Starting phenix.real_space_refine on Wed Mar 4 14:13:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p37_13178/03_2026/7p37_13178_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p37_13178/03_2026/7p37_13178.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7p37_13178/03_2026/7p37_13178_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p37_13178/03_2026/7p37_13178_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7p37_13178/03_2026/7p37_13178.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p37_13178/03_2026/7p37_13178.map" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.080 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: 6 Type Number sf(0) Gaussians Zn 12 6.06 5 P 72 5.49 5 S 96 5.16 5 C 8652 2.51 5 N 2712 2.21 5 O 2952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14496 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1145 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain: "B" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1145 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 24 SG CYS A 3 24.063 31.536 29.041 1.00 41.20 S ATOM 48 SG CYS A 6 21.180 29.864 27.166 1.00 45.02 S ATOM 254 SG CYS A 31 22.367 33.208 26.023 1.00 41.51 S ATOM 275 SG CYS A 34 20.540 32.972 29.312 1.00 44.03 S ATOM 6894 SG CYS B 3 74.054 42.619 65.365 1.00 11.76 S ATOM 6918 SG CYS B 6 72.100 45.890 65.731 1.00 12.15 S ATOM 7124 SG CYS B 31 75.196 45.364 67.758 1.00 13.45 S ATOM 7145 SG CYS B 34 72.067 43.335 68.534 1.00 13.85 S Restraints were copied for chains: C, E, G, I, K, D, F, H, J, L Time building chain proxies: 1.92, per 1000 atoms: 0.13 Number of scatterers: 14496 At special positions: 0 Unit cell: (129.31, 114.57, 89.11, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 12 29.99 S 96 16.00 P 72 15.00 O 2952 8.00 N 2712 7.00 C 8652 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 44 " - pdb=" SG CYS E 44 " distance=0.00 Simple disulfide: pdb=" SG CYS E 71 " - pdb=" SG CYS E 71 " distance=0.00 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: 1.27 Conformation dependent library (CDL) restraints added in 500.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 203 " pdb="ZN ZN A 203 " - pdb=" SG CYS A 31 " pdb="ZN ZN A 203 " - pdb=" SG CYS A 6 " pdb="ZN ZN A 203 " - pdb=" SG CYS A 34 " pdb="ZN ZN A 203 " - pdb=" SG CYS A 3 " pdb=" ZN B 203 " pdb="ZN ZN B 203 " - pdb=" SG CYS B 31 " pdb="ZN ZN B 203 " - pdb=" SG CYS B 6 " pdb="ZN ZN B 203 " - pdb=" SG CYS B 34 " pdb="ZN ZN B 203 " - pdb=" SG CYS B 3 " pdb=" ZN C 203 " pdb="ZN ZN C 203 " - pdb=" SG CYS C 31 " pdb="ZN ZN C 203 " - pdb=" SG CYS C 6 " pdb="ZN ZN C 203 " - pdb=" SG CYS C 34 " pdb="ZN ZN C 203 " - pdb=" SG CYS C 3 " pdb=" ZN D 203 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 6 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 31 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 34 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 3 " pdb=" ZN E 203 " pdb="ZN ZN E 203 " - pdb=" SG CYS E 31 " pdb="ZN ZN E 203 " - pdb=" SG CYS E 6 " pdb="ZN ZN E 203 " - pdb=" SG CYS E 34 " pdb="ZN ZN E 203 " - pdb=" SG CYS E 3 " pdb=" ZN F 203 " pdb="ZN ZN F 203 " - pdb=" SG CYS F 6 " pdb="ZN ZN F 203 " - pdb=" SG CYS F 34 " pdb="ZN ZN F 203 " - pdb=" SG CYS F 31 " pdb="ZN ZN F 203 " - pdb=" SG CYS F 3 " pdb=" ZN G 203 " pdb="ZN ZN G 203 " - pdb=" SG CYS G 31 " pdb="ZN ZN G 203 " - pdb=" SG CYS G 6 " pdb="ZN ZN G 203 " - pdb=" SG CYS G 34 " pdb="ZN ZN G 203 " - pdb=" SG CYS G 3 " pdb=" ZN H 203 " pdb="ZN ZN H 203 " - pdb=" SG CYS H 6 " pdb="ZN ZN H 203 " - pdb=" SG CYS H 31 " pdb="ZN ZN H 203 " - pdb=" SG CYS H 34 " pdb="ZN ZN H 203 " - pdb=" SG CYS H 3 " pdb=" ZN I 203 " pdb="ZN ZN I 203 " - pdb=" SG CYS I 31 " pdb="ZN ZN I 203 " - pdb=" SG CYS I 6 " pdb="ZN ZN I 203 " - pdb=" SG CYS I 34 " pdb="ZN ZN I 203 " - pdb=" SG CYS I 3 " pdb=" ZN J 203 " pdb="ZN ZN J 203 " - pdb=" SG CYS J 6 " pdb="ZN ZN J 203 " - pdb=" SG CYS J 34 " pdb="ZN ZN J 203 " - pdb=" SG CYS J 31 " pdb="ZN ZN J 203 " - pdb=" SG CYS J 3 " pdb=" ZN K 203 " pdb="ZN ZN K 203 " - pdb=" SG CYS K 31 " pdb="ZN ZN K 203 " - pdb=" SG CYS K 6 " pdb="ZN ZN K 203 " - pdb=" SG CYS K 34 " pdb="ZN ZN K 203 " - pdb=" SG CYS K 3 " pdb=" ZN L 203 " pdb="ZN ZN L 203 " - pdb=" SG CYS L 6 " pdb="ZN ZN L 203 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 203 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 203 " - pdb=" SG CYS L 3 " Number of angles added : 72 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3336 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 18 sheets defined 52.0% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 59 through 71 removed outlier: 3.719A pdb=" N VAL A 63 " --> pdb=" O SER A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 95 removed outlier: 3.860A pdb=" N THR A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 117 removed outlier: 3.934A pdb=" N GLY A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Proline residue: A 112 - end of helix removed outlier: 3.765A pdb=" N GLU A 115 " --> pdb=" O GLY A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 129 removed outlier: 4.376A pdb=" N VAL A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 147 removed outlier: 3.627A pdb=" N PHE A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 71 removed outlier: 3.719A pdb=" N VAL E 63 " --> pdb=" O SER E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 95 removed outlier: 3.860A pdb=" N THR E 95 " --> pdb=" O ALA E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 117 removed outlier: 3.935A pdb=" N GLY E 111 " --> pdb=" O LEU E 107 " (cutoff:3.500A) Proline residue: E 112 - end of helix removed outlier: 3.764A pdb=" N GLU E 115 " --> pdb=" O GLY E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 129 removed outlier: 4.377A pdb=" N VAL E 127 " --> pdb=" O ARG E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 147 removed outlier: 3.627A pdb=" N PHE E 137 " --> pdb=" O SER E 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 71 removed outlier: 3.720A pdb=" N VAL I 63 " --> pdb=" O SER I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 95 removed outlier: 3.859A pdb=" N THR I 95 " --> pdb=" O ALA I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 117 removed outlier: 3.934A pdb=" N GLY I 111 " --> pdb=" O LEU I 107 " (cutoff:3.500A) Proline residue: I 112 - end of helix removed outlier: 3.765A pdb=" N GLU I 115 " --> pdb=" O GLY I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 129 removed outlier: 4.376A pdb=" N VAL I 127 " --> pdb=" O ARG I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 133 through 147 removed outlier: 3.627A pdb=" N PHE I 137 " --> pdb=" O SER I 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 71 removed outlier: 3.720A pdb=" N VAL C 63 " --> pdb=" O SER C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 95 removed outlier: 3.860A pdb=" N THR C 95 " --> pdb=" O ALA C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 117 removed outlier: 3.934A pdb=" N GLY C 111 " --> pdb=" O LEU C 107 " (cutoff:3.500A) Proline residue: C 112 - end of helix removed outlier: 3.765A pdb=" N GLU C 115 " --> pdb=" O GLY C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 129 removed outlier: 4.376A pdb=" N VAL C 127 " --> pdb=" O ARG C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 147 removed outlier: 3.627A pdb=" N PHE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 71 removed outlier: 3.718A pdb=" N VAL G 63 " --> pdb=" O SER G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 95 removed outlier: 3.860A pdb=" N THR G 95 " --> pdb=" O ALA G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 117 removed outlier: 3.934A pdb=" N GLY G 111 " --> pdb=" O LEU G 107 " (cutoff:3.500A) Proline residue: G 112 - end of helix removed outlier: 3.765A pdb=" N GLU G 115 " --> pdb=" O GLY G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 129 removed outlier: 4.377A pdb=" N VAL G 127 " --> pdb=" O ARG G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 147 removed outlier: 3.627A pdb=" N PHE G 137 " --> pdb=" O SER G 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 71 removed outlier: 3.720A pdb=" N VAL K 63 " --> pdb=" O SER K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 95 removed outlier: 3.860A pdb=" N THR K 95 " --> pdb=" O ALA K 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 117 removed outlier: 3.934A pdb=" N GLY K 111 " --> pdb=" O LEU K 107 " (cutoff:3.500A) Proline residue: K 112 - end of helix removed outlier: 3.765A pdb=" N GLU K 115 " --> pdb=" O GLY K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 117 through 129 removed outlier: 4.377A pdb=" N VAL K 127 " --> pdb=" O ARG K 123 " (cutoff:3.500A) Processing helix chain 'K' and resid 133 through 147 removed outlier: 3.628A pdb=" N PHE K 137 " --> pdb=" O SER K 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 71 removed outlier: 3.651A pdb=" N VAL B 63 " --> pdb=" O SER B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 96 removed outlier: 3.752A pdb=" N GLY B 96 " --> pdb=" O VAL B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 108 Processing helix chain 'B' and resid 109 through 117 removed outlier: 3.894A pdb=" N GLU B 115 " --> pdb=" O GLY B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 129 removed outlier: 4.062A pdb=" N VAL B 127 " --> pdb=" O ARG B 123 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR B 128 " --> pdb=" O PHE B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 147 Processing helix chain 'F' and resid 59 through 71 removed outlier: 3.651A pdb=" N VAL F 63 " --> pdb=" O SER F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 96 removed outlier: 3.751A pdb=" N GLY F 96 " --> pdb=" O VAL F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 108 Processing helix chain 'F' and resid 109 through 117 removed outlier: 3.894A pdb=" N GLU F 115 " --> pdb=" O GLY F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 129 removed outlier: 4.062A pdb=" N VAL F 127 " --> pdb=" O ARG F 123 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR F 128 " --> pdb=" O PHE F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 147 Processing helix chain 'J' and resid 59 through 71 removed outlier: 3.651A pdb=" N VAL J 63 " --> pdb=" O SER J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 96 removed outlier: 3.752A pdb=" N GLY J 96 " --> pdb=" O VAL J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 108 Processing helix chain 'J' and resid 109 through 117 removed outlier: 3.895A pdb=" N GLU J 115 " --> pdb=" O GLY J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 118 through 129 removed outlier: 4.062A pdb=" N VAL J 127 " --> pdb=" O ARG J 123 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR J 128 " --> pdb=" O PHE J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 147 Processing helix chain 'D' and resid 59 through 71 removed outlier: 3.650A pdb=" N VAL D 63 " --> pdb=" O SER D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 96 removed outlier: 3.752A pdb=" N GLY D 96 " --> pdb=" O VAL D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 108 Processing helix chain 'D' and resid 109 through 117 removed outlier: 3.895A pdb=" N GLU D 115 " --> pdb=" O GLY D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 129 removed outlier: 4.062A pdb=" N VAL D 127 " --> pdb=" O ARG D 123 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR D 128 " --> pdb=" O PHE D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 147 Processing helix chain 'H' and resid 59 through 71 removed outlier: 3.651A pdb=" N VAL H 63 " --> pdb=" O SER H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 96 removed outlier: 3.752A pdb=" N GLY H 96 " --> pdb=" O VAL H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 108 Processing helix chain 'H' and resid 109 through 117 removed outlier: 3.895A pdb=" N GLU H 115 " --> pdb=" O GLY H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 129 removed outlier: 4.062A pdb=" N VAL H 127 " --> pdb=" O ARG H 123 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR H 128 " --> pdb=" O PHE H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 147 Processing helix chain 'L' and resid 59 through 71 removed outlier: 3.650A pdb=" N VAL L 63 " --> pdb=" O SER L 59 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 96 removed outlier: 3.751A pdb=" N GLY L 96 " --> pdb=" O VAL L 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 101 through 108 Processing helix chain 'L' and resid 109 through 117 removed outlier: 3.895A pdb=" N GLU L 115 " --> pdb=" O GLY L 111 " (cutoff:3.500A) Processing helix chain 'L' and resid 118 through 129 removed outlier: 4.062A pdb=" N VAL L 127 " --> pdb=" O ARG L 123 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR L 128 " --> pdb=" O PHE L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 133 through 147 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 18 removed outlier: 6.422A pdb=" N ARG A 28 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER A 16 " --> pdb=" O ARG A 26 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ARG A 26 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLN D 30 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N VAL D 13 " --> pdb=" O GLN D 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 55 through 57 Processing sheet with id=AA3, first strand: chain 'E' and resid 12 through 18 removed outlier: 6.421A pdb=" N ARG E 28 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N SER E 16 " --> pdb=" O ARG E 26 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ARG E 26 " --> pdb=" O SER E 16 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLN H 30 " --> pdb=" O VAL H 13 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N VAL H 13 " --> pdb=" O GLN H 30 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 55 through 57 Processing sheet with id=AA5, first strand: chain 'I' and resid 12 through 18 removed outlier: 6.421A pdb=" N ARG I 28 " --> pdb=" O VAL I 14 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER I 16 " --> pdb=" O ARG I 26 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ARG I 26 " --> pdb=" O SER I 16 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLN L 30 " --> pdb=" O VAL L 13 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N VAL L 13 " --> pdb=" O GLN L 30 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 55 through 57 Processing sheet with id=AA7, first strand: chain 'C' and resid 12 through 18 removed outlier: 6.421A pdb=" N ARG C 28 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER C 16 " --> pdb=" O ARG C 26 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ARG C 26 " --> pdb=" O SER C 16 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL C 41 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLN B 30 " --> pdb=" O VAL B 13 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N VAL B 13 " --> pdb=" O GLN B 30 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 55 through 57 Processing sheet with id=AA9, first strand: chain 'G' and resid 12 through 18 removed outlier: 6.422A pdb=" N ARG G 28 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER G 16 " --> pdb=" O ARG G 26 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ARG G 26 " --> pdb=" O SER G 16 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLN F 30 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N VAL F 13 " --> pdb=" O GLN F 30 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 55 through 57 Processing sheet with id=AB2, first strand: chain 'K' and resid 12 through 18 removed outlier: 6.422A pdb=" N ARG K 28 " --> pdb=" O VAL K 14 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER K 16 " --> pdb=" O ARG K 26 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ARG K 26 " --> pdb=" O SER K 16 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLN J 30 " --> pdb=" O VAL J 13 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N VAL J 13 " --> pdb=" O GLN J 30 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 55 through 57 Processing sheet with id=AB4, first strand: chain 'B' and resid 47 through 49 Processing sheet with id=AB5, first strand: chain 'F' and resid 47 through 49 Processing sheet with id=AB6, first strand: chain 'J' and resid 47 through 49 Processing sheet with id=AB7, first strand: chain 'D' and resid 47 through 49 Processing sheet with id=AB8, first strand: chain 'H' and resid 47 through 49 Processing sheet with id=AB9, first strand: chain 'L' and resid 47 through 49 743 hydrogen bonds defined for protein. 2193 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: 2.23 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4948 1.34 - 1.46: 1802 1.46 - 1.57: 7740 1.57 - 1.69: 114 1.69 - 1.81: 120 Bond restraints: 14724 Sorted by residual: bond pdb=" O5' ATP H 201 " pdb=" PA ATP H 201 " ideal model delta sigma weight residual 1.579 1.615 -0.036 1.10e-02 8.26e+03 1.06e+01 bond pdb=" O5' ATP J 201 " pdb=" PA ATP J 201 " ideal model delta sigma weight residual 1.579 1.614 -0.035 1.10e-02 8.26e+03 1.03e+01 bond pdb=" O5' ATP D 201 " pdb=" PA ATP D 201 " ideal model delta sigma weight residual 1.579 1.614 -0.035 1.10e-02 8.26e+03 1.01e+01 bond pdb=" O5' ATP B 201 " pdb=" PA ATP B 201 " ideal model delta sigma weight residual 1.579 1.614 -0.035 1.10e-02 8.26e+03 1.00e+01 bond pdb=" O5' ATP F 201 " pdb=" PA ATP F 201 " ideal model delta sigma weight residual 1.579 1.614 -0.035 1.10e-02 8.26e+03 9.95e+00 ... (remaining 14719 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 19597 2.57 - 5.14: 419 5.14 - 7.71: 36 7.71 - 10.29: 18 10.29 - 12.86: 6 Bond angle restraints: 20076 Sorted by residual: angle pdb=" PB ATP H 202 " pdb=" O3B ATP H 202 " pdb=" PG ATP H 202 " ideal model delta sigma weight residual 139.87 127.01 12.86 1.00e+00 1.00e+00 1.65e+02 angle pdb=" PB ATP F 202 " pdb=" O3B ATP F 202 " pdb=" PG ATP F 202 " ideal model delta sigma weight residual 139.87 127.02 12.85 1.00e+00 1.00e+00 1.65e+02 angle pdb=" PB ATP J 202 " pdb=" O3B ATP J 202 " pdb=" PG ATP J 202 " ideal model delta sigma weight residual 139.87 127.03 12.84 1.00e+00 1.00e+00 1.65e+02 angle pdb=" PB ATP L 202 " pdb=" O3B ATP L 202 " pdb=" PG ATP L 202 " ideal model delta sigma weight residual 139.87 127.04 12.83 1.00e+00 1.00e+00 1.65e+02 angle pdb=" PB ATP B 202 " pdb=" O3B ATP B 202 " pdb=" PG ATP B 202 " ideal model delta sigma weight residual 139.87 127.04 12.83 1.00e+00 1.00e+00 1.65e+02 ... (remaining 20071 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 8434 17.45 - 34.90: 552 34.90 - 52.35: 336 52.35 - 69.81: 84 69.81 - 87.26: 42 Dihedral angle restraints: 9448 sinusoidal: 4336 harmonic: 5112 Sorted by residual: dihedral pdb=" C PHE L 137 " pdb=" N PHE L 137 " pdb=" CA PHE L 137 " pdb=" CB PHE L 137 " ideal model delta harmonic sigma weight residual -122.60 -114.26 -8.34 0 2.50e+00 1.60e-01 1.11e+01 dihedral pdb=" C PHE D 137 " pdb=" N PHE D 137 " pdb=" CA PHE D 137 " pdb=" CB PHE D 137 " ideal model delta harmonic sigma weight residual -122.60 -114.28 -8.32 0 2.50e+00 1.60e-01 1.11e+01 dihedral pdb=" C PHE B 137 " pdb=" N PHE B 137 " pdb=" CA PHE B 137 " pdb=" CB PHE B 137 " ideal model delta harmonic sigma weight residual -122.60 -114.31 -8.29 0 2.50e+00 1.60e-01 1.10e+01 ... (remaining 9445 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1765 0.051 - 0.102: 371 0.102 - 0.154: 96 0.154 - 0.205: 28 0.205 - 0.256: 20 Chirality restraints: 2280 Sorted by residual: chirality pdb=" CA PHE D 137 " pdb=" N PHE D 137 " pdb=" C PHE D 137 " pdb=" CB PHE D 137 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA PHE L 137 " pdb=" N PHE L 137 " pdb=" C PHE L 137 " pdb=" CB PHE L 137 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA PHE H 137 " pdb=" N PHE H 137 " pdb=" C PHE H 137 " pdb=" CB PHE H 137 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 2277 not shown) Planarity restraints: 2520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE E 141 " -0.019 2.00e-02 2.50e+03 3.95e-02 1.56e+01 pdb=" C ILE E 141 " 0.068 2.00e-02 2.50e+03 pdb=" O ILE E 141 " -0.026 2.00e-02 2.50e+03 pdb=" N ALA E 142 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 141 " 0.019 2.00e-02 2.50e+03 3.94e-02 1.56e+01 pdb=" C ILE C 141 " -0.068 2.00e-02 2.50e+03 pdb=" O ILE C 141 " 0.026 2.00e-02 2.50e+03 pdb=" N ALA C 142 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 141 " -0.019 2.00e-02 2.50e+03 3.94e-02 1.56e+01 pdb=" C ILE A 141 " 0.068 2.00e-02 2.50e+03 pdb=" O ILE A 141 " -0.026 2.00e-02 2.50e+03 pdb=" N ALA A 142 " -0.023 2.00e-02 2.50e+03 ... (remaining 2517 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3185 2.80 - 3.33: 13955 3.33 - 3.85: 23807 3.85 - 4.38: 29236 4.38 - 4.90: 48898 Nonbonded interactions: 119081 Sorted by model distance: nonbonded pdb=" O SER E 126 " pdb=" NH2 ARG F 123 " model vdw 2.280 3.120 nonbonded pdb=" OD2 ASP F 21 " pdb=" OG1 THR F 23 " model vdw 2.285 3.040 nonbonded pdb=" OD2 ASP J 21 " pdb=" OG1 THR J 23 " model vdw 2.285 3.040 nonbonded pdb=" OD2 ASP B 21 " pdb=" OG1 THR B 23 " model vdw 2.286 3.040 nonbonded pdb=" OD2 ASP H 21 " pdb=" OG1 THR H 23 " model vdw 2.286 3.040 ... (remaining 119076 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: 0.02 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' selection = chain 'K' selection = chain 'L' } 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: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.520 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.020 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:5.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 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 : 0.005 0.038 14772 Z= 0.360 Angle : 0.850 12.857 20150 Z= 0.638 Chirality : 0.052 0.256 2280 Planarity : 0.004 0.040 2520 Dihedral : 16.905 87.257 6108 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.22), residues: 1740 helix: 1.95 (0.20), residues: 810 sheet: 0.76 (0.29), residues: 336 loop : 0.51 (0.28), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 129 TYR 0.013 0.002 TYR E 128 PHE 0.018 0.002 PHE H 137 HIS 0.002 0.001 HIS F 2 Details of bonding type rmsd covalent geometry : bond 0.00487 (14724) covalent geometry : angle 0.84760 (20076) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.14207 ( 743) hydrogen bonds : angle 5.14877 ( 2193) metal coordination : bond 0.00343 ( 48) metal coordination : angle 1.43467 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 0.501 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.6908 time to fit residues: 227.6420 Evaluate side-chains 228 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.0170 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.4980 overall best weight: 1.0222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 114 GLN I 114 GLN B 114 GLN F 114 GLN J 114 GLN D 114 GLN H 114 GLN L 114 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.192227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.162750 restraints weight = 13773.016| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 1.53 r_work: 0.3772 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3626 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 14772 Z= 0.112 Angle : 0.483 5.375 20150 Z= 0.262 Chirality : 0.037 0.130 2280 Planarity : 0.004 0.025 2520 Dihedral : 17.078 87.462 2808 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.19 % Allowed : 12.50 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.22), residues: 1740 helix: 1.86 (0.19), residues: 858 sheet: 0.72 (0.27), residues: 396 loop : 0.36 (0.32), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 36 TYR 0.017 0.003 TYR G 128 PHE 0.010 0.002 PHE J 137 HIS 0.001 0.000 HIS F 103 Details of bonding type rmsd covalent geometry : bond 0.00245 (14724) covalent geometry : angle 0.47038 (20076) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03503 ( 743) hydrogen bonds : angle 4.14181 ( 2193) metal coordination : bond 0.00355 ( 48) metal coordination : angle 1.89480 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 231 time to evaluate : 0.555 Fit side-chains REVERT: A 21 ASP cc_start: 0.8057 (p0) cc_final: 0.7818 (p0) REVERT: I 7 ARG cc_start: 0.7446 (mpt180) cc_final: 0.6996 (mpt180) REVERT: C 99 GLU cc_start: 0.7978 (tt0) cc_final: 0.7713 (tt0) REVERT: B 37 ARG cc_start: 0.7402 (mtt-85) cc_final: 0.7144 (mtp-110) outliers start: 18 outliers final: 10 residues processed: 242 average time/residue: 0.7589 time to fit residues: 197.1987 Evaluate side-chains 201 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 191 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain J residue 45 SER Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain L residue 45 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 44 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 130 optimal weight: 0.2980 chunk 8 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 114 GLN I 86 GLN I 114 GLN C 86 GLN G 114 GLN B 72 GLN H 72 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.190709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.160554 restraints weight = 13836.064| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 1.54 r_work: 0.3749 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3600 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 14772 Z= 0.118 Angle : 0.478 4.572 20150 Z= 0.258 Chirality : 0.037 0.129 2280 Planarity : 0.004 0.027 2520 Dihedral : 15.868 88.260 2808 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.78 % Allowed : 13.43 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.22), residues: 1740 helix: 1.86 (0.19), residues: 846 sheet: 0.62 (0.27), residues: 396 loop : 0.29 (0.32), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 36 TYR 0.017 0.003 TYR G 128 PHE 0.011 0.002 PHE L 38 HIS 0.002 0.000 HIS J 2 Details of bonding type rmsd covalent geometry : bond 0.00263 (14724) covalent geometry : angle 0.46626 (20076) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03447 ( 743) hydrogen bonds : angle 3.99514 ( 2193) metal coordination : bond 0.00382 ( 48) metal coordination : angle 1.84705 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 196 time to evaluate : 0.630 Fit side-chains REVERT: A 21 ASP cc_start: 0.8127 (p0) cc_final: 0.7890 (p0) REVERT: E 12 ARG cc_start: 0.7933 (ptm-80) cc_final: 0.7481 (ptt-90) REVERT: I 7 ARG cc_start: 0.7467 (mpt180) cc_final: 0.6948 (mpt180) REVERT: C 12 ARG cc_start: 0.7817 (ptm-80) cc_final: 0.7435 (ptt-90) REVERT: G 21 ASP cc_start: 0.8005 (p0) cc_final: 0.7793 (p0) REVERT: K 12 ARG cc_start: 0.7906 (ptm-80) cc_final: 0.7451 (ptt-90) REVERT: F 7 ARG cc_start: 0.7333 (mtp85) cc_final: 0.7037 (mmp-170) REVERT: H 72 GLN cc_start: 0.5118 (OUTLIER) cc_final: 0.4204 (mt0) REVERT: L 72 GLN cc_start: 0.5080 (pt0) cc_final: 0.4254 (mt0) outliers start: 42 outliers final: 17 residues processed: 221 average time/residue: 0.6780 time to fit residues: 162.5641 Evaluate side-chains 203 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 185 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain J residue 45 SER Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 72 GLN Chi-restraints excluded: chain L residue 45 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 133 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 51 optimal weight: 0.0870 chunk 24 optimal weight: 1.9990 chunk 117 optimal weight: 0.4980 chunk 140 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 159 optimal weight: 0.6980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 114 GLN I 114 GLN G 114 GLN F 72 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.195311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.165930 restraints weight = 13764.172| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 1.50 r_work: 0.3798 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3651 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 14772 Z= 0.093 Angle : 0.437 4.310 20150 Z= 0.238 Chirality : 0.036 0.123 2280 Planarity : 0.003 0.025 2520 Dihedral : 14.898 89.079 2808 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.31 % Allowed : 14.02 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.22), residues: 1740 helix: 1.96 (0.19), residues: 852 sheet: 0.81 (0.27), residues: 396 loop : 0.42 (0.32), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 7 TYR 0.015 0.002 TYR G 128 PHE 0.009 0.001 PHE E 124 HIS 0.001 0.000 HIS J 103 Details of bonding type rmsd covalent geometry : bond 0.00188 (14724) covalent geometry : angle 0.42681 (20076) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.02797 ( 743) hydrogen bonds : angle 3.75414 ( 2193) metal coordination : bond 0.00271 ( 48) metal coordination : angle 1.64673 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 205 time to evaluate : 0.533 Fit side-chains REVERT: A 7 ARG cc_start: 0.7587 (mpt180) cc_final: 0.7292 (mpt180) REVERT: A 12 ARG cc_start: 0.7827 (ptt-90) cc_final: 0.7455 (ptt-90) REVERT: I 7 ARG cc_start: 0.7473 (mpt180) cc_final: 0.6908 (mpt180) REVERT: I 21 ASP cc_start: 0.8147 (p0) cc_final: 0.7631 (p0) REVERT: G 42 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7612 (tt0) REVERT: F 7 ARG cc_start: 0.7346 (mtp85) cc_final: 0.7052 (mmp-170) REVERT: F 72 GLN cc_start: 0.5275 (OUTLIER) cc_final: 0.4420 (mt0) outliers start: 35 outliers final: 12 residues processed: 224 average time/residue: 0.7135 time to fit residues: 172.3178 Evaluate side-chains 211 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 197 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain D residue 101 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 145 optimal weight: 0.4980 chunk 119 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 126 optimal weight: 0.1980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 86 GLN I 114 GLN G 86 GLN G 114 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.194834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.165195 restraints weight = 13733.687| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 1.51 r_work: 0.3791 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3645 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 14772 Z= 0.098 Angle : 0.446 4.179 20150 Z= 0.241 Chirality : 0.036 0.121 2280 Planarity : 0.003 0.023 2520 Dihedral : 14.498 88.862 2808 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.18 % Allowed : 15.74 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.22), residues: 1740 helix: 2.03 (0.19), residues: 852 sheet: 0.84 (0.27), residues: 396 loop : 0.40 (0.32), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 36 TYR 0.014 0.002 TYR G 128 PHE 0.009 0.001 PHE B 38 HIS 0.001 0.000 HIS H 2 Details of bonding type rmsd covalent geometry : bond 0.00206 (14724) covalent geometry : angle 0.43635 (20076) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.02851 ( 743) hydrogen bonds : angle 3.71178 ( 2193) metal coordination : bond 0.00294 ( 48) metal coordination : angle 1.60050 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 202 time to evaluate : 0.523 Fit side-chains REVERT: A 110 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8399 (mp) REVERT: E 7 ARG cc_start: 0.7690 (mpt180) cc_final: 0.7480 (mpt180) REVERT: E 12 ARG cc_start: 0.7819 (ptt-90) cc_final: 0.7420 (ptt-90) REVERT: I 21 ASP cc_start: 0.8092 (p0) cc_final: 0.7729 (p0) REVERT: C 12 ARG cc_start: 0.7812 (ptt-90) cc_final: 0.7447 (ptt-90) REVERT: C 110 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8416 (mp) REVERT: G 42 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7623 (tt0) REVERT: K 7 ARG cc_start: 0.7661 (mpt180) cc_final: 0.7454 (mpt180) REVERT: K 12 ARG cc_start: 0.7822 (ptt-90) cc_final: 0.7444 (ptt-90) REVERT: F 7 ARG cc_start: 0.7356 (mtp85) cc_final: 0.7062 (mmp-170) outliers start: 33 outliers final: 18 residues processed: 223 average time/residue: 0.6340 time to fit residues: 153.6838 Evaluate side-chains 218 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 197 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain E residue 17 ARG Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 17 ARG Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain L residue 45 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 37 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 81 optimal weight: 0.3980 chunk 39 optimal weight: 8.9990 chunk 134 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 141 optimal weight: 0.6980 chunk 84 optimal weight: 0.0770 chunk 79 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 overall best weight: 2.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN E 2 HIS I 114 GLN G 114 GLN K 86 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.187589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.156849 restraints weight = 13729.478| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 1.53 r_work: 0.3696 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14772 Z= 0.182 Angle : 0.546 4.620 20150 Z= 0.291 Chirality : 0.039 0.147 2280 Planarity : 0.005 0.041 2520 Dihedral : 15.644 88.072 2808 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.11 % Allowed : 15.74 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.22), residues: 1740 helix: 1.73 (0.19), residues: 852 sheet: 0.47 (0.26), residues: 396 loop : 0.37 (0.32), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 29 TYR 0.022 0.004 TYR G 128 PHE 0.017 0.002 PHE B 38 HIS 0.005 0.001 HIS D 2 Details of bonding type rmsd covalent geometry : bond 0.00434 (14724) covalent geometry : angle 0.53342 (20076) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.04172 ( 743) hydrogen bonds : angle 4.10537 ( 2193) metal coordination : bond 0.00568 ( 48) metal coordination : angle 2.02342 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 187 time to evaluate : 0.537 Fit side-chains REVERT: A 110 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8353 (mp) REVERT: E 7 ARG cc_start: 0.7679 (mpt180) cc_final: 0.7379 (mpt180) REVERT: I 7 ARG cc_start: 0.7609 (mpt180) cc_final: 0.7066 (mpt180) REVERT: C 110 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8407 (mp) REVERT: K 7 ARG cc_start: 0.7675 (mpt180) cc_final: 0.7371 (mpt180) REVERT: F 7 ARG cc_start: 0.7368 (mtp85) cc_final: 0.7042 (mmp-170) outliers start: 47 outliers final: 31 residues processed: 213 average time/residue: 0.7219 time to fit residues: 165.7121 Evaluate side-chains 217 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain E residue 17 ARG Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain I residue 17 ARG Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 17 ARG Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain L residue 45 SER Chi-restraints excluded: chain L residue 61 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 88 optimal weight: 10.0000 chunk 102 optimal weight: 0.0050 chunk 125 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 114 GLN G 114 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.193467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.163708 restraints weight = 13776.132| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 1.50 r_work: 0.3772 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3626 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 14772 Z= 0.101 Angle : 0.464 4.625 20150 Z= 0.250 Chirality : 0.037 0.134 2280 Planarity : 0.003 0.028 2520 Dihedral : 14.713 89.975 2808 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.65 % Allowed : 16.47 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.22), residues: 1740 helix: 1.91 (0.19), residues: 852 sheet: 0.74 (0.27), residues: 396 loop : 0.41 (0.33), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 12 TYR 0.015 0.003 TYR K 128 PHE 0.009 0.001 PHE B 38 HIS 0.001 0.000 HIS L 8 Details of bonding type rmsd covalent geometry : bond 0.00214 (14724) covalent geometry : angle 0.45373 (20076) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.02914 ( 743) hydrogen bonds : angle 3.72615 ( 2193) metal coordination : bond 0.00300 ( 48) metal coordination : angle 1.70292 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 194 time to evaluate : 0.600 Fit side-chains REVERT: E 21 ASP cc_start: 0.8071 (p0) cc_final: 0.7784 (p0) REVERT: I 7 ARG cc_start: 0.7594 (mpt180) cc_final: 0.7359 (mpt180) REVERT: I 21 ASP cc_start: 0.8162 (p0) cc_final: 0.7634 (p0) REVERT: K 21 ASP cc_start: 0.8073 (p0) cc_final: 0.7807 (p0) REVERT: B 45 SER cc_start: 0.7355 (OUTLIER) cc_final: 0.7070 (m) outliers start: 40 outliers final: 18 residues processed: 217 average time/residue: 0.7442 time to fit residues: 173.8516 Evaluate side-chains 204 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain I residue 17 ARG Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain L residue 45 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 121 optimal weight: 0.0060 chunk 145 optimal weight: 5.9990 chunk 160 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 111 optimal weight: 8.9990 overall best weight: 2.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 114 GLN G 114 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.185195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.155405 restraints weight = 13892.586| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 1.50 r_work: 0.3675 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 14772 Z= 0.176 Angle : 0.559 8.189 20150 Z= 0.295 Chirality : 0.040 0.182 2280 Planarity : 0.004 0.033 2520 Dihedral : 15.418 87.965 2808 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.51 % Allowed : 17.33 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.22), residues: 1740 helix: 1.73 (0.18), residues: 846 sheet: 0.61 (0.26), residues: 396 loop : 0.36 (0.33), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 12 TYR 0.027 0.004 TYR K 128 PHE 0.016 0.002 PHE F 38 HIS 0.006 0.001 HIS J 2 Details of bonding type rmsd covalent geometry : bond 0.00417 (14724) covalent geometry : angle 0.54693 (20076) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.04085 ( 743) hydrogen bonds : angle 4.07588 ( 2193) metal coordination : bond 0.00577 ( 48) metal coordination : angle 1.99368 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 182 time to evaluate : 0.590 Fit side-chains REVERT: A 17 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7181 (ttm170) REVERT: A 110 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8335 (mp) REVERT: E 7 ARG cc_start: 0.7591 (mpt180) cc_final: 0.7361 (mpt180) REVERT: E 21 ASP cc_start: 0.8053 (p0) cc_final: 0.7727 (p0) REVERT: I 7 ARG cc_start: 0.7588 (mpt180) cc_final: 0.7338 (mpt180) REVERT: C 110 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8332 (mp) REVERT: K 7 ARG cc_start: 0.7634 (mpt180) cc_final: 0.7406 (mpt180) REVERT: K 21 ASP cc_start: 0.8026 (p0) cc_final: 0.7798 (p0) REVERT: F 7 ARG cc_start: 0.7353 (mtp85) cc_final: 0.7073 (mmp-170) outliers start: 38 outliers final: 26 residues processed: 208 average time/residue: 0.7410 time to fit residues: 165.8080 Evaluate side-chains 207 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 178 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain I residue 17 ARG Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain L residue 45 SER Chi-restraints excluded: chain L residue 61 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 150 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 102 optimal weight: 0.0370 chunk 30 optimal weight: 5.9990 chunk 125 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 155 optimal weight: 0.1980 chunk 64 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 114 GLN G 114 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.193773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.164009 restraints weight = 13879.752| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 1.51 r_work: 0.3771 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3626 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 14772 Z= 0.101 Angle : 0.478 7.161 20150 Z= 0.254 Chirality : 0.037 0.223 2280 Planarity : 0.003 0.032 2520 Dihedral : 14.548 89.826 2808 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.79 % Allowed : 18.25 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.22), residues: 1740 helix: 1.88 (0.19), residues: 852 sheet: 0.84 (0.27), residues: 396 loop : 0.45 (0.33), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 12 TYR 0.018 0.003 TYR K 128 PHE 0.011 0.001 PHE K 124 HIS 0.001 0.000 HIS G 8 Details of bonding type rmsd covalent geometry : bond 0.00210 (14724) covalent geometry : angle 0.46711 (20076) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.02890 ( 743) hydrogen bonds : angle 3.72623 ( 2193) metal coordination : bond 0.00287 ( 48) metal coordination : angle 1.72608 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 184 time to evaluate : 0.559 Fit side-chains REVERT: E 7 ARG cc_start: 0.7655 (mpt180) cc_final: 0.7411 (mpt180) REVERT: I 21 ASP cc_start: 0.8188 (p0) cc_final: 0.7632 (p0) REVERT: K 7 ARG cc_start: 0.7652 (mpt180) cc_final: 0.7412 (mpt180) REVERT: F 7 ARG cc_start: 0.7302 (mtp85) cc_final: 0.7041 (mmp-170) outliers start: 27 outliers final: 22 residues processed: 203 average time/residue: 0.7679 time to fit residues: 167.5110 Evaluate side-chains 196 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain I residue 17 ARG Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 110 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain L residue 45 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 22 optimal weight: 3.9990 chunk 5 optimal weight: 0.4980 chunk 88 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 155 optimal weight: 0.0670 chunk 82 optimal weight: 0.7980 chunk 100 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 158 optimal weight: 9.9990 chunk 122 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 114 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.195239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.165603 restraints weight = 13857.226| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 1.51 r_work: 0.3801 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3655 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14772 Z= 0.100 Angle : 0.476 9.189 20150 Z= 0.254 Chirality : 0.037 0.281 2280 Planarity : 0.003 0.027 2520 Dihedral : 14.025 89.241 2808 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.52 % Allowed : 18.65 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.22), residues: 1740 helix: 1.93 (0.19), residues: 858 sheet: 0.95 (0.27), residues: 396 loop : 0.33 (0.33), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 12 TYR 0.016 0.002 TYR E 128 PHE 0.014 0.001 PHE K 124 HIS 0.001 0.000 HIS D 2 Details of bonding type rmsd covalent geometry : bond 0.00209 (14724) covalent geometry : angle 0.46876 (20076) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.02803 ( 743) hydrogen bonds : angle 3.65612 ( 2193) metal coordination : bond 0.00271 ( 48) metal coordination : angle 1.49962 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 194 time to evaluate : 0.364 Fit side-chains REVERT: E 7 ARG cc_start: 0.7656 (mpt180) cc_final: 0.7411 (mpt180) REVERT: I 7 ARG cc_start: 0.7488 (mpt180) cc_final: 0.7250 (mpt180) REVERT: K 7 ARG cc_start: 0.7661 (mpt180) cc_final: 0.7417 (mpt180) REVERT: B 45 SER cc_start: 0.7270 (OUTLIER) cc_final: 0.7006 (m) REVERT: F 7 ARG cc_start: 0.7321 (mtp85) cc_final: 0.7096 (mmp-170) outliers start: 23 outliers final: 19 residues processed: 209 average time/residue: 0.7630 time to fit residues: 171.1070 Evaluate side-chains 201 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 181 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain I residue 17 ARG Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain H residue 17 ARG Chi-restraints excluded: chain L residue 45 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 118 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 163 optimal weight: 10.0000 chunk 103 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 114 GLN K 2 HIS F 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.188724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.158269 restraints weight = 13810.330| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 1.52 r_work: 0.3718 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3571 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14772 Z= 0.168 Angle : 0.559 10.200 20150 Z= 0.295 Chirality : 0.040 0.273 2280 Planarity : 0.004 0.040 2520 Dihedral : 14.751 87.962 2808 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.59 % Allowed : 18.72 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.22), residues: 1740 helix: 1.78 (0.19), residues: 846 sheet: 0.72 (0.27), residues: 396 loop : 0.48 (0.33), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 129 TYR 0.027 0.004 TYR K 128 PHE 0.016 0.002 PHE B 38 HIS 0.005 0.001 HIS J 2 Details of bonding type rmsd covalent geometry : bond 0.00398 (14724) covalent geometry : angle 0.54883 (20076) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03875 ( 743) hydrogen bonds : angle 3.97570 ( 2193) metal coordination : bond 0.00550 ( 48) metal coordination : angle 1.84292 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5037.23 seconds wall clock time: 86 minutes 21.87 seconds (5181.87 seconds total)