Starting phenix.real_space_refine on Fri May 9 23:37:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ufr_20759/05_2025/6ufr_20759.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ufr_20759/05_2025/6ufr_20759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ufr_20759/05_2025/6ufr_20759.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ufr_20759/05_2025/6ufr_20759.map" model { file = "/net/cci-nas-00/data/ceres_data/6ufr_20759/05_2025/6ufr_20759.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ufr_20759/05_2025/6ufr_20759.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 2720 2.51 5 N 760 2.21 5 O 940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 4420 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 433 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "G" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "I" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "F" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "J" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "H" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Restraints were copied for chains: C, B, E, D, G, F, I, H, J Time building chain proxies: 1.76, per 1000 atoms: 0.40 Number of scatterers: 4420 At special positions: 0 Unit cell: (103.074, 96.37, 41.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 940 8.00 N 760 7.00 C 2720 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 604.0 milliseconds 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1060 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 68.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'E' and resid 37 through 57 removed outlier: 9.090A pdb=" N VAL E 37 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 9.953A pdb=" N VAL D 40 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N TYR E 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 10.066A pdb=" N SER D 42 " --> pdb=" O TYR E 39 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N GLY E 41 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 10.099A pdb=" N THR D 44 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N LYS E 43 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 9.767A pdb=" N LYS D 46 " --> pdb=" O LYS E 43 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LYS E 45 " --> pdb=" O LYS D 46 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N VAL D 48 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLY E 47 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N HIS D 50 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL E 49 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N VAL D 52 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N GLY E 51 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 10.333A pdb=" N THR D 54 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 9.061A pdb=" N ALA E 53 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 10.023A pdb=" N ALA D 56 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 9.023A pdb=" N VAL E 55 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU A 38 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N TYR D 39 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL A 40 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N GLY D 41 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER A 42 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LYS D 43 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N THR A 44 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LYS D 45 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL A 52 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ALA D 53 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N THR A 54 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL D 55 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ALA A 56 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLU D 57 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LEU H 38 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR A 39 " --> pdb=" O LEU H 38 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL H 40 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N GLY A 41 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N SER H 42 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LYS A 43 " --> pdb=" O SER H 42 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR H 44 " --> pdb=" O LYS A 43 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LYS A 45 " --> pdb=" O THR H 44 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL H 52 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ALA A 53 " --> pdb=" O VAL H 52 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR H 54 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL A 55 " --> pdb=" O THR H 54 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ALA H 56 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N GLU A 57 " --> pdb=" O ALA H 56 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N LEU I 38 " --> pdb=" O TYR H 39 " (cutoff:3.500A) removed outlier: 10.139A pdb=" N GLY H 41 " --> pdb=" O LEU I 38 " (cutoff:3.500A) removed outlier: 9.145A pdb=" N VAL I 40 " --> pdb=" O GLY H 41 " (cutoff:3.500A) removed outlier: 10.437A pdb=" N LYS H 43 " --> pdb=" O VAL I 40 " (cutoff:3.500A) removed outlier: 9.214A pdb=" N SER I 42 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 10.083A pdb=" N LYS H 45 " --> pdb=" O SER I 42 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N THR I 44 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N GLY H 47 " --> pdb=" O THR I 44 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LYS I 46 " --> pdb=" O GLY H 47 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N VAL H 49 " --> pdb=" O LYS I 46 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL I 48 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N GLY H 51 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N HIS I 50 " --> pdb=" O GLY H 51 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ALA H 53 " --> pdb=" O HIS I 50 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N VAL I 52 " --> pdb=" O ALA H 53 " (cutoff:3.500A) removed outlier: 10.221A pdb=" N VAL H 55 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 9.171A pdb=" N THR I 54 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 10.341A pdb=" N GLU H 57 " --> pdb=" O THR I 54 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N ALA I 56 " --> pdb=" O GLU H 57 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 61 through 66 removed outlier: 6.751A pdb=" N GLU A 61 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N THR D 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL A 63 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N VAL D 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN A 65 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLU I 61 " --> pdb=" O GLN H 62 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N THR H 64 " --> pdb=" O GLU I 61 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL I 63 " --> pdb=" O THR H 64 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N VAL H 66 " --> pdb=" O VAL I 63 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN I 65 " --> pdb=" O VAL H 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 70 through 72 removed outlier: 6.395A pdb=" N VAL A 70 " --> pdb=" O VAL H 71 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 76 through 83 removed outlier: 6.616A pdb=" N ALA A 76 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N GLN D 79 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA A 78 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N THR D 81 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LYS A 80 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N GLU D 83 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL A 82 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA I 76 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N GLN H 79 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA I 78 " --> pdb=" O GLN H 79 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N THR H 81 " --> pdb=" O ALA I 78 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LYS I 80 " --> pdb=" O THR H 81 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N GLU H 83 " --> pdb=" O LYS I 80 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL I 82 " --> pdb=" O GLU H 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 88 through 97 removed outlier: 6.335A pdb=" N ILE E 88 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ALA D 91 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ALA E 90 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N GLY D 93 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N THR E 92 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N VAL D 95 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 9.332A pdb=" N PHE E 94 " --> pdb=" O VAL D 95 " (cutoff:3.500A) removed outlier: 10.295A pdb=" N LYS D 97 " --> pdb=" O PHE E 94 " (cutoff:3.500A) removed outlier: 9.330A pdb=" N LYS E 96 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N PHE D 94 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL A 95 " --> pdb=" O PHE D 94 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LYS D 96 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LYS A 97 " --> pdb=" O LYS D 96 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE A 88 " --> pdb=" O ALA H 89 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ALA H 91 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA A 90 " --> pdb=" O ALA H 91 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N GLY H 93 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N THR A 92 " --> pdb=" O GLY H 93 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N VAL H 95 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 9.317A pdb=" N PHE A 94 " --> pdb=" O VAL H 95 " (cutoff:3.500A) removed outlier: 10.275A pdb=" N LYS H 97 " --> pdb=" O PHE A 94 " (cutoff:3.500A) removed outlier: 9.298A pdb=" N LYS A 96 " --> pdb=" O LYS H 97 " (cutoff:3.500A) removed outlier: 9.097A pdb=" N ILE I 88 " --> pdb=" O ALA H 89 " (cutoff:3.500A) removed outlier: 10.126A pdb=" N ALA H 91 " --> pdb=" O ILE I 88 " (cutoff:3.500A) removed outlier: 9.023A pdb=" N ALA I 90 " --> pdb=" O ALA H 91 " (cutoff:3.500A) removed outlier: 10.241A pdb=" N GLY H 93 " --> pdb=" O ALA I 90 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N THR I 92 " --> pdb=" O GLY H 93 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL H 95 " --> pdb=" O THR I 92 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N PHE I 94 " --> pdb=" O VAL H 95 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N LYS H 97 " --> pdb=" O PHE I 94 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LYS I 96 " --> pdb=" O LYS H 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 37 through 57 removed outlier: 9.128A pdb=" N LEU C 38 " --> pdb=" O TYR F 39 " (cutoff:3.500A) removed outlier: 10.126A pdb=" N GLY F 41 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 9.115A pdb=" N VAL C 40 " --> pdb=" O GLY F 41 " (cutoff:3.500A) removed outlier: 10.409A pdb=" N LYS F 43 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 9.175A pdb=" N SER C 42 " --> pdb=" O LYS F 43 " (cutoff:3.500A) removed outlier: 10.060A pdb=" N LYS F 45 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N THR C 44 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N GLY F 47 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LYS C 46 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N VAL F 49 " --> pdb=" O LYS C 46 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL C 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N GLY F 51 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N HIS C 50 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ALA F 53 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 9.099A pdb=" N VAL C 52 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 10.255A pdb=" N VAL F 55 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N THR C 54 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 10.382A pdb=" N GLU F 57 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N ALA C 56 " --> pdb=" O GLU F 57 " (cutoff:3.500A) removed outlier: 9.155A pdb=" N VAL C 37 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 10.025A pdb=" N VAL B 40 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 9.105A pdb=" N TYR C 39 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 10.146A pdb=" N SER B 42 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 9.078A pdb=" N GLY C 41 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 10.185A pdb=" N THR B 44 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N LYS C 43 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 9.860A pdb=" N LYS B 46 " --> pdb=" O LYS C 43 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LYS C 45 " --> pdb=" O LYS B 46 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N VAL B 48 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLY C 47 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N HIS B 50 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL C 49 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N VAL B 52 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N GLY C 51 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 10.363A pdb=" N THR B 54 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 9.086A pdb=" N ALA C 53 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 10.042A pdb=" N ALA B 56 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 9.040A pdb=" N VAL C 55 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N LEU G 38 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 10.088A pdb=" N GLY B 41 " --> pdb=" O LEU G 38 " (cutoff:3.500A) removed outlier: 9.078A pdb=" N VAL G 40 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 10.357A pdb=" N LYS B 43 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 9.116A pdb=" N SER G 42 " --> pdb=" O LYS B 43 " (cutoff:3.500A) removed outlier: 9.985A pdb=" N LYS B 45 " --> pdb=" O SER G 42 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N THR G 44 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N GLY B 47 " --> pdb=" O THR G 44 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LYS G 46 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N VAL B 49 " --> pdb=" O LYS G 46 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL G 48 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N GLY B 51 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N HIS G 50 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ALA B 53 " --> pdb=" O HIS G 50 " (cutoff:3.500A) removed outlier: 9.068A pdb=" N VAL G 52 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 10.223A pdb=" N VAL B 55 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 9.177A pdb=" N THR G 54 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 10.355A pdb=" N GLU B 57 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 9.105A pdb=" N ALA G 56 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LEU J 38 " --> pdb=" O VAL G 37 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N TYR G 39 " --> pdb=" O LEU J 38 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL J 40 " --> pdb=" O TYR G 39 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLY G 41 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N SER J 42 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LYS G 43 " --> pdb=" O SER J 42 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N THR J 44 " --> pdb=" O LYS G 43 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS G 45 " --> pdb=" O THR J 44 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL J 52 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ALA G 53 " --> pdb=" O VAL J 52 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR J 54 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL G 55 " --> pdb=" O THR J 54 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ALA J 56 " --> pdb=" O VAL G 55 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLU G 57 " --> pdb=" O ALA J 56 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 61 through 66 removed outlier: 6.717A pdb=" N GLU C 61 " --> pdb=" O GLN F 62 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N THR F 64 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL C 63 " --> pdb=" O THR F 64 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL F 66 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASN C 65 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLU G 61 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N THR B 64 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL G 63 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N VAL B 66 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASN G 65 " --> pdb=" O VAL B 66 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 70 through 72 removed outlier: 6.433A pdb=" N VAL C 70 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL G 70 " --> pdb=" O VAL J 71 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 76 through 83 removed outlier: 6.620A pdb=" N ALA C 76 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N GLN F 79 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA C 78 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N THR F 81 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LYS C 80 " --> pdb=" O THR F 81 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N GLU F 83 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL C 82 " --> pdb=" O GLU F 83 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA G 76 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N GLN B 79 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA G 78 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N THR B 81 " --> pdb=" O ALA G 78 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LYS G 80 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N GLU B 83 " --> pdb=" O LYS G 80 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL G 82 " --> pdb=" O GLU B 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 88 through 97 removed outlier: 6.755A pdb=" N PHE F 94 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL C 95 " --> pdb=" O PHE F 94 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LYS F 96 " --> pdb=" O VAL C 95 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LYS C 97 " --> pdb=" O LYS F 96 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE C 88 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ALA B 91 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA C 90 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N GLY B 93 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N THR C 92 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N VAL B 95 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 9.315A pdb=" N PHE C 94 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 10.269A pdb=" N LYS B 97 " --> pdb=" O PHE C 94 " (cutoff:3.500A) removed outlier: 9.299A pdb=" N LYS C 96 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N PHE B 94 " --> pdb=" O GLY G 93 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL G 95 " --> pdb=" O PHE B 94 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LYS B 96 " --> pdb=" O VAL G 95 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LYS G 97 " --> pdb=" O LYS B 96 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ALA G 89 " --> pdb=" O ILE J 88 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ALA J 90 " --> pdb=" O ALA G 89 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ALA G 91 " --> pdb=" O ALA J 90 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N THR J 92 " --> pdb=" O ALA G 91 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLY G 93 " --> pdb=" O THR J 92 " (cutoff:3.500A) 95 hydrogen bonds defined for protein. 285 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.05 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.28: 740 1.28 - 1.35: 670 1.35 - 1.41: 170 1.41 - 1.48: 769 1.48 - 1.54: 2001 Bond restraints: 4350 Sorted by residual: bond pdb=" N GLU J 83 " pdb=" CA GLU J 83 " ideal model delta sigma weight residual 1.460 1.488 -0.028 1.20e-02 6.94e+03 5.52e+00 bond pdb=" N GLU F 83 " pdb=" CA GLU F 83 " ideal model delta sigma weight residual 1.460 1.488 -0.028 1.20e-02 6.94e+03 5.30e+00 bond pdb=" N GLU G 83 " pdb=" CA GLU G 83 " ideal model delta sigma weight residual 1.460 1.487 -0.028 1.20e-02 6.94e+03 5.28e+00 bond pdb=" N GLU A 83 " pdb=" CA GLU A 83 " ideal model delta sigma weight residual 1.460 1.487 -0.027 1.20e-02 6.94e+03 5.19e+00 bond pdb=" N GLU H 83 " pdb=" CA GLU H 83 " ideal model delta sigma weight residual 1.460 1.487 -0.027 1.20e-02 6.94e+03 5.18e+00 ... (remaining 4345 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 4955 1.19 - 2.38: 701 2.38 - 3.58: 177 3.58 - 4.77: 27 4.77 - 5.96: 10 Bond angle restraints: 5870 Sorted by residual: angle pdb=" C THR H 59 " pdb=" N LYS H 60 " pdb=" CA LYS H 60 " ideal model delta sigma weight residual 122.42 118.11 4.31 1.55e+00 4.16e-01 7.74e+00 angle pdb=" C THR F 59 " pdb=" N LYS F 60 " pdb=" CA LYS F 60 " ideal model delta sigma weight residual 122.42 118.12 4.30 1.55e+00 4.16e-01 7.69e+00 angle pdb=" C THR J 59 " pdb=" N LYS J 60 " pdb=" CA LYS J 60 " ideal model delta sigma weight residual 122.42 118.13 4.29 1.55e+00 4.16e-01 7.64e+00 angle pdb=" C THR E 59 " pdb=" N LYS E 60 " pdb=" CA LYS E 60 " ideal model delta sigma weight residual 122.42 118.14 4.28 1.55e+00 4.16e-01 7.62e+00 angle pdb=" C THR B 59 " pdb=" N LYS B 60 " pdb=" CA LYS B 60 " ideal model delta sigma weight residual 122.42 118.15 4.27 1.55e+00 4.16e-01 7.59e+00 ... (remaining 5865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.90: 2330 14.90 - 29.80: 150 29.80 - 44.70: 20 44.70 - 59.60: 30 59.60 - 74.50: 10 Dihedral angle restraints: 2540 sinusoidal: 850 harmonic: 1690 Sorted by residual: dihedral pdb=" CA GLY E 73 " pdb=" C GLY E 73 " pdb=" N VAL E 74 " pdb=" CA VAL E 74 " ideal model delta harmonic sigma weight residual 180.00 159.69 20.31 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA GLY C 73 " pdb=" C GLY C 73 " pdb=" N VAL C 74 " pdb=" CA VAL C 74 " ideal model delta harmonic sigma weight residual 180.00 159.71 20.29 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA GLY A 73 " pdb=" C GLY A 73 " pdb=" N VAL A 74 " pdb=" CA VAL A 74 " ideal model delta harmonic sigma weight residual 180.00 159.71 20.29 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 2537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 289 0.040 - 0.079: 232 0.079 - 0.118: 199 0.118 - 0.157: 35 0.157 - 0.197: 15 Chirality restraints: 770 Sorted by residual: chirality pdb=" CB THR E 44 " pdb=" CA THR E 44 " pdb=" OG1 THR E 44 " pdb=" CG2 THR E 44 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.20 2.00e-01 2.50e+01 9.67e-01 chirality pdb=" CB THR B 44 " pdb=" CA THR B 44 " pdb=" OG1 THR B 44 " pdb=" CG2 THR B 44 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.49e-01 chirality pdb=" CB THR H 44 " pdb=" CA THR H 44 " pdb=" OG1 THR H 44 " pdb=" CG2 THR H 44 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.39e-01 ... (remaining 767 not shown) Planarity restraints: 720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 75 " -0.019 2.00e-02 2.50e+03 3.72e-02 1.39e+01 pdb=" C THR C 75 " 0.064 2.00e-02 2.50e+03 pdb=" O THR C 75 " -0.024 2.00e-02 2.50e+03 pdb=" N ALA C 76 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 75 " 0.019 2.00e-02 2.50e+03 3.72e-02 1.39e+01 pdb=" C THR D 75 " -0.064 2.00e-02 2.50e+03 pdb=" O THR D 75 " 0.024 2.00e-02 2.50e+03 pdb=" N ALA D 76 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 75 " -0.018 2.00e-02 2.50e+03 3.71e-02 1.38e+01 pdb=" C THR B 75 " 0.064 2.00e-02 2.50e+03 pdb=" O THR B 75 " -0.024 2.00e-02 2.50e+03 pdb=" N ALA B 76 " -0.022 2.00e-02 2.50e+03 ... (remaining 717 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 351 2.75 - 3.29: 3533 3.29 - 3.82: 7636 3.82 - 4.36: 8344 4.36 - 4.90: 16105 Nonbonded interactions: 35969 Sorted by model distance: nonbonded pdb=" O GLY D 67 " pdb=" O HOH D 201 " model vdw 2.209 3.040 nonbonded pdb=" O GLY J 67 " pdb=" O HOH J 201 " model vdw 2.209 3.040 nonbonded pdb=" O GLY C 67 " pdb=" O HOH C 201 " model vdw 2.209 3.040 nonbonded pdb=" O GLY H 67 " pdb=" O HOH H 201 " model vdw 2.209 3.040 nonbonded pdb=" O GLY I 67 " pdb=" O HOH I 201 " model vdw 2.209 3.040 ... (remaining 35964 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.460 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:10.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 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 : 0.012 0.061 4350 Z= 0.493 Angle : 0.960 5.959 5870 Z= 0.568 Chirality : 0.071 0.197 770 Planarity : 0.009 0.037 720 Dihedral : 13.714 74.498 1480 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.27), residues: 610 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.51 (0.21), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS H 50 PHE 0.018 0.005 PHE G 94 TYR 0.006 0.003 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.09747 ( 95) hydrogen bonds : angle 8.56883 ( 285) covalent geometry : bond 0.01228 ( 4350) covalent geometry : angle 0.96006 ( 5870) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.516 Fit side-chains REVERT: A 43 LYS cc_start: 0.8214 (mttt) cc_final: 0.7968 (mptt) REVERT: A 57 GLU cc_start: 0.8060 (tt0) cc_final: 0.7850 (tm-30) REVERT: A 83 GLU cc_start: 0.7374 (mt-10) cc_final: 0.7070 (mp0) REVERT: C 43 LYS cc_start: 0.8461 (mttt) cc_final: 0.8154 (mptt) REVERT: C 57 GLU cc_start: 0.8094 (tt0) cc_final: 0.7891 (tm-30) REVERT: C 81 THR cc_start: 0.9027 (m) cc_final: 0.8503 (m) REVERT: C 83 GLU cc_start: 0.7334 (mt-10) cc_final: 0.6879 (mp0) REVERT: E 43 LYS cc_start: 0.8360 (mttt) cc_final: 0.8145 (mptt) REVERT: E 57 GLU cc_start: 0.7880 (tt0) cc_final: 0.7613 (tm-30) REVERT: G 43 LYS cc_start: 0.8243 (mttt) cc_final: 0.8006 (mptt) REVERT: G 46 LYS cc_start: 0.8557 (tttt) cc_final: 0.7979 (tmtm) REVERT: G 83 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6892 (mp0) REVERT: I 46 LYS cc_start: 0.8667 (tttt) cc_final: 0.8032 (tmtm) REVERT: F 43 LYS cc_start: 0.8309 (mttt) cc_final: 0.8090 (mptt) REVERT: F 57 GLU cc_start: 0.7929 (tt0) cc_final: 0.7633 (tm-30) REVERT: J 46 LYS cc_start: 0.8686 (tttt) cc_final: 0.8038 (tmtm) REVERT: D 43 LYS cc_start: 0.8330 (mttt) cc_final: 0.8046 (mptt) REVERT: D 57 GLU cc_start: 0.8098 (tt0) cc_final: 0.7898 (tm-30) REVERT: D 81 THR cc_start: 0.9061 (m) cc_final: 0.8495 (m) REVERT: D 83 GLU cc_start: 0.7359 (mt-10) cc_final: 0.6922 (mp0) REVERT: H 43 LYS cc_start: 0.8130 (mttt) cc_final: 0.7882 (mptt) REVERT: H 46 LYS cc_start: 0.8564 (tttt) cc_final: 0.8072 (tmtm) REVERT: H 83 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6717 (mp0) REVERT: B 43 LYS cc_start: 0.8388 (mttt) cc_final: 0.8147 (mptt) REVERT: B 46 LYS cc_start: 0.8597 (tttt) cc_final: 0.8348 (tmtp) REVERT: B 57 GLU cc_start: 0.7998 (tt0) cc_final: 0.7795 (tm-30) REVERT: B 83 GLU cc_start: 0.7364 (mt-10) cc_final: 0.6901 (mp0) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 1.0620 time to fit residues: 153.1474 Evaluate side-chains 128 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.140507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.124371 restraints weight = 3841.613| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 1.59 r_work: 0.3628 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3528 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4350 Z= 0.121 Angle : 0.524 5.861 5870 Z= 0.295 Chirality : 0.054 0.128 770 Planarity : 0.002 0.008 720 Dihedral : 5.594 17.286 630 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 5.00 % Allowed : 14.77 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.98 (0.33), residues: 610 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.74 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS D 50 PHE 0.014 0.003 PHE J 94 TYR 0.009 0.002 TYR A 39 Details of bonding type rmsd hydrogen bonds : bond 0.02069 ( 95) hydrogen bonds : angle 6.33082 ( 285) covalent geometry : bond 0.00241 ( 4350) covalent geometry : angle 0.52387 ( 5870) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.468 Fit side-chains REVERT: A 43 LYS cc_start: 0.8569 (mttt) cc_final: 0.7992 (mptt) REVERT: A 57 GLU cc_start: 0.8621 (tt0) cc_final: 0.8214 (tm-30) REVERT: A 83 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7251 (mp0) REVERT: C 43 LYS cc_start: 0.8613 (mttt) cc_final: 0.7992 (mptt) REVERT: C 57 GLU cc_start: 0.8650 (tt0) cc_final: 0.8297 (tm-30) REVERT: C 81 THR cc_start: 0.9061 (m) cc_final: 0.8818 (m) REVERT: C 83 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7185 (mp0) REVERT: E 57 GLU cc_start: 0.8355 (tt0) cc_final: 0.7961 (tm-30) REVERT: G 43 LYS cc_start: 0.8601 (mttt) cc_final: 0.8035 (mptt) REVERT: G 46 LYS cc_start: 0.8935 (tttt) cc_final: 0.8344 (tmtm) REVERT: G 83 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7145 (mp0) REVERT: I 43 LYS cc_start: 0.8476 (mptt) cc_final: 0.8167 (mptt) REVERT: F 57 GLU cc_start: 0.8382 (tt0) cc_final: 0.7966 (tm-30) REVERT: J 46 LYS cc_start: 0.8880 (tttt) cc_final: 0.8256 (tmtm) REVERT: J 57 GLU cc_start: 0.8577 (tt0) cc_final: 0.8164 (tm-30) REVERT: D 43 LYS cc_start: 0.8589 (mttt) cc_final: 0.7963 (mptt) REVERT: D 57 GLU cc_start: 0.8648 (tt0) cc_final: 0.8289 (tm-30) REVERT: D 81 THR cc_start: 0.9081 (m) cc_final: 0.8732 (m) REVERT: D 83 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7199 (mp0) REVERT: H 43 LYS cc_start: 0.8613 (mttt) cc_final: 0.8041 (mptt) REVERT: H 46 LYS cc_start: 0.8817 (tttt) cc_final: 0.8292 (tmtm) REVERT: H 83 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7145 (mp0) REVERT: B 43 LYS cc_start: 0.8636 (mttt) cc_final: 0.8046 (mptt) REVERT: B 57 GLU cc_start: 0.8623 (tt0) cc_final: 0.8178 (tm-30) REVERT: B 83 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7297 (mp0) outliers start: 22 outliers final: 4 residues processed: 128 average time/residue: 1.0509 time to fit residues: 139.6346 Evaluate side-chains 120 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 116 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 27 optimal weight: 20.0000 chunk 4 optimal weight: 40.0000 chunk 5 optimal weight: 40.0000 chunk 37 optimal weight: 20.0000 chunk 22 optimal weight: 40.0000 chunk 11 optimal weight: 50.0000 chunk 52 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 20 optimal weight: 40.0000 chunk 16 optimal weight: 6.9990 chunk 8 optimal weight: 40.0000 overall best weight: 12.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.131199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.115202 restraints weight = 3963.852| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.59 r_work: 0.3526 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 4350 Z= 0.227 Angle : 0.660 6.742 5870 Z= 0.369 Chirality : 0.057 0.153 770 Planarity : 0.003 0.011 720 Dihedral : 6.302 19.766 630 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 5.23 % Allowed : 14.55 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.83 (0.34), residues: 610 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.62 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 50 PHE 0.016 0.004 PHE G 94 TYR 0.012 0.002 TYR E 39 Details of bonding type rmsd hydrogen bonds : bond 0.02695 ( 95) hydrogen bonds : angle 6.10048 ( 285) covalent geometry : bond 0.00528 ( 4350) covalent geometry : angle 0.66009 ( 5870) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.463 Fit side-chains REVERT: A 43 LYS cc_start: 0.8747 (mttt) cc_final: 0.8091 (mptt) REVERT: A 46 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8192 (tmtp) REVERT: A 57 GLU cc_start: 0.8684 (tt0) cc_final: 0.8158 (tm-30) REVERT: A 83 GLU cc_start: 0.8392 (mt-10) cc_final: 0.7632 (mp0) REVERT: C 43 LYS cc_start: 0.8725 (mttt) cc_final: 0.8014 (mptt) REVERT: C 57 GLU cc_start: 0.8717 (tt0) cc_final: 0.8280 (tm-30) REVERT: E 43 LYS cc_start: 0.8641 (mttt) cc_final: 0.7986 (mptt) REVERT: E 57 GLU cc_start: 0.8428 (tt0) cc_final: 0.7991 (tm-30) REVERT: G 43 LYS cc_start: 0.8567 (mttt) cc_final: 0.7912 (mptt) REVERT: G 46 LYS cc_start: 0.8874 (tttt) cc_final: 0.8240 (tmtm) REVERT: G 83 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7261 (mp0) REVERT: I 46 LYS cc_start: 0.8873 (tmtp) cc_final: 0.8292 (tmtm) REVERT: I 57 GLU cc_start: 0.8584 (tt0) cc_final: 0.8232 (tm-30) REVERT: I 83 GLU cc_start: 0.8477 (mt-10) cc_final: 0.7503 (mp0) REVERT: F 43 LYS cc_start: 0.8626 (mttt) cc_final: 0.7964 (mptt) REVERT: F 57 GLU cc_start: 0.8422 (tt0) cc_final: 0.7976 (tm-30) REVERT: J 46 LYS cc_start: 0.8884 (tttt) cc_final: 0.8146 (tmtm) REVERT: J 57 GLU cc_start: 0.8633 (tt0) cc_final: 0.8221 (tm-30) REVERT: J 83 GLU cc_start: 0.8465 (mt-10) cc_final: 0.7558 (mp0) REVERT: D 43 LYS cc_start: 0.8716 (mttt) cc_final: 0.8012 (mptt) REVERT: D 57 GLU cc_start: 0.8707 (tt0) cc_final: 0.8267 (tm-30) REVERT: H 43 LYS cc_start: 0.8605 (mttt) cc_final: 0.7957 (mptt) REVERT: H 46 LYS cc_start: 0.8809 (tttt) cc_final: 0.8144 (tmtm) REVERT: H 83 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7287 (mp0) REVERT: B 43 LYS cc_start: 0.8746 (mttt) cc_final: 0.8083 (mptt) REVERT: B 57 GLU cc_start: 0.8692 (tt0) cc_final: 0.8211 (tm-30) REVERT: B 83 GLU cc_start: 0.8416 (mt-10) cc_final: 0.7626 (mp0) outliers start: 23 outliers final: 15 residues processed: 124 average time/residue: 1.1232 time to fit residues: 144.2752 Evaluate side-chains 125 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 30.0000 chunk 43 optimal weight: 30.0000 chunk 50 optimal weight: 20.0000 chunk 38 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 11 optimal weight: 30.0000 chunk 13 optimal weight: 5.9990 chunk 39 optimal weight: 20.0000 chunk 56 optimal weight: 30.0000 chunk 32 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.134621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.118712 restraints weight = 3939.420| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.59 r_work: 0.3565 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4350 Z= 0.150 Angle : 0.556 6.044 5870 Z= 0.310 Chirality : 0.055 0.138 770 Planarity : 0.002 0.008 720 Dihedral : 5.765 18.294 630 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 5.45 % Allowed : 14.09 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.80 (0.34), residues: 610 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.60 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 50 PHE 0.015 0.004 PHE J 94 TYR 0.013 0.002 TYR E 39 Details of bonding type rmsd hydrogen bonds : bond 0.02236 ( 95) hydrogen bonds : angle 5.75374 ( 285) covalent geometry : bond 0.00335 ( 4350) covalent geometry : angle 0.55646 ( 5870) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.509 Fit side-chains REVERT: A 43 LYS cc_start: 0.8700 (mttt) cc_final: 0.8051 (mptt) REVERT: A 46 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8212 (tmtp) REVERT: A 57 GLU cc_start: 0.8668 (tt0) cc_final: 0.8176 (tm-30) REVERT: C 43 LYS cc_start: 0.8686 (mttt) cc_final: 0.7940 (mptt) REVERT: C 46 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8478 (tmtp) REVERT: C 57 GLU cc_start: 0.8716 (tt0) cc_final: 0.8261 (tm-30) REVERT: E 43 LYS cc_start: 0.8619 (mttt) cc_final: 0.7959 (mptt) REVERT: E 57 GLU cc_start: 0.8419 (tt0) cc_final: 0.8024 (tm-30) REVERT: G 43 LYS cc_start: 0.8619 (mttt) cc_final: 0.7995 (mptt) REVERT: G 46 LYS cc_start: 0.8884 (tttt) cc_final: 0.8310 (tmtm) REVERT: G 83 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7266 (mp0) REVERT: I 46 LYS cc_start: 0.8897 (tmtp) cc_final: 0.8239 (tmtm) REVERT: I 57 GLU cc_start: 0.8606 (tt0) cc_final: 0.8290 (tm-30) REVERT: I 83 GLU cc_start: 0.8492 (mt-10) cc_final: 0.7557 (mp0) REVERT: F 43 LYS cc_start: 0.8616 (mttt) cc_final: 0.7944 (mptt) REVERT: F 57 GLU cc_start: 0.8431 (tt0) cc_final: 0.8031 (tm-30) REVERT: J 46 LYS cc_start: 0.8893 (tttt) cc_final: 0.8210 (tmtm) REVERT: J 57 GLU cc_start: 0.8639 (tt0) cc_final: 0.8257 (tm-30) REVERT: D 43 LYS cc_start: 0.8664 (mttt) cc_final: 0.7964 (mptt) REVERT: D 57 GLU cc_start: 0.8718 (tt0) cc_final: 0.8258 (tm-30) REVERT: H 43 LYS cc_start: 0.8638 (mttt) cc_final: 0.8004 (mptt) REVERT: H 46 LYS cc_start: 0.8809 (tttt) cc_final: 0.8230 (tmtm) REVERT: H 83 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7289 (mp0) REVERT: B 43 LYS cc_start: 0.8721 (mttt) cc_final: 0.8060 (mptt) REVERT: B 57 GLU cc_start: 0.8690 (tt0) cc_final: 0.8184 (tm-30) outliers start: 24 outliers final: 16 residues processed: 119 average time/residue: 1.1102 time to fit residues: 136.9430 Evaluate side-chains 127 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 55 optimal weight: 40.0000 chunk 12 optimal weight: 30.0000 chunk 59 optimal weight: 50.0000 chunk 40 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 21 optimal weight: 0.6980 chunk 2 optimal weight: 40.0000 chunk 44 optimal weight: 8.9990 chunk 24 optimal weight: 30.0000 chunk 52 optimal weight: 20.0000 chunk 41 optimal weight: 30.0000 overall best weight: 9.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.132779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.116768 restraints weight = 3989.059| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.60 r_work: 0.3542 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4350 Z= 0.182 Angle : 0.598 6.242 5870 Z= 0.333 Chirality : 0.056 0.145 770 Planarity : 0.002 0.009 720 Dihedral : 5.958 18.844 630 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 5.91 % Allowed : 14.32 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.82 (0.34), residues: 610 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.61 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 50 PHE 0.016 0.004 PHE G 94 TYR 0.010 0.002 TYR B 39 Details of bonding type rmsd hydrogen bonds : bond 0.02444 ( 95) hydrogen bonds : angle 5.72504 ( 285) covalent geometry : bond 0.00417 ( 4350) covalent geometry : angle 0.59760 ( 5870) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.579 Fit side-chains REVERT: A 43 LYS cc_start: 0.8773 (mttt) cc_final: 0.8061 (mptt) REVERT: A 46 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8211 (tmtp) REVERT: A 57 GLU cc_start: 0.8657 (tt0) cc_final: 0.8185 (tm-30) REVERT: C 43 LYS cc_start: 0.8720 (mttt) cc_final: 0.7975 (mptt) REVERT: C 46 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8251 (tmtp) REVERT: C 57 GLU cc_start: 0.8744 (tt0) cc_final: 0.8289 (tm-30) REVERT: E 43 LYS cc_start: 0.8610 (mttt) cc_final: 0.7920 (mptt) REVERT: E 57 GLU cc_start: 0.8420 (tt0) cc_final: 0.8025 (tm-30) REVERT: G 43 LYS cc_start: 0.8655 (mttt) cc_final: 0.7984 (mptt) REVERT: G 46 LYS cc_start: 0.8880 (tttt) cc_final: 0.8299 (tmtm) REVERT: I 46 LYS cc_start: 0.8935 (tmtp) cc_final: 0.8278 (tmtm) REVERT: I 57 GLU cc_start: 0.8623 (tt0) cc_final: 0.8308 (tm-30) REVERT: F 43 LYS cc_start: 0.8643 (mttt) cc_final: 0.7974 (mptt) REVERT: F 57 GLU cc_start: 0.8431 (tt0) cc_final: 0.8028 (tm-30) REVERT: J 46 LYS cc_start: 0.8913 (tttt) cc_final: 0.8225 (tmtm) REVERT: J 57 GLU cc_start: 0.8671 (tt0) cc_final: 0.8255 (tm-30) REVERT: D 43 LYS cc_start: 0.8706 (mttt) cc_final: 0.7955 (mptt) REVERT: D 46 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8274 (tmtp) REVERT: D 57 GLU cc_start: 0.8729 (tt0) cc_final: 0.8272 (tm-30) REVERT: H 43 LYS cc_start: 0.8659 (mttt) cc_final: 0.7983 (mptt) REVERT: H 46 LYS cc_start: 0.8789 (tttt) cc_final: 0.8200 (tmtm) REVERT: B 43 LYS cc_start: 0.8755 (mttt) cc_final: 0.8061 (mptt) REVERT: B 54 THR cc_start: 0.8327 (OUTLIER) cc_final: 0.8000 (m) REVERT: B 57 GLU cc_start: 0.8677 (tt0) cc_final: 0.8209 (tm-30) outliers start: 26 outliers final: 17 residues processed: 120 average time/residue: 1.1495 time to fit residues: 143.2832 Evaluate side-chains 129 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 36 optimal weight: 30.0000 chunk 47 optimal weight: 50.0000 chunk 7 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 58 optimal weight: 30.0000 chunk 45 optimal weight: 40.0000 chunk 20 optimal weight: 30.0000 chunk 12 optimal weight: 20.0000 chunk 39 optimal weight: 30.0000 chunk 55 optimal weight: 20.0000 overall best weight: 14.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.130387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.114472 restraints weight = 3931.323| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.58 r_work: 0.3518 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 4350 Z= 0.250 Angle : 0.688 7.028 5870 Z= 0.384 Chirality : 0.058 0.157 770 Planarity : 0.003 0.012 720 Dihedral : 6.323 19.837 630 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 6.14 % Allowed : 15.91 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.90 (0.33), residues: 610 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.67 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 50 PHE 0.017 0.005 PHE G 94 TYR 0.013 0.003 TYR B 39 Details of bonding type rmsd hydrogen bonds : bond 0.02861 ( 95) hydrogen bonds : angle 5.83213 ( 285) covalent geometry : bond 0.00581 ( 4350) covalent geometry : angle 0.68817 ( 5870) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.481 Fit side-chains REVERT: A 43 LYS cc_start: 0.8808 (mttt) cc_final: 0.8090 (mptt) REVERT: A 46 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8202 (tmtp) REVERT: A 54 THR cc_start: 0.8336 (OUTLIER) cc_final: 0.8008 (m) REVERT: A 57 GLU cc_start: 0.8689 (tt0) cc_final: 0.8173 (tm-30) REVERT: C 43 LYS cc_start: 0.8718 (mttt) cc_final: 0.7922 (mptt) REVERT: C 46 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8195 (tmtp) REVERT: C 57 GLU cc_start: 0.8749 (tt0) cc_final: 0.8287 (tm-30) REVERT: E 43 LYS cc_start: 0.8671 (mttt) cc_final: 0.7970 (mptt) REVERT: E 57 GLU cc_start: 0.8429 (tt0) cc_final: 0.8008 (tm-30) REVERT: G 43 LYS cc_start: 0.8621 (mttt) cc_final: 0.7941 (mptt) REVERT: G 46 LYS cc_start: 0.8859 (tttt) cc_final: 0.8244 (tmtm) REVERT: I 46 LYS cc_start: 0.8942 (tmtp) cc_final: 0.8340 (tmtm) REVERT: I 57 GLU cc_start: 0.8643 (tt0) cc_final: 0.8282 (tm-30) REVERT: F 43 LYS cc_start: 0.8658 (mttt) cc_final: 0.7941 (mptt) REVERT: F 57 GLU cc_start: 0.8435 (tt0) cc_final: 0.8008 (tm-30) REVERT: J 46 LYS cc_start: 0.8875 (tttt) cc_final: 0.8158 (tmtm) REVERT: D 43 LYS cc_start: 0.8728 (mttt) cc_final: 0.7959 (mptt) REVERT: D 46 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8267 (tmtp) REVERT: D 57 GLU cc_start: 0.8738 (tt0) cc_final: 0.8277 (tm-30) REVERT: H 43 LYS cc_start: 0.8633 (mttt) cc_final: 0.7954 (mptt) REVERT: H 46 LYS cc_start: 0.8769 (tttt) cc_final: 0.8161 (tmtm) REVERT: B 43 LYS cc_start: 0.8781 (mttt) cc_final: 0.8069 (mptt) REVERT: B 54 THR cc_start: 0.8348 (OUTLIER) cc_final: 0.8012 (m) REVERT: B 57 GLU cc_start: 0.8717 (tt0) cc_final: 0.8255 (tm-30) outliers start: 27 outliers final: 16 residues processed: 121 average time/residue: 1.1275 time to fit residues: 141.2462 Evaluate side-chains 129 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/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-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.7215 > 50: distance: 14 - 16: 22.669 distance: 16 - 17: 13.382 distance: 17 - 18: 7.195 distance: 17 - 20: 38.679 distance: 18 - 19: 37.539 distance: 18 - 21: 18.856 distance: 21 - 22: 15.882 distance: 22 - 23: 36.728 distance: 23 - 24: 28.132 distance: 23 - 25: 24.811 distance: 25 - 26: 17.579 distance: 26 - 27: 24.571 distance: 26 - 29: 33.273 distance: 27 - 28: 28.572 distance: 27 - 31: 17.497 distance: 29 - 30: 18.485 distance: 31 - 32: 7.109 distance: 32 - 33: 13.715 distance: 32 - 35: 11.992 distance: 33 - 34: 11.978 distance: 33 - 39: 18.952 distance: 35 - 36: 18.593 distance: 35 - 37: 8.513 distance: 36 - 38: 5.758 distance: 39 - 40: 11.888 distance: 39 - 128: 15.567 distance: 40 - 41: 11.706 distance: 40 - 43: 4.526 distance: 41 - 42: 7.455 distance: 41 - 44: 14.403 distance: 42 - 138: 10.543 distance: 44 - 45: 8.097 distance: 45 - 46: 24.928 distance: 45 - 48: 18.333 distance: 46 - 47: 20.797 distance: 46 - 49: 10.596 distance: 49 - 50: 13.249 distance: 49 - 141: 9.391 distance: 50 - 51: 12.570 distance: 50 - 53: 10.826 distance: 51 - 52: 13.004 distance: 51 - 54: 12.745 distance: 52 - 148: 14.451 distance: 54 - 55: 26.331 distance: 55 - 56: 11.386 distance: 55 - 58: 6.599 distance: 56 - 57: 6.249 distance: 56 - 61: 20.303 distance: 58 - 59: 14.290 distance: 58 - 60: 5.623 distance: 61 - 62: 17.246 distance: 61 - 151: 13.965 distance: 62 - 63: 13.787 distance: 63 - 64: 4.358 distance: 63 - 65: 15.805 distance: 65 - 66: 11.478 distance: 66 - 67: 16.824 distance: 66 - 69: 25.278 distance: 67 - 68: 12.668 distance: 67 - 76: 11.803 distance: 69 - 70: 17.854 distance: 70 - 71: 18.338 distance: 70 - 72: 9.040 distance: 71 - 73: 6.071 distance: 72 - 74: 8.941 distance: 73 - 75: 10.681 distance: 74 - 75: 14.325