Starting phenix.real_space_refine on Mon Sep 23 17:43:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ufr_20759/09_2024/6ufr_20759.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ufr_20759/09_2024/6ufr_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ufr_20759/09_2024/6ufr_20759.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ufr_20759/09_2024/6ufr_20759.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ufr_20759/09_2024/6ufr_20759.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ufr_20759/09_2024/6ufr_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-5461/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: 1.84, per 1000 atoms: 0.42 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: 1.04 Conformation dependent library (CDL) restraints added in 588.8 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: 0.49 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: 1.00 Time building geometry restraints manager: 1.22 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = 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=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: 0.200 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 13.430 Find NCS groups from input model: 0.150 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:17.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.960 ------------------------------------------------------------------------------- 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= 0.847 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 0.484 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: 0.8582 time to fit residues: 123.6855 Evaluate side-chains 128 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 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= 0.165 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 *********************** 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 fitting. rotamer outliers: 22 poor density : 122 time to evaluate : 0.418 Fit side-chains REVERT: A 43 LYS cc_start: 0.8310 (mttt) cc_final: 0.8016 (mptt) REVERT: A 57 GLU cc_start: 0.8144 (tt0) cc_final: 0.7784 (tm-30) REVERT: A 83 GLU cc_start: 0.7454 (mt-10) cc_final: 0.6941 (mp0) REVERT: C 43 LYS cc_start: 0.8325 (mttt) cc_final: 0.7980 (mptt) REVERT: C 57 GLU cc_start: 0.8184 (tt0) cc_final: 0.7877 (tm-30) REVERT: C 81 THR cc_start: 0.8993 (m) cc_final: 0.8552 (m) REVERT: C 83 GLU cc_start: 0.7369 (mt-10) cc_final: 0.7010 (mp0) REVERT: E 57 GLU cc_start: 0.7936 (tt0) cc_final: 0.7603 (tm-30) REVERT: G 43 LYS cc_start: 0.8287 (mttt) cc_final: 0.8054 (mptt) REVERT: G 46 LYS cc_start: 0.8676 (tttt) cc_final: 0.8173 (tmtm) REVERT: G 83 GLU cc_start: 0.7317 (mt-10) cc_final: 0.6994 (mp0) REVERT: I 43 LYS cc_start: 0.8356 (mptt) cc_final: 0.8033 (mptt) REVERT: F 57 GLU cc_start: 0.7967 (tt0) cc_final: 0.7616 (tm-30) REVERT: J 46 LYS cc_start: 0.8644 (tttt) cc_final: 0.8102 (tmtm) REVERT: J 57 GLU cc_start: 0.8141 (tt0) cc_final: 0.7745 (tm-30) REVERT: D 43 LYS cc_start: 0.8314 (mttt) cc_final: 0.7969 (mptt) REVERT: D 57 GLU cc_start: 0.8189 (tt0) cc_final: 0.7870 (tm-30) REVERT: D 81 THR cc_start: 0.9008 (m) cc_final: 0.8469 (m) REVERT: D 83 GLU cc_start: 0.7386 (mt-10) cc_final: 0.6989 (mp0) REVERT: H 43 LYS cc_start: 0.8288 (mttt) cc_final: 0.8035 (mptt) REVERT: H 46 LYS cc_start: 0.8537 (tttt) cc_final: 0.8110 (tmtm) REVERT: H 83 GLU cc_start: 0.7360 (mt-10) cc_final: 0.7007 (mp0) REVERT: B 43 LYS cc_start: 0.8378 (mttt) cc_final: 0.8072 (mptt) REVERT: B 57 GLU cc_start: 0.8150 (tt0) cc_final: 0.7756 (tm-30) REVERT: B 83 GLU cc_start: 0.7522 (mt-10) cc_final: 0.6989 (mp0) outliers start: 22 outliers final: 4 residues processed: 128 average time/residue: 0.9349 time to fit residues: 124.2854 Evaluate side-chains 120 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 116 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 30 optimal weight: 20.0000 chunk 16 optimal weight: 6.9990 chunk 45 optimal weight: 30.0000 chunk 37 optimal weight: 20.0000 chunk 15 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 58 optimal weight: 40.0000 chunk 48 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 chunk 43 optimal weight: 30.0000 chunk 53 optimal weight: 50.0000 overall best weight: 9.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4350 Z= 0.293 Angle : 0.603 6.288 5870 Z= 0.337 Chirality : 0.056 0.145 770 Planarity : 0.002 0.009 720 Dihedral : 6.040 19.006 630 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 5.45 % Allowed : 14.77 % 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: -0.81 (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 0.015 0.004 PHE G 94 TYR 0.012 0.002 TYR E 39 *********************** 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 fitting. rotamer outliers: 24 poor density : 113 time to evaluate : 0.490 Fit side-chains REVERT: A 43 LYS cc_start: 0.8492 (mttt) cc_final: 0.8107 (mptt) REVERT: A 46 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.7998 (tmtp) REVERT: A 57 GLU cc_start: 0.8194 (tt0) cc_final: 0.7746 (tm-30) REVERT: A 83 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7232 (mp0) REVERT: C 43 LYS cc_start: 0.8418 (mttt) cc_final: 0.7996 (mptt) REVERT: C 57 GLU cc_start: 0.8247 (tt0) cc_final: 0.7864 (tm-30) REVERT: E 43 LYS cc_start: 0.8287 (mttt) cc_final: 0.7911 (mptt) REVERT: E 57 GLU cc_start: 0.7995 (tt0) cc_final: 0.7635 (tm-30) REVERT: G 43 LYS cc_start: 0.8276 (mttt) cc_final: 0.7973 (mptt) REVERT: G 46 LYS cc_start: 0.8646 (tttt) cc_final: 0.8115 (tmtm) REVERT: G 83 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7073 (mp0) REVERT: I 46 LYS cc_start: 0.8721 (tmtp) cc_final: 0.8158 (tmtm) REVERT: I 57 GLU cc_start: 0.8167 (tt0) cc_final: 0.7833 (tm-30) REVERT: I 83 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7215 (mp0) REVERT: F 43 LYS cc_start: 0.8287 (mttt) cc_final: 0.7905 (mptt) REVERT: F 57 GLU cc_start: 0.8011 (tt0) cc_final: 0.7639 (tm-30) REVERT: J 57 GLU cc_start: 0.8204 (tt0) cc_final: 0.7818 (tm-30) REVERT: J 83 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7272 (mp0) REVERT: D 43 LYS cc_start: 0.8415 (mttt) cc_final: 0.7984 (mptt) REVERT: D 57 GLU cc_start: 0.8249 (tt0) cc_final: 0.7862 (tm-30) REVERT: H 43 LYS cc_start: 0.8290 (mttt) cc_final: 0.7983 (mptt) REVERT: H 46 LYS cc_start: 0.8568 (tttt) cc_final: 0.8070 (tmtm) REVERT: H 83 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7131 (mp0) REVERT: B 43 LYS cc_start: 0.8492 (mttt) cc_final: 0.8121 (mptt) REVERT: B 57 GLU cc_start: 0.8197 (tt0) cc_final: 0.7734 (tm-30) REVERT: B 83 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7244 (mp0) outliers start: 24 outliers final: 16 residues processed: 124 average time/residue: 1.1390 time to fit residues: 146.2411 Evaluate side-chains 129 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 112 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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 74 VAL 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 41 optimal weight: 40.0000 chunk 28 optimal weight: 30.0000 chunk 6 optimal weight: 30.0000 chunk 26 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 57 optimal weight: 30.0000 chunk 51 optimal weight: 7.9990 chunk 15 optimal weight: 20.0000 chunk 48 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 overall best weight: 5.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4350 Z= 0.174 Angle : 0.500 5.474 5870 Z= 0.280 Chirality : 0.054 0.128 770 Planarity : 0.002 0.006 720 Dihedral : 5.386 16.742 630 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 5.23 % Allowed : 14.77 % Favored : 80.00 % 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: -0.78 (0.34), residues: 610 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.58 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 50 PHE 0.015 0.003 PHE J 94 TYR 0.012 0.002 TYR E 39 *********************** 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 133 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 110 time to evaluate : 0.488 Fit side-chains REVERT: A 43 LYS cc_start: 0.8464 (mttt) cc_final: 0.8058 (mptt) REVERT: A 46 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.7996 (tmtp) REVERT: A 57 GLU cc_start: 0.8177 (tt0) cc_final: 0.7769 (tm-30) REVERT: A 83 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7194 (mp0) REVERT: C 43 LYS cc_start: 0.8370 (mttt) cc_final: 0.7936 (mptt) REVERT: C 46 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8271 (tmtp) REVERT: C 57 GLU cc_start: 0.8217 (tt0) cc_final: 0.7804 (tm-30) REVERT: E 43 LYS cc_start: 0.8268 (mttt) cc_final: 0.7861 (mptt) REVERT: E 57 GLU cc_start: 0.7968 (tt0) cc_final: 0.7680 (tm-30) REVERT: G 43 LYS cc_start: 0.8348 (mttt) cc_final: 0.7997 (mptt) REVERT: G 83 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7030 (mp0) REVERT: I 46 LYS cc_start: 0.8736 (tmtp) cc_final: 0.8107 (tmtm) REVERT: I 57 GLU cc_start: 0.8153 (tt0) cc_final: 0.7843 (tm-30) REVERT: I 83 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7238 (mp0) REVERT: F 43 LYS cc_start: 0.8278 (mttt) cc_final: 0.7865 (mptt) REVERT: F 57 GLU cc_start: 0.7990 (tt0) cc_final: 0.7663 (tm-30) REVERT: J 46 LYS cc_start: 0.8625 (tmtp) cc_final: 0.7975 (tmtm) REVERT: J 57 GLU cc_start: 0.8173 (tt0) cc_final: 0.7808 (tm-30) REVERT: J 83 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7338 (mp0) REVERT: D 43 LYS cc_start: 0.8379 (mttt) cc_final: 0.7947 (mptt) REVERT: D 57 GLU cc_start: 0.8221 (tt0) cc_final: 0.7805 (tm-30) REVERT: H 43 LYS cc_start: 0.8335 (mttt) cc_final: 0.7987 (mptt) REVERT: H 46 LYS cc_start: 0.8541 (tttt) cc_final: 0.8042 (tmtm) REVERT: H 83 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7110 (mp0) REVERT: B 43 LYS cc_start: 0.8457 (mttt) cc_final: 0.8041 (mptt) REVERT: B 57 GLU cc_start: 0.8186 (tt0) cc_final: 0.7750 (tm-30) REVERT: B 83 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7212 (mp0) outliers start: 23 outliers final: 17 residues processed: 119 average time/residue: 1.0949 time to fit residues: 135.1519 Evaluate side-chains 128 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 109 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 74 VAL 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 0 optimal weight: 30.0000 chunk 43 optimal weight: 50.0000 chunk 23 optimal weight: 50.0000 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 30.0000 chunk 52 optimal weight: 30.0000 chunk 14 optimal weight: 30.0000 chunk 19 optimal weight: 50.0000 chunk 11 optimal weight: 50.0000 chunk 34 optimal weight: 8.9990 overall best weight: 14.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 4350 Z= 0.409 Angle : 0.677 6.817 5870 Z= 0.378 Chirality : 0.058 0.155 770 Planarity : 0.003 0.012 720 Dihedral : 6.254 19.532 630 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 6.14 % Allowed : 14.09 % 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: -0.85 (0.34), residues: 610 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.64 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 50 PHE 0.018 0.005 PHE G 94 TYR 0.011 0.003 TYR B 39 *********************** 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 135 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 108 time to evaluate : 0.476 Fit side-chains REVERT: A 43 LYS cc_start: 0.8537 (mttt) cc_final: 0.8079 (mptt) REVERT: A 46 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.7970 (tmtp) REVERT: A 57 GLU cc_start: 0.8244 (tt0) cc_final: 0.7800 (tm-30) REVERT: C 43 LYS cc_start: 0.8467 (mttt) cc_final: 0.7985 (mptt) REVERT: C 46 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.7998 (tmtp) REVERT: C 57 GLU cc_start: 0.8272 (tt0) cc_final: 0.7843 (tm-30) REVERT: E 43 LYS cc_start: 0.8361 (mttt) cc_final: 0.7921 (mptt) REVERT: E 57 GLU cc_start: 0.8018 (tt0) cc_final: 0.7671 (tm-30) REVERT: G 43 LYS cc_start: 0.8388 (mttt) cc_final: 0.8009 (mptt) REVERT: G 46 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8100 (tmtm) REVERT: G 83 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7105 (mp0) REVERT: I 46 LYS cc_start: 0.8775 (tmtp) cc_final: 0.8211 (tmtm) REVERT: I 57 GLU cc_start: 0.8211 (tt0) cc_final: 0.7903 (tm-30) REVERT: F 43 LYS cc_start: 0.8379 (mttt) cc_final: 0.7942 (mptt) REVERT: F 57 GLU cc_start: 0.8016 (tt0) cc_final: 0.7662 (tm-30) REVERT: J 46 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8053 (tmtm) REVERT: J 57 GLU cc_start: 0.8249 (tt0) cc_final: 0.7885 (tm-30) REVERT: D 43 LYS cc_start: 0.8445 (mttt) cc_final: 0.7988 (mptt) REVERT: D 46 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8053 (tmtp) REVERT: D 57 GLU cc_start: 0.8273 (tt0) cc_final: 0.7844 (tm-30) REVERT: H 43 LYS cc_start: 0.8385 (mttt) cc_final: 0.8021 (mptt) REVERT: H 46 LYS cc_start: 0.8555 (tttt) cc_final: 0.8011 (tmtm) REVERT: B 43 LYS cc_start: 0.8535 (mttt) cc_final: 0.8069 (mptt) REVERT: B 57 GLU cc_start: 0.8246 (tt0) cc_final: 0.7802 (tm-30) outliers start: 27 outliers final: 16 residues processed: 119 average time/residue: 1.1479 time to fit residues: 141.5998 Evaluate side-chains 128 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 107 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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 G residue 46 LYS 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 46 LYS 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 75 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 30.0000 chunk 58 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 20.0000 chunk 19 optimal weight: 40.0000 chunk 30 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 6 optimal weight: 20.0000 chunk 33 optimal weight: 8.9990 chunk 42 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4350 Z= 0.222 Angle : 0.546 5.808 5870 Z= 0.304 Chirality : 0.055 0.137 770 Planarity : 0.002 0.008 720 Dihedral : 5.649 17.750 630 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 6.14 % Allowed : 15.00 % Favored : 78.86 % 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: -0.81 (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 0.015 0.004 PHE G 94 TYR 0.011 0.002 TYR A 39 *********************** 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 fitting. rotamer outliers: 27 poor density : 111 time to evaluate : 0.462 Fit side-chains REVERT: A 43 LYS cc_start: 0.8550 (mttt) cc_final: 0.8109 (mptt) REVERT: A 46 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.7963 (tmtp) REVERT: A 57 GLU cc_start: 0.8184 (tt0) cc_final: 0.7755 (tm-30) REVERT: C 43 LYS cc_start: 0.8426 (mttt) cc_final: 0.7924 (mptt) REVERT: C 46 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8018 (tmtp) REVERT: C 57 GLU cc_start: 0.8233 (tt0) cc_final: 0.7889 (tm-30) REVERT: E 43 LYS cc_start: 0.8266 (mttt) cc_final: 0.7843 (mptt) REVERT: E 57 GLU cc_start: 0.7997 (tt0) cc_final: 0.7725 (tm-30) REVERT: G 43 LYS cc_start: 0.8337 (mttt) cc_final: 0.7940 (mptt) REVERT: G 46 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8113 (tmtm) REVERT: I 46 LYS cc_start: 0.8758 (tmtp) cc_final: 0.8131 (tmtm) REVERT: I 57 GLU cc_start: 0.8168 (tt0) cc_final: 0.7829 (tm-30) REVERT: F 43 LYS cc_start: 0.8271 (mttt) cc_final: 0.7845 (mptt) REVERT: F 57 GLU cc_start: 0.7996 (tt0) cc_final: 0.7723 (tm-30) REVERT: J 46 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8063 (tmtm) REVERT: D 43 LYS cc_start: 0.8409 (mttt) cc_final: 0.7921 (mptt) REVERT: D 57 GLU cc_start: 0.8226 (tt0) cc_final: 0.7862 (tm-30) REVERT: H 43 LYS cc_start: 0.8322 (mttt) cc_final: 0.7954 (mptt) REVERT: H 46 LYS cc_start: 0.8546 (tttt) cc_final: 0.8085 (tmtm) REVERT: B 43 LYS cc_start: 0.8531 (mttt) cc_final: 0.8102 (mptt) REVERT: B 57 GLU cc_start: 0.8204 (tt0) cc_final: 0.7764 (tm-30) outliers start: 27 outliers final: 17 residues processed: 120 average time/residue: 1.0791 time to fit residues: 134.4017 Evaluate side-chains 130 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 109 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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 G residue 46 LYS 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 46 LYS Chi-restraints excluded: chain J residue 54 THR 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 54 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 20.0000 chunk 48 optimal weight: 3.9990 chunk 57 optimal weight: 30.0000 chunk 36 optimal weight: 30.0000 chunk 35 optimal weight: 30.0000 chunk 26 optimal weight: 30.0000 chunk 23 optimal weight: 40.0000 chunk 34 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 39 optimal weight: 30.0000 overall best weight: 16.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 4350 Z= 0.462 Angle : 0.723 6.962 5870 Z= 0.404 Chirality : 0.060 0.161 770 Planarity : 0.003 0.013 720 Dihedral : 6.425 20.088 630 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 6.59 % Allowed : 15.91 % Favored : 77.50 % 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: -0.91 (0.33), residues: 610 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.68 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 50 PHE 0.018 0.005 PHE G 94 TYR 0.014 0.003 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 7 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 fitting. rotamer outliers: 29 poor density : 108 time to evaluate : 0.449 Fit side-chains REVERT: A 43 LYS cc_start: 0.8580 (mttt) cc_final: 0.8098 (mptt) REVERT: A 46 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.7959 (tmtp) REVERT: A 54 THR cc_start: 0.8110 (OUTLIER) cc_final: 0.7791 (m) REVERT: A 57 GLU cc_start: 0.8266 (tt0) cc_final: 0.7840 (tm-30) REVERT: C 43 LYS cc_start: 0.8495 (mttt) cc_final: 0.7989 (mptt) REVERT: C 46 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.7994 (tmtp) REVERT: C 57 GLU cc_start: 0.8299 (tt0) cc_final: 0.7882 (tm-30) REVERT: E 43 LYS cc_start: 0.8375 (mttt) cc_final: 0.7924 (mptt) REVERT: E 57 GLU cc_start: 0.8039 (tt0) cc_final: 0.7669 (tm-30) REVERT: G 43 LYS cc_start: 0.8361 (mttt) cc_final: 0.7962 (mptt) REVERT: G 46 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8142 (tmtm) REVERT: I 46 LYS cc_start: 0.8789 (tmtp) cc_final: 0.8221 (tmtm) REVERT: I 57 GLU cc_start: 0.8223 (tt0) cc_final: 0.7916 (tm-30) REVERT: F 43 LYS cc_start: 0.8370 (mttt) cc_final: 0.7933 (mptt) REVERT: F 57 GLU cc_start: 0.8046 (tt0) cc_final: 0.7669 (tm-30) REVERT: J 46 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8068 (tmtm) REVERT: D 43 LYS cc_start: 0.8453 (mttt) cc_final: 0.7970 (mptt) REVERT: D 57 GLU cc_start: 0.8297 (tt0) cc_final: 0.7875 (tm-30) REVERT: H 43 LYS cc_start: 0.8349 (mttt) cc_final: 0.7972 (mptt) REVERT: H 46 LYS cc_start: 0.8542 (tttt) cc_final: 0.7996 (tmtm) REVERT: B 43 LYS cc_start: 0.8591 (mttt) cc_final: 0.8112 (mptt) REVERT: B 46 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8439 (tmtp) REVERT: B 54 THR cc_start: 0.8107 (OUTLIER) cc_final: 0.7778 (m) REVERT: B 57 GLU cc_start: 0.8271 (tt0) cc_final: 0.7850 (tm-30) outliers start: 29 outliers final: 18 residues processed: 118 average time/residue: 1.1606 time to fit residues: 141.7040 Evaluate side-chains 130 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 105 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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 54 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain G residue 46 LYS 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 54 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain J residue 46 LYS 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 46 LYS Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 30.0000 chunk 5 optimal weight: 50.0000 chunk 45 optimal weight: 30.0000 chunk 52 optimal weight: 6.9990 chunk 55 optimal weight: 20.0000 chunk 50 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 32 optimal weight: 0.2980 chunk 23 optimal weight: 40.0000 chunk 42 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 overall best weight: 6.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4350 Z= 0.209 Angle : 0.538 5.732 5870 Z= 0.301 Chirality : 0.055 0.135 770 Planarity : 0.002 0.007 720 Dihedral : 5.607 17.668 630 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 6.59 % Allowed : 15.23 % Favored : 78.18 % 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: -0.85 (0.33), residues: 610 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.63 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 50 PHE 0.015 0.003 PHE G 94 TYR 0.013 0.002 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 8 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 136 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 107 time to evaluate : 0.486 Fit side-chains REVERT: A 43 LYS cc_start: 0.8505 (mttt) cc_final: 0.8044 (mptt) REVERT: A 46 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.7960 (tmtp) REVERT: A 54 THR cc_start: 0.8048 (OUTLIER) cc_final: 0.7734 (m) REVERT: A 57 GLU cc_start: 0.8184 (tt0) cc_final: 0.7783 (tm-30) REVERT: C 43 LYS cc_start: 0.8395 (mttt) cc_final: 0.7920 (mptt) REVERT: C 46 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.7968 (tmtp) REVERT: C 57 GLU cc_start: 0.8246 (tt0) cc_final: 0.7908 (tm-30) REVERT: E 43 LYS cc_start: 0.8286 (mttt) cc_final: 0.7812 (mptt) REVERT: E 57 GLU cc_start: 0.8001 (tt0) cc_final: 0.7726 (tm-30) REVERT: G 43 LYS cc_start: 0.8340 (mttt) cc_final: 0.7992 (mptt) REVERT: G 46 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8063 (tmtm) REVERT: I 46 LYS cc_start: 0.8776 (tmtp) cc_final: 0.8142 (tmtm) REVERT: I 57 GLU cc_start: 0.8164 (tt0) cc_final: 0.7840 (tm-30) REVERT: F 43 LYS cc_start: 0.8276 (mttt) cc_final: 0.7821 (mptt) REVERT: F 57 GLU cc_start: 0.7999 (tt0) cc_final: 0.7722 (tm-30) REVERT: J 46 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8055 (tmtm) REVERT: D 43 LYS cc_start: 0.8379 (mttt) cc_final: 0.7899 (mptt) REVERT: D 57 GLU cc_start: 0.8242 (tt0) cc_final: 0.7906 (tm-30) REVERT: H 43 LYS cc_start: 0.8349 (mttt) cc_final: 0.7988 (mptt) REVERT: H 46 LYS cc_start: 0.8532 (tttt) cc_final: 0.8096 (tmtm) REVERT: B 43 LYS cc_start: 0.8508 (mttt) cc_final: 0.8046 (mptt) REVERT: B 54 THR cc_start: 0.8063 (OUTLIER) cc_final: 0.7740 (m) REVERT: B 57 GLU cc_start: 0.8201 (tt0) cc_final: 0.7798 (tm-30) outliers start: 29 outliers final: 20 residues processed: 116 average time/residue: 1.1311 time to fit residues: 136.0332 Evaluate side-chains 132 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 106 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 54 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain J residue 46 LYS 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 54 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 20.0000 chunk 50 optimal weight: 40.0000 chunk 53 optimal weight: 50.0000 chunk 35 optimal weight: 20.0000 chunk 56 optimal weight: 30.0000 chunk 34 optimal weight: 20.0000 chunk 27 optimal weight: 30.0000 chunk 39 optimal weight: 30.0000 chunk 59 optimal weight: 50.0000 chunk 55 optimal weight: 30.0000 chunk 47 optimal weight: 50.0000 overall best weight: 24.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.075 4350 Z= 0.640 Angle : 0.849 7.816 5870 Z= 0.476 Chirality : 0.064 0.175 770 Planarity : 0.004 0.017 720 Dihedral : 6.798 21.103 630 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 6.59 % Allowed : 15.23 % Favored : 78.18 % 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: -1.02 (0.33), residues: 610 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.77 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS F 50 PHE 0.019 0.006 PHE G 94 TYR 0.017 0.004 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 9 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 133 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 104 time to evaluate : 0.482 Fit side-chains REVERT: A 43 LYS cc_start: 0.8597 (mttt) cc_final: 0.8097 (mptt) REVERT: A 46 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.7976 (tmtp) REVERT: A 57 GLU cc_start: 0.8295 (tt0) cc_final: 0.7849 (tm-30) REVERT: C 43 LYS cc_start: 0.8513 (mttt) cc_final: 0.7994 (mptt) REVERT: C 46 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.7972 (tmtp) REVERT: C 57 GLU cc_start: 0.8302 (tt0) cc_final: 0.7873 (tm-30) REVERT: E 43 LYS cc_start: 0.8454 (mttt) cc_final: 0.7981 (mptt) REVERT: E 57 GLU cc_start: 0.8102 (tt0) cc_final: 0.7674 (tm-30) REVERT: G 43 LYS cc_start: 0.8352 (mttt) cc_final: 0.7996 (mptt) REVERT: G 46 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8157 (tmtm) REVERT: I 46 LYS cc_start: 0.8795 (tmtp) cc_final: 0.8220 (tmtm) REVERT: I 57 GLU cc_start: 0.8216 (tt0) cc_final: 0.7902 (tm-30) REVERT: F 43 LYS cc_start: 0.8457 (mttt) cc_final: 0.7986 (mptt) REVERT: F 57 GLU cc_start: 0.8100 (tt0) cc_final: 0.7668 (tm-30) REVERT: J 46 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8127 (tmtm) REVERT: D 43 LYS cc_start: 0.8512 (mttt) cc_final: 0.7993 (mptt) REVERT: D 46 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8008 (tmtp) REVERT: D 57 GLU cc_start: 0.8315 (tt0) cc_final: 0.7874 (tm-30) REVERT: D 97 LYS cc_start: 0.8084 (mttt) cc_final: 0.7778 (mtpt) REVERT: H 43 LYS cc_start: 0.8332 (mttt) cc_final: 0.7955 (mptt) REVERT: H 46 LYS cc_start: 0.8518 (tttt) cc_final: 0.7958 (tmtm) REVERT: B 43 LYS cc_start: 0.8575 (mttt) cc_final: 0.8084 (mptt) REVERT: B 57 GLU cc_start: 0.8302 (tt0) cc_final: 0.7859 (tm-30) outliers start: 29 outliers final: 17 residues processed: 115 average time/residue: 1.2124 time to fit residues: 144.1960 Evaluate side-chains 122 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 100 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS 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 54 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G 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 54 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain J residue 46 LYS 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 14 optimal weight: 20.0000 chunk 43 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 47 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4350 Z= 0.161 Angle : 0.506 5.529 5870 Z= 0.284 Chirality : 0.054 0.126 770 Planarity : 0.002 0.007 720 Dihedral : 5.414 16.772 630 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.18 % Allowed : 18.64 % Favored : 78.18 % 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: -0.85 (0.33), residues: 610 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.64 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 50 PHE 0.014 0.003 PHE G 94 TYR 0.016 0.003 TYR B 39 ********************** REFINEMENT MACRO_CYCLE 10 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 124 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 110 time to evaluate : 0.480 Fit side-chains REVERT: A 43 LYS cc_start: 0.8463 (mttt) cc_final: 0.8036 (mptt) REVERT: A 54 THR cc_start: 0.8070 (m) cc_final: 0.7761 (m) REVERT: A 57 GLU cc_start: 0.8190 (tt0) cc_final: 0.7818 (tm-30) REVERT: C 43 LYS cc_start: 0.8392 (mttt) cc_final: 0.7910 (mptt) REVERT: C 57 GLU cc_start: 0.8236 (tt0) cc_final: 0.7931 (tm-30) REVERT: E 43 LYS cc_start: 0.8242 (mttt) cc_final: 0.7767 (mptt) REVERT: E 57 GLU cc_start: 0.8012 (tt0) cc_final: 0.7738 (tm-30) REVERT: G 43 LYS cc_start: 0.8356 (mttt) cc_final: 0.8008 (mptt) REVERT: G 46 LYS cc_start: 0.8746 (tmtp) cc_final: 0.8078 (tmtm) REVERT: I 46 LYS cc_start: 0.8746 (tmtp) cc_final: 0.8135 (tmtm) REVERT: I 57 GLU cc_start: 0.8172 (tt0) cc_final: 0.7844 (tm-30) REVERT: F 43 LYS cc_start: 0.8248 (mttt) cc_final: 0.7763 (mptt) REVERT: F 57 GLU cc_start: 0.8011 (tt0) cc_final: 0.7733 (tm-30) REVERT: J 46 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8035 (tmtm) REVERT: D 43 LYS cc_start: 0.8383 (mttt) cc_final: 0.7889 (mptt) REVERT: D 57 GLU cc_start: 0.8230 (tt0) cc_final: 0.7930 (tm-30) REVERT: H 43 LYS cc_start: 0.8330 (mttt) cc_final: 0.7995 (mptt) REVERT: H 46 LYS cc_start: 0.8524 (tttt) cc_final: 0.8078 (tmtm) REVERT: B 43 LYS cc_start: 0.8511 (mttt) cc_final: 0.8054 (mptt) outliers start: 14 outliers final: 12 residues processed: 115 average time/residue: 1.2587 time to fit residues: 149.6703 Evaluate side-chains 121 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain E residue 54 THR 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 54 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 20.0000 chunk 6 optimal weight: 30.0000 chunk 8 optimal weight: 30.0000 chunk 41 optimal weight: 10.0000 chunk 2 optimal weight: 40.0000 chunk 34 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 1 optimal weight: 40.0000 chunk 38 optimal weight: 0.0470 overall best weight: 5.0088 ------------------------------------------------------------------------------- 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 = 0.3885 r_free = 0.3885 target = 0.137615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.122262 restraints weight = 3927.329| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 1.57 r_work: 0.3609 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4350 Z= 0.166 Angle : 0.492 5.186 5870 Z= 0.277 Chirality : 0.054 0.127 770 Planarity : 0.002 0.007 720 Dihedral : 5.235 16.037 630 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.18 % Allowed : 20.00 % Favored : 76.82 % 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: -0.79 (0.34), residues: 610 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.59 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS G 50 PHE 0.014 0.003 PHE J 94 TYR 0.016 0.002 TYR B 39 =============================================================================== Job complete usr+sys time: 2277.16 seconds wall clock time: 40 minutes 32.51 seconds (2432.51 seconds total)