.8135 (t0) cc_final: 0.7500 (p0) REVERT: D 162 MET cc_start: 0.8897 (tpt) cc_final: 0.8355 (tpp) REVERT: D 280 GLU cc_start: 0.8906 (pm20) cc_final: 0.8679 (pm20) REVERT: D 310 GLU cc_start: 0.8374 (tt0) cc_final: 0.8101 (tp30) REVERT: D 317 TRP cc_start: 0.8033 (p-90) cc_final: 0.7486 (p-90) REVERT: D 318 PHE cc_start: 0.7991 (p90) cc_final: 0.7692 (p90) REVERT: D 324 LYS cc_start: 0.8725 (mttp) cc_final: 0.8448 (mmmt) outliers start: 6 outliers final: 1 residues processed: 431 average time/residue: 0.3549 time to fit residues: 226.5250 Evaluate side-chains 283 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 282 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 108 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 161 optimal weight: 10.0000 chunk 132 optimal weight: 0.9990 chunk 53 optimal weight: 20.0000 chunk 194 optimal weight: 10.0000 chunk 210 optimal weight: 10.0000 chunk 173 optimal weight: 20.0000 chunk 193 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 156 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 817 HIS A 822 ASN ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1000 GLN B 33 GLN B 117 ASN B 195 HIS ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN ** C 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 858 GLN C 910 GLN C 937 GLN ** D 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 GLN D 306 GLN ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20880 Z= 0.283 Angle : 0.777 10.453 29159 Z= 0.426 Chirality : 0.043 0.208 3192 Planarity : 0.006 0.075 2994 Dihedral : 24.772 176.149 4568 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 22.93 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.44 % Favored : 95.25 % Rotamer: Outliers : 0.06 % Allowed : 4.58 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 1.62 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.10 (0.17), residues: 1938 helix: -0.29 (0.20), residues: 617 sheet: 0.39 (0.28), residues: 304 loop : -1.36 (0.18), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 538 HIS 0.010 0.002 HIS B 207 PHE 0.021 0.002 PHE A 681 TYR 0.025 0.002 TYR D 29 ARG 0.018 0.001 ARG C 848 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 355 time to evaluate : 1.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 LEU cc_start: 0.8536 (mt) cc_final: 0.8232 (mt) REVERT: A 431 LYS cc_start: 0.8021 (mtmm) cc_final: 0.7792 (tppt) REVERT: A 524 ASN cc_start: 0.9199 (t0) cc_final: 0.8800 (m110) REVERT: A 527 LYS cc_start: 0.8862 (mttm) cc_final: 0.7997 (tptt) REVERT: A 565 ASP cc_start: 0.8345 (p0) cc_final: 0.7861 (p0) REVERT: A 572 ILE cc_start: 0.9722 (mt) cc_final: 0.9410 (tt) REVERT: A 677 LEU cc_start: 0.9255 (tt) cc_final: 0.9045 (tp) REVERT: A 705 MET cc_start: 0.8689 (mmm) cc_final: 0.8471 (mmm) REVERT: A 807 MET cc_start: 0.8687 (mpp) cc_final: 0.8175 (mpp) REVERT: A 817 HIS cc_start: 0.9054 (m90) cc_final: 0.8703 (m-70) REVERT: A 872 ASN cc_start: 0.9036 (p0) cc_final: 0.8752 (p0) REVERT: A 895 GLU cc_start: 0.8955 (mp0) cc_final: 0.8525 (tp30) REVERT: A 911 MET cc_start: 0.9582 (ptm) cc_final: 0.9351 (ptt) REVERT: A 945 MET cc_start: 0.8755 (mtp) cc_final: 0.8335 (mmt) REVERT: A 947 LYS cc_start: 0.8874 (tttt) cc_final: 0.8367 (tppt) REVERT: A 955 THR cc_start: 0.8433 (t) cc_final: 0.7910 (m) REVERT: A 960 LYS cc_start: 0.9508 (mttt) cc_final: 0.8367 (tttm) REVERT: A 1005 GLU cc_start: 0.9146 (pt0) cc_final: 0.8682 (pt0) REVERT: B 81 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7385 (mm-30) REVERT: B 150 LYS cc_start: 0.8951 (mptt) cc_final: 0.8663 (mppt) REVERT: B 173 ASN cc_start: 0.8530 (t0) cc_final: 0.8296 (t0) REVERT: B 222 HIS cc_start: 0.8927 (t-90) cc_final: 0.8548 (t-170) REVERT: B 271 TYR cc_start: 0.8710 (m-80) cc_final: 0.8401 (m-10) REVERT: C 455 LEU cc_start: 0.8440 (mp) cc_final: 0.7976 (pp) REVERT: C 495 LEU cc_start: 0.9142 (mt) cc_final: 0.8781 (mt) REVERT: C 555 ASP cc_start: 0.8259 (m-30) cc_final: 0.7910 (m-30) REVERT: C 594 MET cc_start: 0.8202 (mmm) cc_final: 0.7910 (mtp) REVERT: C 598 ARG cc_start: 0.8665 (ptp-110) cc_final: 0.8415 (mtm110) REVERT: C 777 GLU cc_start: 0.9371 (pt0) cc_final: 0.9148 (pt0) REVERT: C 872 ASN cc_start: 0.9434 (p0) cc_final: 0.9195 (p0) REVERT: C 905 MET cc_start: 0.8846 (tmm) cc_final: 0.8538 (tmm) REVERT: C 915 TRP cc_start: 0.8967 (p-90) cc_final: 0.8070 (p-90) REVERT: C 916 ARG cc_start: 0.9250 (tpt170) cc_final: 0.8993 (tpp-160) REVERT: C 926 ASP cc_start: 0.9120 (p0) cc_final: 0.8825 (p0) REVERT: C 938 PHE cc_start: 0.9322 (t80) cc_final: 0.8920 (t80) REVERT: C 995 LYS cc_start: 0.9289 (mttp) cc_final: 0.8989 (mmtm) REVERT: C 1005 GLU cc_start: 0.8489 (tt0) cc_final: 0.7833 (tp30) REVERT: D 45 ILE cc_start: 0.9313 (mm) cc_final: 0.9078 (mm) REVERT: D 91 LEU cc_start: 0.9034 (mm) cc_final: 0.8568 (mm) REVERT: D 108 MET cc_start: 0.8322 (tpt) cc_final: 0.7832 (tpt) REVERT: D 117 ASN cc_start: 0.8243 (t0) cc_final: 0.7877 (p0) REVERT: D 162 MET cc_start: 0.8961 (tpt) cc_final: 0.8401 (tpp) REVERT: D 268 TYR cc_start: 0.7632 (t80) cc_final: 0.7382 (m-80) REVERT: D 324 LYS cc_start: 0.8898 (mttp) cc_final: 0.8424 (mmmt) outliers start: 1 outliers final: 0 residues processed: 356 average time/residue: 0.3365 time to fit residues: 180.8530 Evaluate side-chains 256 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 2.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 192 optimal weight: 0.8980 chunk 146 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 92 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 chunk 195 optimal weight: 10.0000 chunk 206 optimal weight: 10.0000 chunk 102 optimal weight: 0.0020 chunk 185 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 overall best weight: 2.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 831 GLN ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 237 HIS D 278 GLN ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.5459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20880 Z= 0.213 Angle : 0.707 10.715 29159 Z= 0.388 Chirality : 0.042 0.205 3192 Planarity : 0.005 0.074 2994 Dihedral : 24.694 179.042 4568 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.08 % Favored : 95.67 % Rotamer: Outliers : 0.12 % Allowed : 3.64 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 1.62 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.18), residues: 1938 helix: -0.04 (0.20), residues: 623 sheet: 0.63 (0.28), residues: 301 loop : -1.26 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 782 HIS 0.005 0.001 HIS A 534 PHE 0.021 0.002 PHE C 681 TYR 0.019 0.002 TYR A 957 ARG 0.008 0.001 ARG D 212 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 331 time to evaluate : 1.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 ARG cc_start: 0.9127 (ptt-90) cc_final: 0.8834 (ptt180) REVERT: A 524 ASN cc_start: 0.9178 (t0) cc_final: 0.8648 (m110) REVERT: A 527 LYS cc_start: 0.8897 (mttm) cc_final: 0.7843 (tptt) REVERT: A 565 ASP cc_start: 0.8357 (p0) cc_final: 0.7945 (p0) REVERT: A 572 ILE cc_start: 0.9702 (mt) cc_final: 0.9494 (tt) REVERT: A 575 ARG cc_start: 0.8382 (ptt90) cc_final: 0.7824 (ptm-80) REVERT: A 644 PHE cc_start: 0.9280 (p90) cc_final: 0.8998 (p90) REVERT: A 688 GLU cc_start: 0.9346 (mm-30) cc_final: 0.9140 (mm-30) REVERT: A 705 MET cc_start: 0.8724 (mmm) cc_final: 0.8495 (mmm) REVERT: A 730 ASP cc_start: 0.6927 (p0) cc_final: 0.6694 (p0) REVERT: A 731 GLU cc_start: 0.8601 (pt0) cc_final: 0.7915 (pp20) REVERT: A 733 MET cc_start: 0.8795 (mtp) cc_final: 0.8580 (mmm) REVERT: A 781 ILE cc_start: 0.9219 (mt) cc_final: 0.8982 (tp) REVERT: A 817 HIS cc_start: 0.8669 (m90) cc_final: 0.8432 (m-70) REVERT: A 869 MET cc_start: 0.9369 (ttt) cc_final: 0.8922 (tmm) REVERT: A 872 ASN cc_start: 0.9163 (p0) cc_final: 0.8816 (p0) REVERT: A 895 GLU cc_start: 0.8917 (mp0) cc_final: 0.8504 (tp30) REVERT: A 911 MET cc_start: 0.9525 (ptm) cc_final: 0.9273 (ptt) REVERT: A 945 MET cc_start: 0.8818 (mtp) cc_final: 0.8305 (mmt) REVERT: A 947 LYS cc_start: 0.8813 (tttt) cc_final: 0.8365 (tppt) REVERT: A 955 THR cc_start: 0.8524 (t) cc_final: 0.7911 (m) REVERT: A 960 LYS cc_start: 0.9471 (mttt) cc_final: 0.8013 (tttm) REVERT: A 1005 GLU cc_start: 0.9192 (pt0) cc_final: 0.8818 (pt0) REVERT: B 64 ASN cc_start: 0.9220 (m-40) cc_final: 0.8926 (m-40) REVERT: B 81 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7351 (mm-30) REVERT: B 128 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7894 (tm-30) REVERT: B 146 ASN cc_start: 0.6700 (p0) cc_final: 0.6382 (t0) REVERT: B 150 LYS cc_start: 0.8939 (mptt) cc_final: 0.8545 (mppt) REVERT: B 173 ASN cc_start: 0.8499 (t0) cc_final: 0.8171 (t0) REVERT: B 222 HIS cc_start: 0.8916 (t-90) cc_final: 0.8464 (t-90) REVERT: B 271 TYR cc_start: 0.8673 (m-80) cc_final: 0.8389 (m-10) REVERT: C 455 LEU cc_start: 0.8593 (mp) cc_final: 0.8102 (pp) REVERT: C 555 ASP cc_start: 0.8405 (m-30) cc_final: 0.7957 (m-30) REVERT: C 647 MET cc_start: 0.8276 (mtp) cc_final: 0.7633 (mtp) REVERT: C 679 LEU cc_start: 0.9238 (mt) cc_final: 0.8995 (mt) REVERT: C 698 VAL cc_start: 0.9509 (p) cc_final: 0.9305 (p) REVERT: C 704 MET cc_start: 0.7517 (ptp) cc_final: 0.6966 (ptp) REVERT: C 915 TRP cc_start: 0.8949 (p-90) cc_final: 0.8051 (p-90) REVERT: C 926 ASP cc_start: 0.9120 (p0) cc_final: 0.8765 (p0) REVERT: C 938 PHE cc_start: 0.9268 (t80) cc_final: 0.9048 (t80) REVERT: C 943 SER cc_start: 0.8805 (m) cc_final: 0.8118 (p) REVERT: C 995 LYS cc_start: 0.9229 (mttp) cc_final: 0.8871 (mmtm) REVERT: C 1005 GLU cc_start: 0.8380 (tt0) cc_final: 0.7813 (tp30) REVERT: D 91 LEU cc_start: 0.9068 (mm) cc_final: 0.8710 (mm) REVERT: D 117 ASN cc_start: 0.8208 (t0) cc_final: 0.7922 (p0) REVERT: D 237 HIS cc_start: 0.8623 (OUTLIER) cc_final: 0.8256 (t-170) REVERT: D 317 TRP cc_start: 0.8185 (p-90) cc_final: 0.7685 (p-90) REVERT: D 324 LYS cc_start: 0.8939 (mttp) cc_final: 0.8460 (mmmt) outliers start: 2 outliers final: 0 residues processed: 332 average time/residue: 0.3408 time to fit residues: 171.3114 Evaluate side-chains 252 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 251 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 172 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 3 optimal weight: 40.0000 chunk 154 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 105 optimal weight: 5.9990 chunk 185 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 GLN ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN B 173 ASN ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 766 HIS C 930 GLN D 278 GLN ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.5922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20880 Z= 0.261 Angle : 0.714 9.812 29159 Z= 0.393 Chirality : 0.041 0.203 3192 Planarity : 0.005 0.077 2994 Dihedral : 24.719 176.302 4568 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 21.85 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.28 % Favored : 95.46 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 1.62 % 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: -0.79 (0.18), residues: 1938 helix: 0.01 (0.20), residues: 626 sheet: 0.80 (0.29), residues: 301 loop : -1.29 (0.18), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 538 HIS 0.010 0.002 HIS A 959 PHE 0.028 0.002 PHE C 454 TYR 0.021 0.002 TYR A 957 ARG 0.010 0.001 ARG A 701 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 1.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 GLN cc_start: 0.8627 (mp-120) cc_final: 0.8394 (mp10) REVERT: A 524 ASN cc_start: 0.9153 (t0) cc_final: 0.8706 (m110) REVERT: A 527 LYS cc_start: 0.8932 (mttm) cc_final: 0.7794 (tptt) REVERT: A 565 ASP cc_start: 0.8420 (p0) cc_final: 0.8026 (p0) REVERT: A 575 ARG cc_start: 0.8560 (ptt90) cc_final: 0.7806 (ptm-80) REVERT: A 644 PHE cc_start: 0.9305 (p90) cc_final: 0.8894 (p90) REVERT: A 688 GLU cc_start: 0.9316 (mm-30) cc_final: 0.9059 (mm-30) REVERT: A 807 MET cc_start: 0.8952 (mpp) cc_final: 0.8472 (mpp) REVERT: A 817 HIS cc_start: 0.8757 (m90) cc_final: 0.8541 (m-70) REVERT: A 863 MET cc_start: 0.8531 (mmp) cc_final: 0.8315 (mmm) REVERT: A 869 MET cc_start: 0.9215 (ttt) cc_final: 0.8855 (tmm) REVERT: A 872 ASN cc_start: 0.9248 (p0) cc_final: 0.8918 (p0) REVERT: A 895 GLU cc_start: 0.8935 (mp0) cc_final: 0.8635 (tp30) REVERT: A 910 GLN cc_start: 0.9283 (mm110) cc_final: 0.8974 (mm-40) REVERT: A 911 MET cc_start: 0.9592 (ptm) cc_final: 0.9349 (ptt) REVERT: A 945 MET cc_start: 0.8834 (mtp) cc_final: 0.8255 (mmt) REVERT: A 955 THR cc_start: 0.8803 (t) cc_final: 0.8302 (m) REVERT: A 960 LYS cc_start: 0.9363 (mttt) cc_final: 0.8469 (mmtp) REVERT: A 987 ASN cc_start: 0.9025 (m-40) cc_final: 0.8270 (p0) REVERT: A 1005 GLU cc_start: 0.9190 (pt0) cc_final: 0.8834 (pt0) REVERT: B 64 ASN cc_start: 0.9210 (m-40) cc_final: 0.8980 (m-40) REVERT: B 81 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7289 (mm-30) REVERT: B 222 HIS cc_start: 0.8792 (t-90) cc_final: 0.8539 (t70) REVERT: B 252 LEU cc_start: 0.9090 (mp) cc_final: 0.8781 (tt) REVERT: C 455 LEU cc_start: 0.8124 (mp) cc_final: 0.7800 (pp) REVERT: C 474 MET cc_start: 0.8817 (mmp) cc_final: 0.7798 (ppp) REVERT: C 495 LEU cc_start: 0.8925 (mt) cc_final: 0.8672 (mt) REVERT: C 555 ASP cc_start: 0.8468 (m-30) cc_final: 0.8044 (m-30) REVERT: C 589 LEU cc_start: 0.9195 (mm) cc_final: 0.8912 (tp) REVERT: C 647 MET cc_start: 0.8319 (mtp) cc_final: 0.7918 (mtp) REVERT: C 677 LEU cc_start: 0.9293 (tt) cc_final: 0.9029 (tp) REVERT: C 680 MET cc_start: 0.8980 (pmm) cc_final: 0.8759 (pmm) REVERT: C 689 THR cc_start: 0.9192 (m) cc_final: 0.8953 (m) REVERT: C 704 MET cc_start: 0.7623 (ptp) cc_final: 0.7044 (ptp) REVERT: C 915 TRP cc_start: 0.8942 (p-90) cc_final: 0.8636 (p-90) REVERT: C 938 PHE cc_start: 0.9248 (t80) cc_final: 0.8939 (t80) REVERT: C 995 LYS cc_start: 0.9221 (mttp) cc_final: 0.8861 (mmtm) REVERT: C 1005 GLU cc_start: 0.8420 (tt0) cc_final: 0.7739 (tp30) REVERT: D 31 PHE cc_start: 0.9180 (t80) cc_final: 0.8972 (t80) REVERT: D 91 LEU cc_start: 0.9176 (mm) cc_final: 0.8678 (mm) REVERT: D 108 MET cc_start: 0.8545 (tpt) cc_final: 0.8163 (tpt) REVERT: D 117 ASN cc_start: 0.8252 (t0) cc_final: 0.8024 (p0) REVERT: D 184 LEU cc_start: 0.8282 (tp) cc_final: 0.8075 (tp) REVERT: D 324 LYS cc_start: 0.8979 (mttp) cc_final: 0.8501 (mmmt) REVERT: D 343 TYR cc_start: 0.8563 (m-80) cc_final: 0.8335 (m-80) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.3034 time to fit residues: 143.6428 Evaluate side-chains 230 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 2.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 69 optimal weight: 7.9990 chunk 186 optimal weight: 20.0000 chunk 40 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 207 optimal weight: 10.0000 chunk 171 optimal weight: 20.0000 chunk 95 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 108 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN B 173 ASN B 195 HIS B 282 GLN ** C 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 524 ASN D 237 HIS D 278 GLN ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.6392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 20880 Z= 0.266 Angle : 0.709 9.074 29159 Z= 0.390 Chirality : 0.041 0.200 3192 Planarity : 0.005 0.075 2994 Dihedral : 24.816 175.803 4568 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 22.69 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.64 % Favored : 95.05 % Rotamer: Outliers : 0.12 % Allowed : 2.35 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 1.62 % 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: -0.77 (0.18), residues: 1938 helix: 0.13 (0.20), residues: 630 sheet: 0.75 (0.29), residues: 310 loop : -1.37 (0.18), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 538 HIS 0.005 0.001 HIS C 959 PHE 0.032 0.002 PHE D 62 TYR 0.022 0.002 TYR A 827 ARG 0.006 0.001 ARG A 877 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 294 time to evaluate : 2.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 ARG cc_start: 0.8629 (mmp80) cc_final: 0.8337 (mmp80) REVERT: A 524 ASN cc_start: 0.9191 (t0) cc_final: 0.8750 (m110) REVERT: A 527 LYS cc_start: 0.9156 (mttm) cc_final: 0.7786 (tptp) REVERT: A 565 ASP cc_start: 0.8497 (p0) cc_final: 0.8284 (p0) REVERT: A 575 ARG cc_start: 0.8673 (ptt90) cc_final: 0.7809 (ptm-80) REVERT: A 644 PHE cc_start: 0.9259 (p90) cc_final: 0.8820 (p90) REVERT: A 688 GLU cc_start: 0.9305 (mm-30) cc_final: 0.9002 (mm-30) REVERT: A 731 GLU cc_start: 0.8847 (pt0) cc_final: 0.8003 (pp20) REVERT: A 817 HIS cc_start: 0.8810 (m90) cc_final: 0.8593 (m-70) REVERT: A 851 TRP cc_start: 0.8738 (m-10) cc_final: 0.8125 (m-90) REVERT: A 863 MET cc_start: 0.8574 (mmp) cc_final: 0.8342 (mmm) REVERT: A 868 VAL cc_start: 0.9379 (m) cc_final: 0.8946 (m) REVERT: A 869 MET cc_start: 0.9216 (ttt) cc_final: 0.8844 (tmm) REVERT: A 872 ASN cc_start: 0.9269 (p0) cc_final: 0.8982 (p0) REVERT: A 895 GLU cc_start: 0.8933 (mp0) cc_final: 0.8548 (tp30) REVERT: A 911 MET cc_start: 0.9574 (ptm) cc_final: 0.9343 (ptt) REVERT: A 955 THR cc_start: 0.8787 (t) cc_final: 0.8363 (m) REVERT: A 960 LYS cc_start: 0.9369 (mttt) cc_final: 0.8248 (mmtp) REVERT: A 1005 GLU cc_start: 0.9122 (pt0) cc_final: 0.8786 (pt0) REVERT: B 252 LEU cc_start: 0.9094 (mp) cc_final: 0.8809 (tt) REVERT: B 280 GLU cc_start: 0.8770 (mt-10) cc_final: 0.7930 (tp30) REVERT: B 282 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7263 (tm-30) REVERT: C 495 LEU cc_start: 0.8913 (mt) cc_final: 0.8711 (mt) REVERT: C 555 ASP cc_start: 0.8523 (m-30) cc_final: 0.8059 (m-30) REVERT: C 589 LEU cc_start: 0.9161 (mm) cc_final: 0.8801 (tp) REVERT: C 647 MET cc_start: 0.8203 (mtp) cc_final: 0.7997 (mtp) REVERT: C 677 LEU cc_start: 0.9273 (tt) cc_final: 0.9005 (tp) REVERT: C 689 THR cc_start: 0.9236 (m) cc_final: 0.9026 (m) REVERT: C 733 MET cc_start: 0.8878 (mmm) cc_final: 0.8336 (mmm) REVERT: C 871 MET cc_start: 0.8808 (tmm) cc_final: 0.8101 (tmm) REVERT: C 938 PHE cc_start: 0.9267 (t80) cc_final: 0.8900 (t80) REVERT: C 995 LYS cc_start: 0.9255 (mttp) cc_final: 0.8907 (mmtm) REVERT: C 1005 GLU cc_start: 0.8405 (tt0) cc_final: 0.7776 (tp30) REVERT: D 108 MET cc_start: 0.8444 (tpt) cc_final: 0.8014 (tpt) REVERT: D 117 ASN cc_start: 0.8239 (t0) cc_final: 0.8027 (p0) REVERT: D 162 MET cc_start: 0.8857 (mmm) cc_final: 0.8443 (tpt) REVERT: D 184 LEU cc_start: 0.8304 (tp) cc_final: 0.8090 (tp) REVERT: D 307 TRP cc_start: 0.7832 (m100) cc_final: 0.7580 (m100) REVERT: D 343 TYR cc_start: 0.8597 (m-80) cc_final: 0.8336 (m-80) outliers start: 2 outliers final: 0 residues processed: 296 average time/residue: 0.3222 time to fit residues: 148.2871 Evaluate side-chains 232 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 231 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 199 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 117 optimal weight: 9.9990 chunk 151 optimal weight: 0.9990 chunk 174 optimal weight: 8.9990 chunk 115 optimal weight: 9.9990 chunk 206 optimal weight: 10.0000 chunk 129 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 127 optimal weight: 7.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 HIS A 910 GLN ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN B 173 ASN B 195 HIS ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.6601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20880 Z= 0.218 Angle : 0.693 9.074 29159 Z= 0.378 Chirality : 0.041 0.200 3192 Planarity : 0.005 0.069 2994 Dihedral : 24.810 177.260 4568 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 21.58 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.70 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 1.62 % 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: -0.73 (0.18), residues: 1938 helix: 0.23 (0.20), residues: 632 sheet: 0.57 (0.29), residues: 317 loop : -1.33 (0.18), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 782 HIS 0.007 0.001 HIS D 140 PHE 0.017 0.002 PHE C 681 TYR 0.018 0.002 TYR A 957 ARG 0.006 0.001 ARG A 897 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 305 time to evaluate : 1.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 ARG cc_start: 0.8521 (mmp80) cc_final: 0.8257 (mmp80) REVERT: A 466 GLN cc_start: 0.8894 (mp10) cc_final: 0.8622 (mp10) REVERT: A 524 ASN cc_start: 0.9163 (t0) cc_final: 0.8919 (m110) REVERT: A 575 ARG cc_start: 0.8633 (ptt90) cc_final: 0.7829 (ptm-80) REVERT: A 644 PHE cc_start: 0.9210 (p90) cc_final: 0.8736 (p90) REVERT: A 688 GLU cc_start: 0.9260 (mm-30) cc_final: 0.9040 (mm-30) REVERT: A 731 GLU cc_start: 0.8819 (pt0) cc_final: 0.8025 (pp20) REVERT: A 817 HIS cc_start: 0.8769 (m90) cc_final: 0.8545 (m-70) REVERT: A 851 TRP cc_start: 0.8742 (m-10) cc_final: 0.8122 (m-90) REVERT: A 863 MET cc_start: 0.8568 (mmp) cc_final: 0.8352 (mmm) REVERT: A 869 MET cc_start: 0.9182 (ttt) cc_final: 0.8910 (tmm) REVERT: A 872 ASN cc_start: 0.9273 (p0) cc_final: 0.8982 (p0) REVERT: A 895 GLU cc_start: 0.8886 (mp0) cc_final: 0.8507 (tp30) REVERT: A 911 MET cc_start: 0.9556 (ptm) cc_final: 0.9323 (ptt) REVERT: A 955 THR cc_start: 0.8791 (t) cc_final: 0.8346 (m) REVERT: A 960 LYS cc_start: 0.9379 (mttt) cc_final: 0.8174 (mmtp) REVERT: A 1005 GLU cc_start: 0.9101 (pt0) cc_final: 0.8745 (pt0) REVERT: B 1 MET cc_start: 0.6850 (tpp) cc_final: 0.5267 (tmm) REVERT: B 84 ASP cc_start: 0.8880 (p0) cc_final: 0.8634 (m-30) REVERT: B 128 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7859 (tm-30) REVERT: B 252 LEU cc_start: 0.9075 (mp) cc_final: 0.8790 (tt) REVERT: B 280 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8089 (tp30) REVERT: B 322 LEU cc_start: 0.8743 (mt) cc_final: 0.7634 (tt) REVERT: C 495 LEU cc_start: 0.8860 (mt) cc_final: 0.8593 (mt) REVERT: C 537 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7969 (tm-30) REVERT: C 555 ASP cc_start: 0.8626 (m-30) cc_final: 0.8318 (m-30) REVERT: C 589 LEU cc_start: 0.9127 (mm) cc_final: 0.8770 (tp) REVERT: C 677 LEU cc_start: 0.9222 (tt) cc_final: 0.8960 (tp) REVERT: C 733 MET cc_start: 0.8804 (mmm) cc_final: 0.8251 (mmm) REVERT: C 783 ARG cc_start: 0.8920 (ptm-80) cc_final: 0.8691 (ptm-80) REVERT: C 836 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7262 (mm-30) REVERT: C 865 LEU cc_start: 0.9159 (mt) cc_final: 0.8928 (mt) REVERT: C 904 LEU cc_start: 0.9427 (tp) cc_final: 0.8635 (pp) REVERT: C 938 PHE cc_start: 0.9237 (t80) cc_final: 0.8771 (t80) REVERT: C 984 GLU cc_start: 0.9240 (tm-30) cc_final: 0.9022 (tp30) REVERT: C 995 LYS cc_start: 0.9260 (mttp) cc_final: 0.8908 (mmtm) REVERT: C 1005 GLU cc_start: 0.8312 (tt0) cc_final: 0.7720 (tp30) REVERT: D 31 PHE cc_start: 0.9168 (t80) cc_final: 0.8760 (t80) REVERT: D 45 ILE cc_start: 0.9403 (mm) cc_final: 0.9131 (mm) REVERT: D 91 LEU cc_start: 0.9234 (mm) cc_final: 0.8975 (mm) REVERT: D 108 MET cc_start: 0.8342 (tpt) cc_final: 0.8017 (tpt) REVERT: D 117 ASN cc_start: 0.8270 (t0) cc_final: 0.8048 (p0) REVERT: D 162 MET cc_start: 0.8809 (mmm) cc_final: 0.8383 (tpt) REVERT: D 184 LEU cc_start: 0.8333 (tp) cc_final: 0.8129 (tp) REVERT: D 343 TYR cc_start: 0.8420 (m-80) cc_final: 0.8204 (m-80) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.3077 time to fit residues: 144.1135 Evaluate side-chains 233 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 82 optimal weight: 40.0000 chunk 123 optimal weight: 0.2980 chunk 62 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 131 optimal weight: 9.9990 chunk 140 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 162 optimal weight: 9.9990 chunk 187 optimal weight: 9.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 810 GLN ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 237 HIS ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.6873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20880 Z= 0.236 Angle : 0.708 8.805 29159 Z= 0.386 Chirality : 0.041 0.197 3192 Planarity : 0.005 0.068 2994 Dihedral : 24.810 177.536 4568 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 22.32 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.80 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 1.62 % 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: -0.75 (0.18), residues: 1938 helix: 0.29 (0.20), residues: 622 sheet: 0.63 (0.29), residues: 300 loop : -1.38 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 538 HIS 0.006 0.001 HIS D 140 PHE 0.018 0.002 PHE A 454 TYR 0.019 0.002 TYR B 29 ARG 0.011 0.001 ARG A 701 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 2.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 ARG cc_start: 0.8737 (mmp80) cc_final: 0.8367 (mmp80) REVERT: A 575 ARG cc_start: 0.8713 (ptt90) cc_final: 0.7852 (ptm-80) REVERT: A 644 PHE cc_start: 0.9179 (p90) cc_final: 0.8668 (p90) REVERT: A 688 GLU cc_start: 0.9216 (mm-30) cc_final: 0.8980 (mm-30) REVERT: A 807 MET cc_start: 0.8994 (mpp) cc_final: 0.8781 (mpp) REVERT: A 851 TRP cc_start: 0.8748 (m-10) cc_final: 0.8069 (m-90) REVERT: A 863 MET cc_start: 0.8571 (mmp) cc_final: 0.8361 (mmm) REVERT: A 869 MET cc_start: 0.9166 (ttt) cc_final: 0.8824 (tmm) REVERT: A 872 ASN cc_start: 0.9298 (p0) cc_final: 0.8986 (p0) REVERT: A 895 GLU cc_start: 0.8892 (mp0) cc_final: 0.8589 (tp30) REVERT: A 911 MET cc_start: 0.9559 (ptm) cc_final: 0.9337 (ptt) REVERT: A 955 THR cc_start: 0.8836 (t) cc_final: 0.8367 (m) REVERT: A 960 LYS cc_start: 0.9399 (mttt) cc_final: 0.8442 (mmtp) REVERT: A 1005 GLU cc_start: 0.9085 (pt0) cc_final: 0.8758 (pt0) REVERT: B 29 TYR cc_start: 0.8375 (m-80) cc_final: 0.7823 (m-80) REVERT: B 84 ASP cc_start: 0.8907 (p0) cc_final: 0.8672 (m-30) REVERT: B 128 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8130 (tm-30) REVERT: B 252 LEU cc_start: 0.9118 (mp) cc_final: 0.8835 (tt) REVERT: B 280 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8081 (tp30) REVERT: B 322 LEU cc_start: 0.8703 (mt) cc_final: 0.7611 (tt) REVERT: C 495 LEU cc_start: 0.8891 (mt) cc_final: 0.8642 (mt) REVERT: C 537 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7942 (tm-30) REVERT: C 555 ASP cc_start: 0.8670 (m-30) cc_final: 0.8375 (m-30) REVERT: C 589 LEU cc_start: 0.9124 (mm) cc_final: 0.8737 (tp) REVERT: C 677 LEU cc_start: 0.9220 (tt) cc_final: 0.8959 (tp) REVERT: C 836 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7171 (mm-30) REVERT: C 904 LEU cc_start: 0.9423 (tp) cc_final: 0.8656 (pp) REVERT: C 938 PHE cc_start: 0.9256 (t80) cc_final: 0.8787 (t80) REVERT: C 984 GLU cc_start: 0.9234 (tm-30) cc_final: 0.9011 (tp30) REVERT: C 995 LYS cc_start: 0.9272 (mttp) cc_final: 0.8901 (mmtm) REVERT: C 1005 GLU cc_start: 0.8318 (tt0) cc_final: 0.7720 (tp30) REVERT: D 31 PHE cc_start: 0.9181 (t80) cc_final: 0.8955 (t80) REVERT: D 45 ILE cc_start: 0.9433 (mm) cc_final: 0.9201 (mm) REVERT: D 91 LEU cc_start: 0.9215 (mm) cc_final: 0.8964 (mm) REVERT: D 108 MET cc_start: 0.8276 (tpt) cc_final: 0.7962 (tpt) REVERT: D 109 LEU cc_start: 0.9184 (tt) cc_final: 0.8979 (tt) REVERT: D 117 ASN cc_start: 0.8308 (t0) cc_final: 0.8087 (p0) REVERT: D 162 MET cc_start: 0.8797 (mmm) cc_final: 0.8363 (tpt) REVERT: D 184 LEU cc_start: 0.8316 (tp) cc_final: 0.8104 (tp) REVERT: D 343 TYR cc_start: 0.8462 (m-80) cc_final: 0.8223 (m-80) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.3151 time to fit residues: 141.2340 Evaluate side-chains 239 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/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-dev-5265/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: 66.3522 > 50: distance: 68 - 86: 6.867 distance: 81 - 86: 3.804 distance: 86 - 87: 21.523 distance: 87 - 88: 9.524 distance: 87 - 90: 20.301 distance: 88 - 89: 13.072 distance: 88 - 91: 10.221 distance: 91 - 92: 46.814 distance: 91 - 188: 21.985 distance: 92 - 93: 41.209 distance: 92 - 95: 21.218 distance: 93 - 94: 41.436 distance: 93 - 99: 40.727 distance: 94 - 185: 31.129 distance: 95 - 96: 21.567 distance: 95 - 97: 23.803 distance: 96 - 98: 17.896 distance: 99 - 100: 14.658 distance: 99 - 105: 26.788 distance: 100 - 101: 26.773 distance: 100 - 103: 16.141 distance: 101 - 102: 13.665 distance: 101 - 106: 25.310 distance: 103 - 104: 27.591 distance: 104 - 105: 17.971 distance: 106 - 107: 16.912 distance: 107 - 108: 24.315 distance: 107 - 110: 33.702 distance: 108 - 109: 22.240 distance: 108 - 112: 23.931 distance: 110 - 111: 31.714 distance: 112 - 113: 28.267 distance: 113 - 114: 25.740 distance: 113 - 116: 44.511 distance: 114 - 115: 15.260 distance: 114 - 121: 20.561 distance: 116 - 117: 47.326 distance: 117 - 118: 18.392 distance: 118 - 119: 32.148 distance: 118 - 120: 14.037 distance: 121 - 122: 16.000 distance: 122 - 123: 18.025 distance: 123 - 124: 10.584 distance: 123 - 125: 20.024 distance: 125 - 126: 7.855 distance: 126 - 127: 14.455 distance: 126 - 129: 18.766 distance: 127 - 128: 27.395 distance: 127 - 133: 15.905 distance: 129 - 130: 15.043 distance: 130 - 131: 21.441 distance: 130 - 132: 16.953 distance: 133 - 134: 37.605 distance: 133 - 139: 21.205 distance: 134 - 135: 43.620 distance: 134 - 137: 26.462 distance: 135 - 136: 45.053 distance: 135 - 140: 57.145 distance: 137 - 138: 6.634 distance: 138 - 139: 31.513 distance: 140 - 141: 16.273 distance: 141 - 142: 13.905 distance: 141 - 144: 34.999 distance: 142 - 143: 23.249 distance: 142 - 147: 11.786 distance: 144 - 145: 16.400 distance: 144 - 146: 14.699 distance: 147 - 148: 10.361 distance: 147 - 153: 5.712 distance: 148 - 149: 8.558 distance: 148 - 151: 7.937 distance: 149 - 150: 11.689 distance: 149 - 154: 11.642 distance: 151 - 152: 6.786 distance: 152 - 153: 9.422