Starting phenix.real_space_refine on Fri Aug 22 23:20:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zmy_60262/08_2025/8zmy_60262.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zmy_60262/08_2025/8zmy_60262.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zmy_60262/08_2025/8zmy_60262.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zmy_60262/08_2025/8zmy_60262.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zmy_60262/08_2025/8zmy_60262.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zmy_60262/08_2025/8zmy_60262.map" } resolution = 2.9 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= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Br 15 7.06 5 S 39 5.16 5 C 5463 2.51 5 N 1446 2.21 5 O 1674 1.98 5 F 15 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8652 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 686 Unusual residues: {'ACE': 1} Classifications: {'peptide': 98, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 97} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'1KI': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'1KI': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'1KI': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'1KI': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'1KI': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'1KI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'1KI': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Time building chain proxies: 1.18, per 1000 atoms: 0.14 Number of scatterers: 8652 At special positions: 0 Unit cell: (139.44, 116.2, 47.31, 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) Br 15 34.99 S 39 16.00 F 15 9.00 O 1674 8.00 N 1446 7.00 C 5463 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: 0.63 Conformation dependent library (CDL) restraints added in 452.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2016 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 45.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 9 Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 18 removed outlier: 7.018A pdb=" N GLU A 13 " --> pdb=" O GLY B 14 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N VAL B 16 " --> pdb=" O GLU A 13 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL A 15 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ALA B 18 " --> pdb=" O VAL A 15 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA A 17 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLU B 13 " --> pdb=" O GLY C 14 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N VAL C 16 " --> pdb=" O GLU B 13 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL B 15 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ALA C 18 " --> pdb=" O VAL B 15 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ALA B 17 " --> pdb=" O ALA C 18 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLU C 13 " --> pdb=" O GLY G 14 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL G 16 " --> pdb=" O GLU C 13 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL C 15 " --> pdb=" O VAL G 16 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ALA G 18 " --> pdb=" O VAL C 15 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ALA C 17 " --> pdb=" O ALA G 18 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLU G 13 " --> pdb=" O GLY H 14 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N VAL H 16 " --> pdb=" O GLU G 13 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL G 15 " --> pdb=" O VAL H 16 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ALA H 18 " --> pdb=" O VAL G 15 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA G 17 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLU H 13 " --> pdb=" O GLY I 14 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N VAL I 16 " --> pdb=" O GLU H 13 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL H 15 " --> pdb=" O VAL I 16 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ALA I 18 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA H 17 " --> pdb=" O ALA I 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 24 through 29 removed outlier: 6.908A pdb=" N GLY A 25 " --> pdb=" O GLN B 24 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLY B 25 " --> pdb=" O GLN C 24 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N GLN C 24 " --> pdb=" O GLY G 25 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N ALA G 27 " --> pdb=" O GLN C 24 " (cutoff:3.500A) removed outlier: 9.052A pdb=" N VAL C 26 " --> pdb=" O ALA G 27 " (cutoff:3.500A) removed outlier: 10.069A pdb=" N ALA G 29 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 8.908A pdb=" N GLU C 28 " --> pdb=" O ALA G 29 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY G 25 " --> pdb=" O GLN H 24 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLY H 25 " --> pdb=" O GLN I 24 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 34 through 40 removed outlier: 6.373A pdb=" N LYS A 34 " --> pdb=" O GLU B 35 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N VAL B 37 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N GLY A 36 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 9.903A pdb=" N TYR B 39 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N LEU A 38 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LYS B 34 " --> pdb=" O GLU C 35 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N VAL C 37 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N GLY B 36 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 9.917A pdb=" N TYR C 39 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N LEU B 38 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LYS C 34 " --> pdb=" O GLU G 35 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N VAL G 37 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N GLY C 36 " --> pdb=" O VAL G 37 " (cutoff:3.500A) removed outlier: 9.928A pdb=" N TYR G 39 " --> pdb=" O GLY C 36 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N LEU C 38 " --> pdb=" O TYR G 39 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LYS G 34 " --> pdb=" O GLU H 35 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N VAL H 37 " --> pdb=" O LYS G 34 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N GLY G 36 " --> pdb=" O VAL H 37 " (cutoff:3.500A) removed outlier: 9.903A pdb=" N TYR H 39 " --> pdb=" O GLY G 36 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N LEU G 38 " --> pdb=" O TYR H 39 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LYS H 34 " --> pdb=" O GLU I 35 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N VAL I 37 " --> pdb=" O LYS H 34 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N GLY H 36 " --> pdb=" O VAL I 37 " (cutoff:3.500A) removed outlier: 9.918A pdb=" N TYR I 39 " --> pdb=" O GLY H 36 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N LEU H 38 " --> pdb=" O TYR I 39 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 46 through 52 removed outlier: 7.030A pdb=" N GLY A 47 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N HIS B 50 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL A 49 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL B 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N GLY A 51 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLY B 47 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N HIS C 50 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL B 49 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL C 52 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N GLY B 51 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLY C 47 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N HIS G 50 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL C 49 " --> pdb=" O HIS G 50 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL G 52 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N GLY C 51 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N GLY G 47 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N HIS H 50 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL G 49 " --> pdb=" O HIS H 50 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL H 52 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N GLY G 51 " --> pdb=" O VAL H 52 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLY H 47 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N HIS I 50 " --> pdb=" O GLY H 47 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL H 49 " --> pdb=" O HIS I 50 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL I 52 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N GLY H 51 " --> pdb=" O VAL I 52 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 63 through 67 removed outlier: 6.255A pdb=" N GLN G 62 " --> pdb=" O VAL H 63 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ASN H 65 " --> pdb=" O GLN G 62 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N THR G 64 " --> pdb=" O ASN H 65 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N GLY H 67 " --> pdb=" O THR G 64 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL G 66 " --> pdb=" O GLY H 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 70 through 71 Processing sheet with id=AA8, first strand: chain 'A' and resid 74 through 78 Processing sheet with id=AA9, first strand: chain 'A' and resid 88 through 95 removed outlier: 6.332A pdb=" N ALA A 89 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N THR B 92 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA A 91 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N PHE B 94 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N GLY A 93 " --> pdb=" O PHE B 94 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA B 89 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N THR C 92 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA B 91 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N PHE C 94 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N GLY B 93 " --> pdb=" O PHE C 94 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA C 89 " --> pdb=" O ALA G 90 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N THR G 92 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA C 91 " --> pdb=" O THR G 92 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N PHE G 94 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 8.940A pdb=" N GLY C 93 " --> pdb=" O PHE G 94 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA G 89 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N THR H 92 " --> pdb=" O ALA G 89 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA G 91 " --> pdb=" O THR H 92 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N PHE H 94 " --> pdb=" O ALA G 91 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N GLY G 93 " --> pdb=" O PHE H 94 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ALA H 89 " --> pdb=" O ALA I 90 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N THR I 92 " --> pdb=" O ALA H 89 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA H 91 " --> pdb=" O THR I 92 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N PHE I 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N GLY H 93 " --> pdb=" O PHE I 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 4 through 9 Processing sheet with id=AB2, first strand: chain 'D' and resid 12 through 18 removed outlier: 7.017A pdb=" N GLU D 13 " --> pdb=" O GLY E 14 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N VAL E 16 " --> pdb=" O GLU D 13 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL D 15 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ALA E 18 " --> pdb=" O VAL D 15 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA D 17 " --> pdb=" O ALA E 18 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N GLU E 13 " --> pdb=" O GLY F 14 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N VAL F 16 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL E 15 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ALA F 18 " --> pdb=" O VAL E 15 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA E 17 " --> pdb=" O ALA F 18 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLU F 13 " --> pdb=" O GLY J 14 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N VAL J 16 " --> pdb=" O GLU F 13 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N VAL F 15 " --> pdb=" O VAL J 16 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ALA J 18 " --> pdb=" O VAL F 15 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ALA F 17 " --> pdb=" O ALA J 18 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLU J 13 " --> pdb=" O GLY K 14 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N VAL K 16 " --> pdb=" O GLU J 13 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL J 15 " --> pdb=" O VAL K 16 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ALA K 18 " --> pdb=" O VAL J 15 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ALA J 17 " --> pdb=" O ALA K 18 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N GLU K 13 " --> pdb=" O GLY L 14 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N VAL L 16 " --> pdb=" O GLU K 13 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL K 15 " --> pdb=" O VAL L 16 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ALA L 18 " --> pdb=" O VAL K 15 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA K 17 " --> pdb=" O ALA L 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 24 through 29 removed outlier: 6.909A pdb=" N GLY D 25 " --> pdb=" O GLN E 24 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLY E 25 " --> pdb=" O GLN F 24 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N GLN F 24 " --> pdb=" O GLY J 25 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N ALA J 27 " --> pdb=" O GLN F 24 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N VAL F 26 " --> pdb=" O ALA J 27 " (cutoff:3.500A) removed outlier: 10.052A pdb=" N ALA J 29 " --> pdb=" O VAL F 26 " (cutoff:3.500A) removed outlier: 8.891A pdb=" N GLU F 28 " --> pdb=" O ALA J 29 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY J 25 " --> pdb=" O GLN K 24 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLY K 25 " --> pdb=" O GLN L 24 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 34 through 40 removed outlier: 6.374A pdb=" N LYS D 34 " --> pdb=" O GLU E 35 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N VAL E 37 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N GLY D 36 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 9.903A pdb=" N TYR E 39 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N LEU D 38 " --> pdb=" O TYR E 39 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LYS E 34 " --> pdb=" O GLU F 35 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N VAL F 37 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N GLY E 36 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 9.926A pdb=" N TYR F 39 " --> pdb=" O GLY E 36 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N LEU E 38 " --> pdb=" O TYR F 39 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LYS F 34 " --> pdb=" O GLU J 35 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL J 37 " --> pdb=" O LYS F 34 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N GLY F 36 " --> pdb=" O VAL J 37 " (cutoff:3.500A) removed outlier: 9.908A pdb=" N TYR J 39 " --> pdb=" O GLY F 36 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N LEU F 38 " --> pdb=" O TYR J 39 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LYS J 34 " --> pdb=" O GLU K 35 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N VAL K 37 " --> pdb=" O LYS J 34 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N GLY J 36 " --> pdb=" O VAL K 37 " (cutoff:3.500A) removed outlier: 9.903A pdb=" N TYR K 39 " --> pdb=" O GLY J 36 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N LEU J 38 " --> pdb=" O TYR K 39 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LYS K 34 " --> pdb=" O GLU L 35 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N VAL L 37 " --> pdb=" O LYS K 34 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N GLY K 36 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 9.927A pdb=" N TYR L 39 " --> pdb=" O GLY K 36 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N LEU K 38 " --> pdb=" O TYR L 39 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 46 through 52 removed outlier: 7.030A pdb=" N GLY D 47 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N HIS E 50 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL D 49 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL E 52 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N GLY D 51 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N GLY E 47 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N HIS F 50 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL E 49 " --> pdb=" O HIS F 50 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL F 52 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N GLY E 51 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N GLY F 47 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N HIS J 50 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL F 49 " --> pdb=" O HIS J 50 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL J 52 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N GLY F 51 " --> pdb=" O VAL J 52 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N GLY J 47 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N HIS K 50 " --> pdb=" O GLY J 47 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL J 49 " --> pdb=" O HIS K 50 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL K 52 " --> pdb=" O VAL J 49 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N GLY J 51 " --> pdb=" O VAL K 52 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N GLY K 47 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N HIS L 50 " --> pdb=" O GLY K 47 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL K 49 " --> pdb=" O HIS L 50 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL L 52 " --> pdb=" O VAL K 49 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N GLY K 51 " --> pdb=" O VAL L 52 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 63 through 67 removed outlier: 6.257A pdb=" N GLN J 62 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ASN K 65 " --> pdb=" O GLN J 62 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR J 64 " --> pdb=" O ASN K 65 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N GLY K 67 " --> pdb=" O THR J 64 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL J 66 " --> pdb=" O GLY K 67 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 70 through 71 Processing sheet with id=AB8, first strand: chain 'D' and resid 74 through 78 Processing sheet with id=AB9, first strand: chain 'D' and resid 88 through 95 removed outlier: 6.333A pdb=" N ALA D 89 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N THR E 92 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ALA D 91 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N PHE E 94 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N GLY D 93 " --> pdb=" O PHE E 94 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA E 89 " --> pdb=" O ALA F 90 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N THR F 92 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA E 91 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N PHE F 94 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N GLY E 93 " --> pdb=" O PHE F 94 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ALA F 89 " --> pdb=" O ALA J 90 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N THR J 92 " --> pdb=" O ALA F 89 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA F 91 " --> pdb=" O THR J 92 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N PHE J 94 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 8.908A pdb=" N GLY F 93 " --> pdb=" O PHE J 94 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA J 89 " --> pdb=" O ALA K 90 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N THR K 92 " --> pdb=" O ALA J 89 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ALA J 91 " --> pdb=" O THR K 92 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N PHE K 94 " --> pdb=" O ALA J 91 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N GLY J 93 " --> pdb=" O PHE K 94 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA K 89 " --> pdb=" O ALA L 90 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N THR L 92 " --> pdb=" O ALA K 89 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ALA K 91 " --> pdb=" O THR L 92 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N PHE L 94 " --> pdb=" O ALA K 91 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N GLY K 93 " --> pdb=" O PHE L 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 166 hydrogen bonds defined for protein. 498 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: 1.32 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 2831 1.37 - 1.51: 2988 1.51 - 1.65: 2806 1.65 - 1.80: 78 1.80 - 1.94: 15 Bond restraints: 8718 Sorted by residual: bond pdb=" C13 1KI H 102 " pdb=" C14 1KI H 102 " ideal model delta sigma weight residual 1.409 1.336 0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C13 1KI J 103 " pdb=" C14 1KI J 103 " ideal model delta sigma weight residual 1.409 1.336 0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C13 1KI F 101 " pdb=" C14 1KI F 101 " ideal model delta sigma weight residual 1.409 1.336 0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C13 1KI J 101 " pdb=" C14 1KI J 101 " ideal model delta sigma weight residual 1.409 1.336 0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C13 1KI G 102 " pdb=" C14 1KI G 102 " ideal model delta sigma weight residual 1.409 1.336 0.073 2.00e-02 2.50e+03 1.32e+01 ... (remaining 8713 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 11280 2.10 - 4.19: 324 4.19 - 6.29: 63 6.29 - 8.38: 34 8.38 - 10.48: 2 Bond angle restraints: 11703 Sorted by residual: angle pdb=" C08 1KI G 102 " pdb=" C09 1KI G 102 " pdb=" F10 1KI G 102 " ideal model delta sigma weight residual 110.24 99.76 10.48 3.00e+00 1.11e-01 1.22e+01 angle pdb=" C08 1KI J 101 " pdb=" C09 1KI J 101 " pdb=" F10 1KI J 101 " ideal model delta sigma weight residual 110.24 99.83 10.41 3.00e+00 1.11e-01 1.20e+01 angle pdb=" C09 1KI H 103 " pdb=" C08 1KI H 103 " pdb=" O07 1KI H 103 " ideal model delta sigma weight residual 109.36 101.14 8.22 3.00e+00 1.11e-01 7.51e+00 angle pdb=" C05 1KI H 102 " pdb=" N04 1KI H 102 " pdb=" C11 1KI H 102 " ideal model delta sigma weight residual 112.35 119.87 -7.52 3.00e+00 1.11e-01 6.28e+00 angle pdb=" C05 1KI H 101 " pdb=" N04 1KI H 101 " pdb=" C11 1KI H 101 " ideal model delta sigma weight residual 112.35 119.85 -7.50 3.00e+00 1.11e-01 6.25e+00 ... (remaining 11698 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 4764 17.81 - 35.63: 201 35.63 - 53.44: 101 53.44 - 71.26: 27 71.26 - 89.07: 25 Dihedral angle restraints: 5118 sinusoidal: 1926 harmonic: 3192 Sorted by residual: dihedral pdb=" CA GLU E 83 " pdb=" C GLU E 83 " pdb=" N GLY E 84 " pdb=" CA GLY E 84 " ideal model delta harmonic sigma weight residual 180.00 161.72 18.28 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA GLU K 83 " pdb=" C GLU K 83 " pdb=" N GLY K 84 " pdb=" CA GLY K 84 " ideal model delta harmonic sigma weight residual 180.00 161.73 18.27 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA GLU B 83 " pdb=" C GLU B 83 " pdb=" N GLY B 84 " pdb=" CA GLY B 84 " ideal model delta harmonic sigma weight residual 180.00 161.74 18.26 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 5115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 756 0.034 - 0.068: 394 0.068 - 0.102: 134 0.102 - 0.136: 84 0.136 - 0.170: 12 Chirality restraints: 1380 Sorted by residual: chirality pdb=" CG LEU I 8 " pdb=" CB LEU I 8 " pdb=" CD1 LEU I 8 " pdb=" CD2 LEU I 8 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.24e-01 chirality pdb=" CG LEU K 8 " pdb=" CB LEU K 8 " pdb=" CD1 LEU K 8 " pdb=" CD2 LEU K 8 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.19e-01 chirality pdb=" CG LEU C 8 " pdb=" CB LEU C 8 " pdb=" CD1 LEU C 8 " pdb=" CD2 LEU C 8 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.13e-01 ... (remaining 1377 not shown) Planarity restraints: 1452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C01 1KI H 103 " 0.004 2.00e-02 2.50e+03 1.28e-02 4.91e+00 pdb=" C02 1KI H 103 " 0.005 2.00e-02 2.50e+03 pdb=" C03 1KI H 103 " 0.017 2.00e-02 2.50e+03 pdb=" C12 1KI H 103 " 0.014 2.00e-02 2.50e+03 pdb=" C13 1KI H 103 " 0.007 2.00e-02 2.50e+03 pdb=" C14 1KI H 103 " 0.001 2.00e-02 2.50e+03 pdb=" C16 1KI H 103 " -0.001 2.00e-02 2.50e+03 pdb=" C17 1KI H 103 " -0.012 2.00e-02 2.50e+03 pdb=" C28 1KI H 103 " -0.002 2.00e-02 2.50e+03 pdb=" N04 1KI H 103 " -0.035 2.00e-02 2.50e+03 pdb=" N15 1KI H 103 " -0.004 2.00e-02 2.50e+03 pdb=" S27 1KI H 103 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C03 1KI L 101 " -0.004 2.00e-02 2.50e+03 6.07e-03 3.69e-01 pdb=" C05 1KI L 101 " -0.003 2.00e-02 2.50e+03 pdb=" C11 1KI L 101 " -0.004 2.00e-02 2.50e+03 pdb=" N04 1KI L 101 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C03 1KI K 102 " 0.003 2.00e-02 2.50e+03 5.97e-03 3.56e-01 pdb=" C05 1KI K 102 " 0.003 2.00e-02 2.50e+03 pdb=" C11 1KI K 102 " 0.003 2.00e-02 2.50e+03 pdb=" N04 1KI K 102 " -0.010 2.00e-02 2.50e+03 ... (remaining 1449 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 765 2.74 - 3.28: 7817 3.28 - 3.82: 13601 3.82 - 4.36: 16478 4.36 - 4.90: 34251 Nonbonded interactions: 72912 Sorted by model distance: nonbonded pdb=" CE MET J 1 " pdb=" C28 1KI H 103 " model vdw 2.203 3.760 nonbonded pdb=" O ALA J 11 " pdb=" C01 1KI J 103 " model vdw 2.214 3.460 nonbonded pdb=" O GLY I 41 " pdb=" F10 1KI H 102 " model vdw 2.270 2.990 nonbonded pdb=" O LYS H 10 " pdb=" F10 1KI G 104 " model vdw 2.302 2.990 nonbonded pdb=" CD LYS G 10 " pdb=" C05 1KI G 102 " model vdw 2.303 3.840 ... (remaining 72907 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' and resid 0 through 98) selection = chain 'D' selection = chain 'E' selection = (chain 'F' and resid 0 through 98) selection = (chain 'G' and resid 0 through 98) selection = (chain 'H' and resid 0 through 98) selection = chain 'I' selection = (chain 'J' and resid 0 through 98) selection = (chain 'K' and resid 0 through 98) selection = (chain 'L' and resid 0 through 98) } 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: 3.010 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: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.770 Find NCS groups from input model: 0.190 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:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 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 : 0.010 0.073 8718 Z= 0.469 Angle : 0.908 10.476 11703 Z= 0.401 Chirality : 0.052 0.170 1380 Planarity : 0.001 0.013 1452 Dihedral : 15.078 89.073 3102 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 29.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % 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 aren not related in a simple way. whole: -4.52 (0.16), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.44 (0.12), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.002 TYR B 39 PHE 0.005 0.001 PHE E 4 HIS 0.003 0.002 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00981 ( 8718) covalent geometry : angle 0.90843 (11703) hydrogen bonds : bond 0.21390 ( 166) hydrogen bonds : angle 8.29770 ( 498) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.324 Fit side-chains REVERT: A 20 GLU cc_start: 0.7021 (tp30) cc_final: 0.6792 (pt0) REVERT: B 83 GLU cc_start: 0.7598 (tt0) cc_final: 0.7197 (tm-30) REVERT: C 83 GLU cc_start: 0.7399 (tt0) cc_final: 0.7007 (tm-30) REVERT: D 20 GLU cc_start: 0.7372 (tp30) cc_final: 0.6983 (pt0) REVERT: E 35 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7556 (tt0) REVERT: G 83 GLU cc_start: 0.7188 (tt0) cc_final: 0.6812 (tm-30) REVERT: I 1 MET cc_start: 0.8025 (ttm) cc_final: 0.7740 (ttm) REVERT: L 1 MET cc_start: 0.8255 (ttm) cc_final: 0.7943 (ttm) REVERT: L 28 GLU cc_start: 0.7335 (mt-10) cc_final: 0.7055 (mp0) REVERT: L 96 LYS cc_start: 0.6597 (ttmm) cc_final: 0.5402 (pptt) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.7091 time to fit residues: 180.6795 Evaluate side-chains 151 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN B 50 HIS B 62 GLN B 79 GLN C 62 GLN C 79 GLN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 HIS ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 62 GLN G 79 GLN H 62 GLN I 62 GLN ** J 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 50 HIS ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.136868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.119766 restraints weight = 7264.787| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 1.57 r_work: 0.3750 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.5633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8718 Z= 0.212 Angle : 0.836 14.495 11703 Z= 0.388 Chirality : 0.052 0.131 1380 Planarity : 0.003 0.017 1452 Dihedral : 11.149 88.791 1350 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 5.51 % Allowed : 18.87 % Favored : 75.61 % 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 aren not related in a simple way. whole: -3.68 (0.19), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.14), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.001 TYR I 39 PHE 0.016 0.003 PHE I 4 HIS 0.004 0.001 HIS L 50 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 8718) covalent geometry : angle 0.83644 (11703) hydrogen bonds : bond 0.03384 ( 166) hydrogen bonds : angle 4.73846 ( 498) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 158 time to evaluate : 0.334 Fit side-chains REVERT: A 20 GLU cc_start: 0.8310 (tp30) cc_final: 0.7447 (pt0) REVERT: A 60 LYS cc_start: 0.8856 (ttpp) cc_final: 0.7428 (pmtt) REVERT: B 35 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8051 (tt0) REVERT: B 83 GLU cc_start: 0.7898 (tt0) cc_final: 0.7583 (tm-30) REVERT: C 13 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8360 (mt-10) REVERT: C 35 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8136 (tt0) REVERT: C 83 GLU cc_start: 0.7979 (tt0) cc_final: 0.7400 (tm-30) REVERT: E 46 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8483 (mt-10) REVERT: F 13 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8529 (mt-10) REVERT: G 13 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8145 (mt-10) REVERT: G 35 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8091 (tt0) REVERT: G 83 GLU cc_start: 0.7932 (tt0) cc_final: 0.7388 (tm-30) REVERT: H 2 ASP cc_start: 0.8186 (m-30) cc_final: 0.7925 (m-30) REVERT: H 13 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8069 (mt-10) REVERT: H 35 GLU cc_start: 0.8407 (mt-10) cc_final: 0.7838 (tt0) REVERT: I 13 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8372 (mt-10) REVERT: I 21 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.7154 (mmpt) REVERT: I 35 GLU cc_start: 0.8452 (mt-10) cc_final: 0.7998 (tm-30) REVERT: I 96 LYS cc_start: 0.7767 (ttmm) cc_final: 0.6318 (mptp) REVERT: J 46 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8503 (mt-10) REVERT: J 61 GLU cc_start: 0.8342 (tt0) cc_final: 0.8104 (tt0) REVERT: K 28 GLU cc_start: 0.8272 (mt-10) cc_final: 0.8021 (mt-10) REVERT: L 21 LYS cc_start: 0.8938 (mttm) cc_final: 0.8733 (mttt) REVERT: L 96 LYS cc_start: 0.7603 (ttmm) cc_final: 0.6048 (pptt) outliers start: 45 outliers final: 21 residues processed: 189 average time/residue: 0.7255 time to fit residues: 143.4017 Evaluate side-chains 170 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain I residue 21 LYS Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 87 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 106 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 90 optimal weight: 0.7980 chunk 27 optimal weight: 9.9990 chunk 46 optimal weight: 0.7980 chunk 94 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 50 HIS H 50 HIS I 50 HIS ** J 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.130302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.114145 restraints weight = 7399.237| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 1.56 r_work: 0.3676 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3542 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.5883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 8718 Z= 0.203 Angle : 0.766 12.967 11703 Z= 0.352 Chirality : 0.051 0.137 1380 Planarity : 0.002 0.009 1452 Dihedral : 10.571 84.427 1350 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.53 % Allowed : 21.45 % Favored : 74.02 % 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 aren not related in a simple way. whole: -3.31 (0.21), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR H 39 PHE 0.010 0.002 PHE I 4 HIS 0.006 0.002 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 8718) covalent geometry : angle 0.76591 (11703) hydrogen bonds : bond 0.03340 ( 166) hydrogen bonds : angle 4.74978 ( 498) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 151 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8406 (tp30) cc_final: 0.7621 (mp0) REVERT: A 60 LYS cc_start: 0.8814 (ttpp) cc_final: 0.7286 (pmtt) REVERT: B 57 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7622 (tt0) REVERT: B 83 GLU cc_start: 0.7955 (tt0) cc_final: 0.7588 (tm-30) REVERT: C 13 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8161 (mt-10) REVERT: C 35 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8036 (tt0) REVERT: C 83 GLU cc_start: 0.8043 (tt0) cc_final: 0.7418 (tm-30) REVERT: F 13 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8395 (mt-10) REVERT: G 5 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.7862 (mpp) REVERT: G 83 GLU cc_start: 0.7999 (tt0) cc_final: 0.7404 (tm-30) REVERT: H 5 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.7958 (mpp) REVERT: I 96 LYS cc_start: 0.8040 (ttmm) cc_final: 0.6500 (mptp) REVERT: J 61 GLU cc_start: 0.8287 (tt0) cc_final: 0.7987 (tt0) REVERT: K 46 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8555 (mt-10) REVERT: L 96 LYS cc_start: 0.7835 (ttmm) cc_final: 0.6170 (pptt) outliers start: 37 outliers final: 23 residues processed: 172 average time/residue: 0.7511 time to fit residues: 135.0733 Evaluate side-chains 171 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain G residue 5 MET Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 5 MET Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 87 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 43 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN F 79 GLN J 79 GLN K 79 GLN L 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.124432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.108741 restraints weight = 7385.739| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 1.51 r_work: 0.3601 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.6432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.049 8718 Z= 0.422 Angle : 0.968 13.540 11703 Z= 0.456 Chirality : 0.055 0.157 1380 Planarity : 0.003 0.015 1452 Dihedral : 11.864 89.549 1350 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 6.25 % Allowed : 19.73 % Favored : 74.02 % 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 aren not related in a simple way. whole: -3.29 (0.21), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR D 39 PHE 0.016 0.003 PHE C 4 HIS 0.005 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00959 ( 8718) covalent geometry : angle 0.96819 (11703) hydrogen bonds : bond 0.03981 ( 166) hydrogen bonds : angle 5.24604 ( 498) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 150 time to evaluate : 0.255 Fit side-chains REVERT: A 20 GLU cc_start: 0.8634 (tp30) cc_final: 0.7712 (pt0) REVERT: A 35 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8099 (tt0) REVERT: A 57 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7874 (tt0) REVERT: A 60 LYS cc_start: 0.8841 (ttpp) cc_final: 0.7271 (pmtt) REVERT: A 97 LYS cc_start: 0.7335 (ptpt) cc_final: 0.5978 (pmtt) REVERT: B 28 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7817 (mt-10) REVERT: B 57 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7710 (tt0) REVERT: B 83 GLU cc_start: 0.7989 (tt0) cc_final: 0.7659 (tm-30) REVERT: B 96 LYS cc_start: 0.7673 (ttmm) cc_final: 0.6735 (tptp) REVERT: C 13 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8343 (mt-10) REVERT: C 57 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7810 (tt0) REVERT: C 83 GLU cc_start: 0.8012 (tt0) cc_final: 0.7496 (tm-30) REVERT: C 97 LYS cc_start: 0.6223 (tptt) cc_final: 0.5742 (mtpp) REVERT: D 35 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7829 (mt-10) REVERT: G 5 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.7953 (mpp) REVERT: G 60 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8408 (tmtt) REVERT: G 83 GLU cc_start: 0.8074 (tt0) cc_final: 0.7549 (tm-30) REVERT: H 5 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.7953 (mpp) REVERT: H 20 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8029 (tm-30) REVERT: I 96 LYS cc_start: 0.8180 (ttmm) cc_final: 0.6475 (mptp) REVERT: J 61 GLU cc_start: 0.8379 (tt0) cc_final: 0.8128 (tt0) REVERT: K 46 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8627 (mt-10) outliers start: 51 outliers final: 29 residues processed: 178 average time/residue: 0.7566 time to fit residues: 140.8418 Evaluate side-chains 181 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 5 MET Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 5 MET Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 87 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 26 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.128944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.113248 restraints weight = 7259.867| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 1.52 r_work: 0.3665 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.6444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 8718 Z= 0.184 Angle : 0.780 12.754 11703 Z= 0.353 Chirality : 0.051 0.143 1380 Planarity : 0.002 0.009 1452 Dihedral : 10.788 84.928 1350 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.66 % Allowed : 22.55 % Favored : 72.79 % 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 aren not related in a simple way. whole: -3.10 (0.22), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR D 39 PHE 0.012 0.002 PHE C 4 HIS 0.003 0.001 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 8718) covalent geometry : angle 0.78027 (11703) hydrogen bonds : bond 0.02798 ( 166) hydrogen bonds : angle 4.89948 ( 498) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 144 time to evaluate : 0.369 Fit side-chains REVERT: A 20 GLU cc_start: 0.8580 (tp30) cc_final: 0.7729 (mp0) REVERT: A 35 GLU cc_start: 0.8362 (mt-10) cc_final: 0.8006 (tt0) REVERT: A 57 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7796 (tt0) REVERT: A 60 LYS cc_start: 0.8798 (ttpp) cc_final: 0.7269 (pmtt) REVERT: A 64 THR cc_start: 0.8801 (OUTLIER) cc_final: 0.8452 (m) REVERT: A 97 LYS cc_start: 0.7462 (ptpt) cc_final: 0.6050 (pmtt) REVERT: B 28 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7857 (mt-10) REVERT: B 57 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7634 (tt0) REVERT: B 83 GLU cc_start: 0.7879 (tt0) cc_final: 0.7561 (tm-30) REVERT: C 13 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8347 (mt-10) REVERT: C 57 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7747 (tt0) REVERT: C 83 GLU cc_start: 0.7938 (tt0) cc_final: 0.7398 (tm-30) REVERT: C 97 LYS cc_start: 0.6220 (tptt) cc_final: 0.5740 (mtpp) REVERT: D 35 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7720 (mt-10) REVERT: G 5 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8031 (mpp) REVERT: G 13 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8191 (mt-10) REVERT: G 83 GLU cc_start: 0.7956 (tt0) cc_final: 0.7418 (tm-30) REVERT: H 5 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8118 (mpp) REVERT: I 96 LYS cc_start: 0.8146 (ttmm) cc_final: 0.6494 (mptp) REVERT: J 61 GLU cc_start: 0.8304 (tt0) cc_final: 0.8073 (tt0) REVERT: K 46 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8631 (mt-10) outliers start: 38 outliers final: 19 residues processed: 165 average time/residue: 0.7886 time to fit residues: 136.1554 Evaluate side-chains 164 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain G residue 5 MET Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 5 MET Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 87 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 14 optimal weight: 0.8980 overall best weight: 7.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.123158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.107621 restraints weight = 7164.772| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 1.50 r_work: 0.3588 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.6581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.042 8718 Z= 0.360 Angle : 0.927 13.471 11703 Z= 0.428 Chirality : 0.053 0.152 1380 Planarity : 0.003 0.013 1452 Dihedral : 11.069 88.109 1350 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 5.76 % Allowed : 21.69 % Favored : 72.55 % 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 aren not related in a simple way. whole: -3.17 (0.21), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.002 TYR D 39 PHE 0.014 0.003 PHE H 4 HIS 0.004 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00819 ( 8718) covalent geometry : angle 0.92676 (11703) hydrogen bonds : bond 0.03690 ( 166) hydrogen bonds : angle 5.10716 ( 498) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 141 time to evaluate : 0.407 Fit side-chains REVERT: A 20 GLU cc_start: 0.8634 (tp30) cc_final: 0.7749 (mp0) REVERT: A 35 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8045 (tt0) REVERT: A 57 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7861 (tt0) REVERT: A 60 LYS cc_start: 0.8793 (ttpp) cc_final: 0.7313 (ptpp) REVERT: A 72 THR cc_start: 0.9049 (m) cc_final: 0.8712 (p) REVERT: A 97 LYS cc_start: 0.7482 (ptpt) cc_final: 0.6223 (pmtt) REVERT: B 28 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7884 (mt-10) REVERT: B 57 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7646 (tt0) REVERT: B 83 GLU cc_start: 0.7955 (tt0) cc_final: 0.7602 (tm-30) REVERT: C 13 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8477 (mt-10) REVERT: C 57 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7839 (tt0) REVERT: C 83 GLU cc_start: 0.8011 (tt0) cc_final: 0.7460 (tm-30) REVERT: C 97 LYS cc_start: 0.6334 (tptt) cc_final: 0.5812 (mtpp) REVERT: D 35 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7816 (mt-10) REVERT: G 5 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.7932 (mpp) REVERT: G 13 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8267 (mt-10) REVERT: G 83 GLU cc_start: 0.8038 (tt0) cc_final: 0.7479 (tm-30) REVERT: H 5 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8005 (mpp) REVERT: H 20 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.7789 (tm-30) REVERT: H 57 GLU cc_start: 0.8075 (mp0) cc_final: 0.7407 (mp0) REVERT: J 61 GLU cc_start: 0.8335 (tt0) cc_final: 0.8112 (tt0) outliers start: 47 outliers final: 30 residues processed: 170 average time/residue: 0.8230 time to fit residues: 146.3325 Evaluate side-chains 177 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 5 MET Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 5 MET Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 87 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 74 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 93 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.126682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.111038 restraints weight = 7246.692| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 1.52 r_work: 0.3635 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.6607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 8718 Z= 0.225 Angle : 0.823 12.989 11703 Z= 0.373 Chirality : 0.051 0.147 1380 Planarity : 0.002 0.011 1452 Dihedral : 10.422 85.822 1350 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 5.76 % Allowed : 22.55 % Favored : 71.69 % 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 aren not related in a simple way. whole: -3.10 (0.22), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR D 39 PHE 0.013 0.003 PHE I 4 HIS 0.003 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00504 ( 8718) covalent geometry : angle 0.82342 (11703) hydrogen bonds : bond 0.03021 ( 166) hydrogen bonds : angle 4.89826 ( 498) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 142 time to evaluate : 0.350 Fit side-chains REVERT: A 20 GLU cc_start: 0.8622 (tp30) cc_final: 0.7727 (mp0) REVERT: A 35 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8003 (tt0) REVERT: A 57 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7819 (tt0) REVERT: A 60 LYS cc_start: 0.8760 (ttpp) cc_final: 0.7280 (ptpp) REVERT: A 64 THR cc_start: 0.8749 (OUTLIER) cc_final: 0.8406 (m) REVERT: A 97 LYS cc_start: 0.7439 (ptpt) cc_final: 0.6352 (pptt) REVERT: B 28 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7871 (mt-10) REVERT: B 57 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7634 (tt0) REVERT: B 83 GLU cc_start: 0.7891 (tt0) cc_final: 0.7537 (tm-30) REVERT: C 13 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8463 (mt-10) REVERT: C 57 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7810 (tt0) REVERT: C 83 GLU cc_start: 0.7946 (tt0) cc_final: 0.7374 (tm-30) REVERT: C 97 LYS cc_start: 0.6324 (tptt) cc_final: 0.5802 (mtpp) REVERT: D 35 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7730 (mt-10) REVERT: F 61 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8215 (tt0) REVERT: G 5 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.7943 (mpp) REVERT: G 13 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8205 (mt-10) REVERT: G 83 GLU cc_start: 0.7975 (tt0) cc_final: 0.7436 (tm-30) REVERT: H 5 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8113 (mpp) REVERT: H 6 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8575 (ttpt) REVERT: H 13 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8509 (mt-10) REVERT: H 57 GLU cc_start: 0.8043 (mp0) cc_final: 0.7416 (mp0) REVERT: I 21 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.7320 (mmtt) outliers start: 47 outliers final: 30 residues processed: 175 average time/residue: 0.8303 time to fit residues: 151.8354 Evaluate side-chains 178 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 141 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain G residue 5 MET Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain H residue 5 MET Chi-restraints excluded: chain H residue 6 LYS Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain I residue 21 LYS Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 87 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 10 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 8 optimal weight: 0.0170 chunk 44 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 68 optimal weight: 20.0000 chunk 78 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 overall best weight: 3.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.129827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.113941 restraints weight = 7270.200| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 1.53 r_work: 0.3659 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3529 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.6653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 8718 Z= 0.179 Angle : 0.777 12.852 11703 Z= 0.349 Chirality : 0.050 0.143 1380 Planarity : 0.002 0.009 1452 Dihedral : 10.008 85.311 1350 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.66 % Allowed : 23.77 % Favored : 71.57 % 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 aren not related in a simple way. whole: -3.01 (0.22), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR A 39 PHE 0.012 0.002 PHE G 4 HIS 0.003 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 8718) covalent geometry : angle 0.77701 (11703) hydrogen bonds : bond 0.02707 ( 166) hydrogen bonds : angle 4.74050 ( 498) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 140 time to evaluate : 0.396 Fit side-chains REVERT: A 20 GLU cc_start: 0.8595 (tp30) cc_final: 0.7690 (mp0) REVERT: A 35 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8004 (tt0) REVERT: A 57 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7796 (tt0) REVERT: A 60 LYS cc_start: 0.8732 (ttpp) cc_final: 0.7269 (ptpp) REVERT: A 64 THR cc_start: 0.8801 (OUTLIER) cc_final: 0.8464 (m) REVERT: B 28 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7835 (mt-10) REVERT: B 83 GLU cc_start: 0.7870 (tt0) cc_final: 0.7540 (tm-30) REVERT: C 13 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8403 (mt-10) REVERT: C 57 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7790 (tt0) REVERT: C 83 GLU cc_start: 0.7939 (tt0) cc_final: 0.7380 (tm-30) REVERT: C 97 LYS cc_start: 0.6328 (tptt) cc_final: 0.5812 (mtpp) REVERT: D 20 GLU cc_start: 0.8905 (mm-30) cc_final: 0.7797 (mp0) REVERT: D 35 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7687 (tt0) REVERT: G 5 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8044 (mpp) REVERT: G 13 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8216 (mt-10) REVERT: G 83 GLU cc_start: 0.7975 (tt0) cc_final: 0.7465 (tm-30) REVERT: H 5 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.8138 (mpp) REVERT: H 6 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8559 (ttpt) REVERT: H 13 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8517 (mt-10) REVERT: I 21 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.7326 (mmtt) REVERT: J 5 MET cc_start: 0.8683 (mmp) cc_final: 0.8440 (mmt) outliers start: 38 outliers final: 28 residues processed: 166 average time/residue: 0.8705 time to fit residues: 150.8143 Evaluate side-chains 172 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain G residue 5 MET Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 5 MET Chi-restraints excluded: chain H residue 6 LYS Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain I residue 21 LYS Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 87 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 39 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 35 optimal weight: 0.0030 overall best weight: 7.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.123082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.107546 restraints weight = 7108.908| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 1.49 r_work: 0.3591 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.6691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.042 8718 Z= 0.357 Angle : 0.924 13.536 11703 Z= 0.428 Chirality : 0.054 0.154 1380 Planarity : 0.003 0.013 1452 Dihedral : 10.573 86.729 1350 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 5.51 % Allowed : 23.65 % Favored : 70.83 % 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 aren not related in a simple way. whole: -3.09 (0.21), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR D 39 PHE 0.013 0.003 PHE G 4 HIS 0.003 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00813 ( 8718) covalent geometry : angle 0.92409 (11703) hydrogen bonds : bond 0.03649 ( 166) hydrogen bonds : angle 5.07127 ( 498) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 141 time to evaluate : 0.343 Fit side-chains REVERT: A 20 GLU cc_start: 0.8639 (tp30) cc_final: 0.7757 (mp0) REVERT: A 28 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7775 (mt-10) REVERT: A 35 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8009 (tt0) REVERT: A 60 LYS cc_start: 0.8749 (ttpp) cc_final: 0.7242 (ptpp) REVERT: A 97 LYS cc_start: 0.7595 (ptpt) cc_final: 0.6522 (pptt) REVERT: B 5 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.7502 (mpp) REVERT: B 28 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7883 (mt-10) REVERT: B 83 GLU cc_start: 0.7890 (tt0) cc_final: 0.7575 (tm-30) REVERT: C 13 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8526 (mt-10) REVERT: C 57 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7839 (tt0) REVERT: C 83 GLU cc_start: 0.8037 (tt0) cc_final: 0.7489 (tm-30) REVERT: C 97 LYS cc_start: 0.6303 (tptt) cc_final: 0.5685 (mtpp) REVERT: D 35 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7812 (mt-10) REVERT: G 5 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8010 (mpp) REVERT: G 13 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8250 (mt-10) REVERT: G 83 GLU cc_start: 0.7992 (tt0) cc_final: 0.7461 (tm-30) REVERT: H 5 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8104 (mpp) REVERT: H 6 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8551 (ttpt) REVERT: I 6 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8656 (ttpt) REVERT: I 21 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.7356 (mmtt) outliers start: 45 outliers final: 29 residues processed: 170 average time/residue: 0.8325 time to fit residues: 147.9090 Evaluate side-chains 177 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 5 MET Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 5 MET Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 5 MET Chi-restraints excluded: chain H residue 6 LYS Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain I residue 6 LYS Chi-restraints excluded: chain I residue 21 LYS Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 48 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 63 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 97 optimal weight: 0.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.130002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.114188 restraints weight = 7223.423| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 1.53 r_work: 0.3671 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3543 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.6704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8718 Z= 0.155 Angle : 0.772 12.839 11703 Z= 0.345 Chirality : 0.050 0.140 1380 Planarity : 0.002 0.009 1452 Dihedral : 9.804 84.848 1350 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.29 % Allowed : 24.88 % Favored : 70.83 % 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 aren not related in a simple way. whole: -2.96 (0.22), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR A 39 PHE 0.012 0.002 PHE I 4 HIS 0.003 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 8718) covalent geometry : angle 0.77200 (11703) hydrogen bonds : bond 0.02620 ( 166) hydrogen bonds : angle 4.70829 ( 498) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 0.346 Fit side-chains REVERT: A 20 GLU cc_start: 0.8595 (tp30) cc_final: 0.7706 (mp0) REVERT: A 35 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7962 (tt0) REVERT: A 60 LYS cc_start: 0.8717 (ttpp) cc_final: 0.7205 (ptpp) REVERT: A 64 THR cc_start: 0.8772 (OUTLIER) cc_final: 0.8527 (m) REVERT: B 28 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7904 (mt-10) REVERT: B 83 GLU cc_start: 0.7824 (tt0) cc_final: 0.7484 (tm-30) REVERT: C 13 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8420 (mt-10) REVERT: C 57 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7808 (tt0) REVERT: C 83 GLU cc_start: 0.7942 (tt0) cc_final: 0.7408 (tm-30) REVERT: C 97 LYS cc_start: 0.6386 (tptt) cc_final: 0.5824 (mtpp) REVERT: D 20 GLU cc_start: 0.8911 (mm-30) cc_final: 0.7815 (mp0) REVERT: D 35 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7680 (tt0) REVERT: F 61 GLU cc_start: 0.8414 (tt0) cc_final: 0.8149 (tp30) REVERT: G 5 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8045 (mpp) REVERT: G 13 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8181 (mt-10) REVERT: G 83 GLU cc_start: 0.7970 (tt0) cc_final: 0.7463 (tm-30) REVERT: H 5 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8182 (mpp) REVERT: H 6 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8506 (ttpt) REVERT: H 13 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8490 (mt-10) REVERT: H 57 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7623 (tt0) REVERT: I 6 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8711 (ttpt) REVERT: I 21 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.7321 (mmtt) outliers start: 35 outliers final: 26 residues processed: 162 average time/residue: 0.8415 time to fit residues: 142.4787 Evaluate side-chains 169 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 136 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain G residue 5 MET Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 5 MET Chi-restraints excluded: chain H residue 6 LYS Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain I residue 6 LYS Chi-restraints excluded: chain I residue 21 LYS Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 56 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 chunk 68 optimal weight: 20.0000 chunk 99 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.126043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.110556 restraints weight = 6998.650| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.48 r_work: 0.3640 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.6715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 8718 Z= 0.222 Angle : 0.819 12.863 11703 Z= 0.370 Chirality : 0.051 0.144 1380 Planarity : 0.002 0.010 1452 Dihedral : 9.912 85.866 1350 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 4.29 % Allowed : 24.88 % Favored : 70.83 % 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 aren not related in a simple way. whole: -2.97 (0.22), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR A 39 PHE 0.012 0.002 PHE I 4 HIS 0.003 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00500 ( 8718) covalent geometry : angle 0.81852 (11703) hydrogen bonds : bond 0.03021 ( 166) hydrogen bonds : angle 4.79952 ( 498) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3190.44 seconds wall clock time: 55 minutes 18.13 seconds (3318.13 seconds total)