Starting phenix.real_space_refine on Wed Jan 15 15:37:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zmy_60262/01_2025/8zmy_60262.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zmy_60262/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8zmy_60262/01_2025/8zmy_60262.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zmy_60262/01_2025/8zmy_60262.map" model { file = "/net/cci-nas-00/data/ceres_data/8zmy_60262/01_2025/8zmy_60262.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zmy_60262/01_2025/8zmy_60262.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 3.60, per 1000 atoms: 0.42 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: 2.35 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.23 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: 2.36 Time building geometry restraints manager: 2.55 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: 3.470 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 20.990 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.030 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:11.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.550 ------------------------------------------------------------------------------- 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= 0.609 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 : 20.23 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.003 0.002 HIS E 50 PHE 0.005 0.001 PHE E 4 TYR 0.004 0.002 TYR B 39 *********************** 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 : 0.913 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: 0.7198 (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: 1.5647 time to fit residues: 399.5872 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 : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 0.3980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 HIS G 62 GLN G 79 GLN ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 62 GLN K 50 HIS L 50 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.151746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.135664 restraints weight = 7047.562| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 1.50 r_work: 0.3960 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3840 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8718 Z= 0.158 Angle : 0.742 12.877 11703 Z= 0.329 Chirality : 0.051 0.131 1380 Planarity : 0.002 0.012 1452 Dihedral : 10.462 88.389 1350 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.17 % Allowed : 18.63 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.19), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.15), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 50 PHE 0.012 0.002 PHE K 4 TYR 0.003 0.001 TYR I 39 *********************** 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 179 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 0.999 Fit side-chains REVERT: A 20 GLU cc_start: 0.7689 (tp30) cc_final: 0.7315 (pt0) REVERT: B 5 MET cc_start: 0.8021 (mpp) cc_final: 0.7652 (mmt) REVERT: B 83 GLU cc_start: 0.7849 (tt0) cc_final: 0.7569 (tm-30) REVERT: C 35 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8066 (tm-30) REVERT: C 83 GLU cc_start: 0.7908 (tt0) cc_final: 0.7362 (tm-30) REVERT: G 83 GLU cc_start: 0.7734 (tt0) cc_final: 0.7347 (tm-30) REVERT: H 13 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7364 (mt-10) REVERT: H 35 GLU cc_start: 0.8400 (mt-10) cc_final: 0.7866 (tt0) REVERT: H 96 LYS cc_start: 0.6754 (ttmm) cc_final: 0.5315 (mptp) REVERT: I 1 MET cc_start: 0.7981 (ttm) cc_final: 0.7730 (ttm) REVERT: I 13 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7224 (mt-10) REVERT: I 21 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.7166 (mmpt) REVERT: I 35 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7892 (tm-30) REVERT: I 96 LYS cc_start: 0.7294 (ttmm) cc_final: 0.5800 (mptp) REVERT: J 5 MET cc_start: 0.8195 (mmt) cc_final: 0.7864 (mmp) REVERT: L 96 LYS cc_start: 0.7009 (ttmm) cc_final: 0.5512 (pptt) outliers start: 34 outliers final: 12 residues processed: 162 average time/residue: 1.6374 time to fit residues: 278.4982 Evaluate side-chains 142 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain I residue 21 LYS Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain L residue 77 VAL 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 30 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 overall best weight: 8.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS D 50 HIS ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.126015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.110026 restraints weight = 6868.234| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 1.50 r_work: 0.3616 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.6103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.057 8718 Z= 0.688 Angle : 1.017 14.055 11703 Z= 0.486 Chirality : 0.057 0.145 1380 Planarity : 0.004 0.018 1452 Dihedral : 11.785 87.888 1350 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 6.74 % Allowed : 17.77 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.21), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 50 PHE 0.020 0.004 PHE C 4 TYR 0.010 0.002 TYR G 39 *********************** 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 215 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 160 time to evaluate : 1.008 Fit side-chains REVERT: A 20 GLU cc_start: 0.8585 (tp30) cc_final: 0.7652 (pt0) REVERT: A 35 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8113 (tt0) REVERT: A 60 LYS cc_start: 0.8845 (ttpp) cc_final: 0.7185 (pmmt) REVERT: A 97 LYS cc_start: 0.6983 (ptpt) cc_final: 0.5689 (pmtt) REVERT: B 57 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7671 (tt0) REVERT: B 83 GLU cc_start: 0.7958 (tt0) cc_final: 0.7609 (tm-30) REVERT: C 83 GLU cc_start: 0.8016 (tt0) cc_final: 0.7514 (tm-30) REVERT: D 35 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7866 (mt-10) REVERT: F 44 THR cc_start: 0.8987 (OUTLIER) cc_final: 0.8776 (m) REVERT: G 83 GLU cc_start: 0.8093 (tt0) cc_final: 0.7551 (tm-30) REVERT: H 5 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.7806 (mpp) REVERT: I 96 LYS cc_start: 0.8158 (ttmm) cc_final: 0.6617 (mptp) REVERT: J 46 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8576 (mt-10) REVERT: K 46 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8618 (mt-10) REVERT: K 83 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8189 (tt0) REVERT: L 96 LYS cc_start: 0.7940 (ttmm) cc_final: 0.6387 (pptt) outliers start: 55 outliers final: 30 residues processed: 192 average time/residue: 1.7109 time to fit residues: 343.7544 Evaluate side-chains 184 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 64 THR 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 64 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 44 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 48 VAL Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 5 MET Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain J residue 44 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 59 THR Chi-restraints excluded: chain K residue 83 GLU 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 5 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 74 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 50 HIS ** D 79 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** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.132309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.116592 restraints weight = 6770.817| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 1.47 r_work: 0.3716 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3589 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.6187 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= 0.188 Angle : 0.736 12.660 11703 Z= 0.332 Chirality : 0.051 0.140 1380 Planarity : 0.002 0.014 1452 Dihedral : 10.799 85.219 1350 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.41 % Allowed : 21.20 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.22), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS I 50 PHE 0.012 0.002 PHE C 4 TYR 0.008 0.001 TYR G 39 *********************** 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 183 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 0.926 Fit side-chains REVERT: A 20 GLU cc_start: 0.8468 (tp30) cc_final: 0.7759 (mt-10) REVERT: A 60 LYS cc_start: 0.8792 (ttpp) cc_final: 0.7297 (pmmt) REVERT: A 64 THR cc_start: 0.8728 (OUTLIER) cc_final: 0.8426 (m) REVERT: A 97 LYS cc_start: 0.7065 (ptpt) cc_final: 0.5695 (pmtt) REVERT: B 57 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7511 (tt0) REVERT: B 83 GLU cc_start: 0.7796 (tt0) cc_final: 0.7525 (tm-30) REVERT: B 96 LYS cc_start: 0.7569 (ttmm) cc_final: 0.6715 (tptp) REVERT: C 57 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7734 (tt0) REVERT: C 83 GLU cc_start: 0.7853 (tt0) cc_final: 0.7329 (tm-30) REVERT: C 97 LYS cc_start: 0.6071 (tptt) cc_final: 0.5607 (mtpt) REVERT: D 20 GLU cc_start: 0.8847 (mm-30) cc_final: 0.7782 (mp0) REVERT: D 35 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7680 (mt-10) REVERT: G 5 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.8023 (mpp) REVERT: G 13 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8019 (mt-10) REVERT: G 83 GLU cc_start: 0.7900 (tt0) cc_final: 0.7334 (tm-30) REVERT: H 5 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.7813 (mpp) REVERT: I 83 GLU cc_start: 0.8388 (pt0) cc_final: 0.8156 (pt0) REVERT: I 96 LYS cc_start: 0.8129 (ttmm) cc_final: 0.6563 (mptp) REVERT: J 44 THR cc_start: 0.8973 (OUTLIER) cc_final: 0.8757 (m) REVERT: J 46 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8512 (mt-10) REVERT: J 64 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8705 (m) outliers start: 36 outliers final: 18 residues processed: 163 average time/residue: 1.7542 time to fit residues: 299.0365 Evaluate side-chains 167 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 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 59 THR Chi-restraints excluded: chain E residue 64 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 48 VAL Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 5 MET Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain J residue 44 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 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 68 optimal weight: 0.5980 chunk 3 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 96 optimal weight: 20.0000 chunk 106 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 79 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** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 50 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.128589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.112896 restraints weight = 7137.948| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 1.51 r_work: 0.3663 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.6359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8718 Z= 0.292 Angle : 0.771 12.577 11703 Z= 0.350 Chirality : 0.051 0.141 1380 Planarity : 0.002 0.014 1452 Dihedral : 10.651 79.664 1350 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 4.66 % Allowed : 20.96 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.22), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS K 50 PHE 0.013 0.002 PHE C 4 TYR 0.007 0.001 TYR G 39 *********************** 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 184 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 0.947 Fit side-chains REVERT: A 13 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8227 (mt-10) REVERT: A 20 GLU cc_start: 0.8526 (tp30) cc_final: 0.7682 (mp0) REVERT: A 35 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8023 (tt0) REVERT: A 60 LYS cc_start: 0.8783 (ttpp) cc_final: 0.7192 (pmmt) REVERT: A 64 THR cc_start: 0.8777 (OUTLIER) cc_final: 0.8462 (m) REVERT: A 97 LYS cc_start: 0.7186 (ptpt) cc_final: 0.5753 (pmtt) REVERT: B 57 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7546 (tt0) REVERT: B 83 GLU cc_start: 0.7936 (tt0) cc_final: 0.7572 (tm-30) REVERT: B 96 LYS cc_start: 0.7583 (ttmm) cc_final: 0.6775 (tptp) REVERT: C 57 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7730 (tt0) REVERT: C 83 GLU cc_start: 0.7938 (tt0) cc_final: 0.7348 (tm-30) REVERT: C 97 LYS cc_start: 0.6217 (tptt) cc_final: 0.5805 (mtpt) REVERT: D 20 GLU cc_start: 0.8915 (mm-30) cc_final: 0.7790 (mp0) REVERT: D 35 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7707 (mt-10) REVERT: G 5 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8016 (mpp) REVERT: G 13 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8126 (mt-10) REVERT: G 83 GLU cc_start: 0.7981 (tt0) cc_final: 0.7409 (tm-30) REVERT: H 5 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.7790 (mpp) REVERT: H 13 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8487 (mt-10) REVERT: I 21 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.7302 (mmpt) REVERT: I 83 GLU cc_start: 0.8464 (pt0) cc_final: 0.8217 (pt0) REVERT: I 96 LYS cc_start: 0.8145 (ttmm) cc_final: 0.6514 (mptp) REVERT: J 5 MET cc_start: 0.8686 (mmp) cc_final: 0.8383 (mmt) REVERT: J 46 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8522 (mt-10) REVERT: L 1 MET cc_start: 0.8026 (ttp) cc_final: 0.7826 (ptm) outliers start: 38 outliers final: 22 residues processed: 169 average time/residue: 1.6654 time to fit residues: 295.0381 Evaluate side-chains 170 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU 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 E residue 59 THR Chi-restraints excluded: chain E residue 64 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 48 VAL Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 5 MET Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain I residue 21 LYS 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 J residue 64 THR Chi-restraints excluded: chain J residue 87 SER 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 12 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 103 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 GLN E 79 GLN F 79 GLN ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 GLN K 50 HIS K 79 GLN L 79 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.124048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.108522 restraints weight = 7128.852| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 1.48 r_work: 0.3607 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.6549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.036 8718 Z= 0.476 Angle : 0.886 13.097 11703 Z= 0.410 Chirality : 0.053 0.148 1380 Planarity : 0.003 0.015 1452 Dihedral : 11.342 86.993 1350 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 5.39 % Allowed : 21.32 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.22), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS K 50 PHE 0.014 0.003 PHE C 4 TYR 0.008 0.002 TYR G 39 *********************** 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 191 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 147 time to evaluate : 0.989 Fit side-chains REVERT: A 20 GLU cc_start: 0.8578 (tp30) cc_final: 0.7637 (pt0) REVERT: A 35 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8066 (tt0) REVERT: A 60 LYS cc_start: 0.8800 (ttpp) cc_final: 0.7305 (ptpp) REVERT: A 97 LYS cc_start: 0.7382 (ptpt) cc_final: 0.6013 (pmtt) REVERT: B 5 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.7489 (mpp) REVERT: B 57 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7620 (tt0) REVERT: B 83 GLU cc_start: 0.7980 (tt0) cc_final: 0.7599 (tm-30) REVERT: B 96 LYS cc_start: 0.7604 (ttmm) cc_final: 0.6807 (tptp) REVERT: C 57 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7769 (tt0) REVERT: C 83 GLU cc_start: 0.8006 (tt0) cc_final: 0.7411 (tm-30) REVERT: C 97 LYS cc_start: 0.6301 (tptt) cc_final: 0.5840 (mtpt) REVERT: D 20 GLU cc_start: 0.8901 (mm-30) cc_final: 0.7766 (mp0) REVERT: D 35 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7804 (mt-10) REVERT: G 5 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8007 (mpp) REVERT: G 13 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8203 (mt-10) REVERT: G 83 GLU cc_start: 0.8030 (tt0) cc_final: 0.7485 (tm-30) REVERT: H 5 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.7888 (mpp) REVERT: H 20 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.7987 (tm-30) REVERT: I 21 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.7381 (mmtt) REVERT: I 83 GLU cc_start: 0.8462 (pt0) cc_final: 0.8194 (pt0) REVERT: I 96 LYS cc_start: 0.8181 (ttmm) cc_final: 0.6527 (mptp) outliers start: 44 outliers final: 27 residues processed: 170 average time/residue: 1.7339 time to fit residues: 309.0140 Evaluate side-chains 177 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 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 64 THR Chi-restraints excluded: chain E residue 75 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 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 H residue 81 THR Chi-restraints excluded: chain I residue 21 LYS 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 62 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 42 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 97 optimal weight: 0.0570 overall best weight: 1.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.132942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.117171 restraints weight = 7261.442| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 1.53 r_work: 0.3708 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.6584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8718 Z= 0.161 Angle : 0.713 12.410 11703 Z= 0.318 Chirality : 0.050 0.138 1380 Planarity : 0.002 0.012 1452 Dihedral : 10.363 87.952 1350 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 5.02 % Allowed : 22.55 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.23), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS K 50 PHE 0.012 0.002 PHE I 4 TYR 0.006 0.001 TYR G 39 *********************** 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 181 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 140 time to evaluate : 0.994 Fit side-chains REVERT: A 20 GLU cc_start: 0.8531 (tp30) cc_final: 0.7805 (mt-10) REVERT: A 60 LYS cc_start: 0.8764 (ttpp) cc_final: 0.7226 (pmtt) REVERT: B 57 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7569 (tt0) REVERT: B 83 GLU cc_start: 0.7841 (tt0) cc_final: 0.7478 (tm-30) REVERT: B 96 LYS cc_start: 0.7492 (ttmm) cc_final: 0.6783 (tttp) REVERT: C 57 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7734 (tt0) REVERT: C 83 GLU cc_start: 0.7879 (tt0) cc_final: 0.7255 (tm-30) REVERT: C 97 LYS cc_start: 0.6303 (tptt) cc_final: 0.5840 (mtpt) REVERT: D 20 GLU cc_start: 0.8889 (mm-30) cc_final: 0.7777 (mp0) REVERT: D 35 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7676 (mt-10) REVERT: E 35 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7870 (tt0) REVERT: F 5 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8236 (mmt) REVERT: G 5 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8085 (mpp) REVERT: G 13 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8063 (mt-10) REVERT: G 83 GLU cc_start: 0.7924 (tt0) cc_final: 0.7346 (tm-30) REVERT: H 5 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.7948 (mpp) REVERT: H 13 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8521 (mt-10) REVERT: I 21 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.7207 (mmpt) REVERT: I 96 LYS cc_start: 0.8122 (ttmm) cc_final: 0.6495 (mptp) REVERT: L 5 MET cc_start: 0.8475 (mmp) cc_final: 0.8234 (mmt) outliers start: 41 outliers final: 23 residues processed: 165 average time/residue: 1.6385 time to fit residues: 283.1492 Evaluate side-chains 167 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 5 MET 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 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 54 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain I residue 21 LYS Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain J residue 59 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 80 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 35 optimal weight: 0.0970 chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 4 optimal weight: 0.9980 chunk 42 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 overall best weight: 4.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 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 = 0.4018 r_free = 0.4018 target = 0.127798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.112258 restraints weight = 7196.337| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 1.50 r_work: 0.3651 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3522 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.6623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 8718 Z= 0.320 Angle : 0.788 12.684 11703 Z= 0.358 Chirality : 0.051 0.142 1380 Planarity : 0.002 0.010 1452 Dihedral : 10.752 88.540 1350 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 4.78 % Allowed : 22.79 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.22), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.011 0.002 PHE I 4 TYR 0.006 0.001 TYR G 39 *********************** 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 181 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 142 time to evaluate : 1.055 Fit side-chains REVERT: A 20 GLU cc_start: 0.8533 (tp30) cc_final: 0.7708 (mp0) REVERT: A 35 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7998 (tt0) REVERT: A 60 LYS cc_start: 0.8776 (ttpp) cc_final: 0.7285 (ptpp) REVERT: B 5 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7465 (mpp) REVERT: B 57 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7607 (tt0) REVERT: B 83 GLU cc_start: 0.7894 (tt0) cc_final: 0.7559 (tm-30) REVERT: B 96 LYS cc_start: 0.7499 (ttmm) cc_final: 0.6762 (tttp) REVERT: C 57 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7785 (tt0) REVERT: C 83 GLU cc_start: 0.7953 (tt0) cc_final: 0.7372 (tm-30) REVERT: C 97 LYS cc_start: 0.6310 (tptt) cc_final: 0.5840 (mtpt) REVERT: D 20 GLU cc_start: 0.8904 (mm-30) cc_final: 0.7794 (mp0) REVERT: D 35 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7746 (mt-10) REVERT: F 64 THR cc_start: 0.8973 (OUTLIER) cc_final: 0.8664 (m) REVERT: G 5 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.7933 (mpp) REVERT: G 13 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8030 (mt-10) REVERT: G 83 GLU cc_start: 0.8003 (tt0) cc_final: 0.7438 (tm-30) REVERT: H 5 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.7885 (mpp) REVERT: I 21 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.7315 (mmpt) outliers start: 39 outliers final: 25 residues processed: 165 average time/residue: 1.7465 time to fit residues: 301.2581 Evaluate side-chains 173 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 59 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 64 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 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 54 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain I residue 21 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 56 optimal weight: 9.9990 chunk 70 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 HIS ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.123607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.108410 restraints weight = 7009.658| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.45 r_work: 0.3602 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3476 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.6692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.041 8718 Z= 0.527 Angle : 0.920 13.283 11703 Z= 0.426 Chirality : 0.053 0.152 1380 Planarity : 0.003 0.013 1452 Dihedral : 11.123 85.273 1350 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 4.90 % Allowed : 22.43 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.22), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 50 PHE 0.012 0.003 PHE B 4 TYR 0.008 0.002 TYR G 39 *********************** 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 182 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 142 time to evaluate : 0.956 Fit side-chains REVERT: A 20 GLU cc_start: 0.8566 (tp30) cc_final: 0.7643 (pt0) REVERT: A 35 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8036 (tt0) REVERT: A 60 LYS cc_start: 0.8763 (ttpp) cc_final: 0.7254 (ptpp) REVERT: A 97 LYS cc_start: 0.7479 (ptpt) cc_final: 0.6341 (pptt) REVERT: B 5 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.7508 (mpp) REVERT: B 57 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7617 (tt0) REVERT: B 83 GLU cc_start: 0.7949 (tt0) cc_final: 0.7573 (tm-30) REVERT: B 97 LYS cc_start: 0.7017 (ptpp) cc_final: 0.6745 (ptpt) REVERT: C 57 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7794 (tt0) REVERT: C 83 GLU cc_start: 0.7996 (tt0) cc_final: 0.7391 (tm-30) REVERT: C 97 LYS cc_start: 0.6364 (tptt) cc_final: 0.5825 (mtpp) REVERT: D 20 GLU cc_start: 0.8914 (mm-30) cc_final: 0.7777 (mp0) REVERT: G 5 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.7995 (mpp) REVERT: G 13 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8147 (mt-10) REVERT: G 83 GLU cc_start: 0.8015 (tt0) cc_final: 0.7484 (tm-30) REVERT: H 5 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.7898 (mpp) REVERT: H 20 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.7751 (tm-30) REVERT: I 6 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8663 (ttpt) REVERT: I 21 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.7363 (mmpt) outliers start: 40 outliers final: 26 residues processed: 166 average time/residue: 1.7278 time to fit residues: 300.1223 Evaluate side-chains 173 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 64 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 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 48 VAL Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 81 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 101 optimal weight: 0.0070 chunk 45 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 63 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 76 optimal weight: 0.7980 chunk 70 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 overall best weight: 2.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 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 = 0.4023 r_free = 0.4023 target = 0.128067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.112825 restraints weight = 6989.823| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 1.46 r_work: 0.3671 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.6692 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= 0.231 Angle : 0.763 12.616 11703 Z= 0.342 Chirality : 0.051 0.141 1380 Planarity : 0.002 0.009 1452 Dihedral : 10.309 87.059 1350 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.80 % Allowed : 23.90 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.22), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 50 PHE 0.012 0.002 PHE I 4 TYR 0.006 0.001 TYR G 39 ********************** 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 171 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.993 Fit side-chains REVERT: A 20 GLU cc_start: 0.8549 (tp30) cc_final: 0.7744 (mp0) REVERT: A 35 GLU cc_start: 0.8344 (mt-10) cc_final: 0.7992 (tt0) REVERT: A 60 LYS cc_start: 0.8719 (ttpp) cc_final: 0.7237 (ptpp) REVERT: A 97 LYS cc_start: 0.7450 (ptpt) cc_final: 0.6298 (pptt) REVERT: B 57 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7569 (tt0) REVERT: B 83 GLU cc_start: 0.7895 (tt0) cc_final: 0.7523 (tm-30) REVERT: B 96 LYS cc_start: 0.7707 (ttmm) cc_final: 0.6802 (tttp) REVERT: C 57 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7748 (tt0) REVERT: C 83 GLU cc_start: 0.7915 (tt0) cc_final: 0.7295 (tm-30) REVERT: C 97 LYS cc_start: 0.6369 (tptt) cc_final: 0.5831 (mtpp) REVERT: D 20 GLU cc_start: 0.8890 (mm-30) cc_final: 0.7782 (mp0) REVERT: F 64 THR cc_start: 0.8946 (OUTLIER) cc_final: 0.8693 (m) REVERT: G 5 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.8058 (mpp) REVERT: G 13 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8006 (mt-10) REVERT: G 83 GLU cc_start: 0.7983 (tt0) cc_final: 0.7432 (tm-30) REVERT: H 5 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.7920 (mpp) REVERT: I 6 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8727 (ttpt) REVERT: I 21 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.7270 (mmpt) REVERT: L 5 MET cc_start: 0.8541 (mmp) cc_final: 0.8272 (mmt) outliers start: 31 outliers final: 22 residues processed: 159 average time/residue: 1.7053 time to fit residues: 283.9369 Evaluate side-chains 166 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 59 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 64 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 48 VAL Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 5 MET Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain I residue 6 LYS Chi-restraints excluded: chain I residue 21 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 105 optimal weight: 9.9990 chunk 14 optimal weight: 0.4980 overall best weight: 6.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 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 = 0.3969 r_free = 0.3969 target = 0.123986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.108819 restraints weight = 6990.294| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.46 r_work: 0.3610 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.6702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 8718 Z= 0.480 Angle : 0.890 13.080 11703 Z= 0.410 Chirality : 0.053 0.149 1380 Planarity : 0.003 0.012 1452 Dihedral : 10.584 87.505 1350 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 3.80 % Allowed : 24.26 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.22), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 50 PHE 0.012 0.003 PHE I 4 TYR 0.007 0.002 TYR G 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6347.33 seconds wall clock time: 113 minutes 20.58 seconds (6800.58 seconds total)