Starting phenix.real_space_refine on Fri Nov 15 07:36:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zmy_60262/11_2024/8zmy_60262.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zmy_60262/11_2024/8zmy_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zmy_60262/11_2024/8zmy_60262.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zmy_60262/11_2024/8zmy_60262.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zmy_60262/11_2024/8zmy_60262.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zmy_60262/11_2024/8zmy_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 3.53, per 1000 atoms: 0.41 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: 2.37 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: 1.38 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: 2.39 Time building geometry restraints manager: 2.58 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: 4.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 21.050 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.290 ------------------------------------------------------------------------------- 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 : 0.875 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: 1.5734 time to fit residues: 401.5751 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 : 1.099 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 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 : 1.597 Fit side-chains REVERT: A 20 GLU cc_start: 0.7434 (tp30) cc_final: 0.7096 (pt0) REVERT: B 5 MET cc_start: 0.7660 (mpp) cc_final: 0.7237 (mmt) REVERT: B 83 GLU cc_start: 0.7365 (tt0) cc_final: 0.7091 (tm-30) REVERT: C 35 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7619 (tm-30) REVERT: C 83 GLU cc_start: 0.7323 (tt0) cc_final: 0.6816 (tm-30) REVERT: G 83 GLU cc_start: 0.7081 (tt0) cc_final: 0.6749 (tm-30) REVERT: H 13 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7014 (mt-10) REVERT: H 35 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7380 (tt0) REVERT: H 96 LYS cc_start: 0.6765 (ttmm) cc_final: 0.5374 (mptp) REVERT: I 1 MET cc_start: 0.7826 (ttm) cc_final: 0.7580 (ttm) REVERT: I 13 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6948 (mt-10) REVERT: I 21 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.6880 (mmpt) REVERT: I 35 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7570 (tm-30) REVERT: I 96 LYS cc_start: 0.7184 (ttmm) cc_final: 0.5802 (mptp) REVERT: J 5 MET cc_start: 0.8155 (mmt) cc_final: 0.7703 (mmp) REVERT: K 20 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8101 (mm-30) REVERT: L 96 LYS cc_start: 0.6901 (ttmm) cc_final: 0.5504 (pptt) outliers start: 34 outliers final: 12 residues processed: 162 average time/residue: 1.6907 time to fit residues: 287.6879 Evaluate side-chains 143 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 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 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 K residue 20 GLU 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 54 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 98 optimal weight: 0.0370 chunk 106 optimal weight: 0.9980 chunk 87 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 78 optimal weight: 7.9990 overall best weight: 4.0064 ------------------------------------------------------------------------------- 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 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** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.5765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 8718 Z= 0.328 Angle : 0.795 12.727 11703 Z= 0.368 Chirality : 0.051 0.130 1380 Planarity : 0.002 0.015 1452 Dihedral : 10.665 89.316 1350 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 5.39 % Allowed : 19.00 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.38 (0.20), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.15), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 50 PHE 0.014 0.002 PHE C 4 TYR 0.007 0.002 TYR D 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 200 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 156 time to evaluate : 1.011 Fit side-chains REVERT: A 20 GLU cc_start: 0.8045 (tp30) cc_final: 0.7230 (mp0) REVERT: A 60 LYS cc_start: 0.8691 (ttpp) cc_final: 0.7270 (pmtt) REVERT: A 72 THR cc_start: 0.8820 (m) cc_final: 0.8382 (p) REVERT: B 83 GLU cc_start: 0.7446 (tt0) cc_final: 0.7116 (tm-30) REVERT: C 13 GLU cc_start: 0.8291 (mt-10) cc_final: 0.8048 (mt-10) REVERT: C 35 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7488 (tt0) REVERT: C 83 GLU cc_start: 0.7351 (tt0) cc_final: 0.6858 (tm-30) REVERT: D 35 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7293 (mt-10) REVERT: F 46 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8074 (mt-10) REVERT: G 13 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7428 (mp0) REVERT: G 83 GLU cc_start: 0.7341 (tt0) cc_final: 0.6790 (tm-30) REVERT: H 2 ASP cc_start: 0.8089 (m-30) cc_final: 0.7747 (m-30) REVERT: H 5 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7360 (mpp) REVERT: H 13 GLU cc_start: 0.8487 (mt-10) cc_final: 0.7955 (mt-10) REVERT: I 21 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.7062 (mmtt) REVERT: I 96 LYS cc_start: 0.7913 (ttmm) cc_final: 0.6468 (mptp) REVERT: J 46 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8211 (mt-10) REVERT: J 61 GLU cc_start: 0.8031 (tt0) cc_final: 0.7758 (tt0) REVERT: K 46 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8227 (mt-10) REVERT: L 13 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8096 (mt-10) REVERT: L 21 LYS cc_start: 0.8707 (mttm) cc_final: 0.8472 (mttt) REVERT: L 96 LYS cc_start: 0.7659 (ttmm) cc_final: 0.6169 (pptt) outliers start: 44 outliers final: 20 residues processed: 182 average time/residue: 1.6649 time to fit residues: 317.2321 Evaluate side-chains 175 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 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 I residue 21 LYS Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 87 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.6272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.035 8718 Z= 0.497 Angle : 0.889 13.098 11703 Z= 0.415 Chirality : 0.053 0.147 1380 Planarity : 0.003 0.015 1452 Dihedral : 11.424 85.871 1350 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 5.64 % Allowed : 19.85 % Favored : 74.51 % 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: -3.23 (0.21), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS D 50 PHE 0.015 0.003 PHE C 4 TYR 0.010 0.002 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 196 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 150 time to evaluate : 0.943 Fit side-chains REVERT: A 20 GLU cc_start: 0.8271 (tp30) cc_final: 0.7335 (pt0) REVERT: A 35 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7553 (tt0) REVERT: A 60 LYS cc_start: 0.8656 (ttpp) cc_final: 0.7116 (pmmt) REVERT: A 97 LYS cc_start: 0.7275 (ptpt) cc_final: 0.5936 (pmtt) REVERT: B 57 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7341 (tt0) REVERT: B 83 GLU cc_start: 0.7471 (tt0) cc_final: 0.7121 (tm-30) REVERT: B 96 LYS cc_start: 0.7581 (ttmm) cc_final: 0.6698 (tptp) REVERT: C 13 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8141 (mt-10) REVERT: C 57 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7441 (tt0) REVERT: C 83 GLU cc_start: 0.7408 (tt0) cc_final: 0.6874 (tm-30) REVERT: D 20 GLU cc_start: 0.8640 (mm-30) cc_final: 0.7448 (mp0) REVERT: D 35 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7281 (mt-10) REVERT: F 61 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7852 (tt0) REVERT: G 83 GLU cc_start: 0.7477 (tt0) cc_final: 0.6924 (tm-30) REVERT: H 5 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7443 (mpp) REVERT: H 13 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8190 (mt-10) REVERT: I 83 GLU cc_start: 0.7954 (pt0) cc_final: 0.7663 (pt0) REVERT: I 96 LYS cc_start: 0.8130 (ttmm) cc_final: 0.6557 (mptp) REVERT: J 61 GLU cc_start: 0.8038 (tt0) cc_final: 0.7822 (tt0) REVERT: K 46 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8345 (mt-10) outliers start: 46 outliers final: 28 residues processed: 177 average time/residue: 1.6336 time to fit residues: 302.7232 Evaluate side-chains 174 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain 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 61 GLU Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 5 MET Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 59 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 44 THR Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 87 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.6446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 8718 Z= 0.417 Angle : 0.855 12.913 11703 Z= 0.393 Chirality : 0.052 0.148 1380 Planarity : 0.002 0.014 1452 Dihedral : 11.296 89.980 1350 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 5.02 % Allowed : 20.71 % Favored : 74.26 % 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: -3.15 (0.22), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 50 PHE 0.014 0.003 PHE C 4 TYR 0.008 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 183 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 142 time to evaluate : 0.921 Fit side-chains REVERT: A 20 GLU cc_start: 0.8336 (tp30) cc_final: 0.7343 (pt0) REVERT: A 35 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7522 (tt0) REVERT: A 57 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7526 (tt0) REVERT: A 60 LYS cc_start: 0.8644 (ttpp) cc_final: 0.7188 (pmtt) REVERT: A 97 LYS cc_start: 0.7406 (ptpt) cc_final: 0.6071 (pmtt) REVERT: B 57 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7328 (tt0) REVERT: B 83 GLU cc_start: 0.7445 (tt0) cc_final: 0.7103 (tm-30) REVERT: B 96 LYS cc_start: 0.7609 (ttmm) cc_final: 0.6708 (tptp) REVERT: C 13 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8132 (mt-10) REVERT: C 57 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7440 (tt0) REVERT: C 83 GLU cc_start: 0.7358 (tt0) cc_final: 0.6774 (tm-30) REVERT: D 20 GLU cc_start: 0.8586 (mm-30) cc_final: 0.7414 (mp0) REVERT: D 35 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7285 (mt-10) REVERT: G 5 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7527 (mpp) REVERT: G 13 GLU cc_start: 0.8452 (mt-10) cc_final: 0.7923 (mt-10) REVERT: G 83 GLU cc_start: 0.7378 (tt0) cc_final: 0.6814 (tm-30) REVERT: H 5 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7409 (mpp) REVERT: I 83 GLU cc_start: 0.7988 (pt0) cc_final: 0.7728 (pt0) REVERT: I 96 LYS cc_start: 0.8090 (ttmm) cc_final: 0.6434 (mptp) REVERT: J 5 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8013 (mmt) REVERT: J 61 GLU cc_start: 0.8037 (tt0) cc_final: 0.7799 (tt0) REVERT: K 46 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8270 (mt-10) outliers start: 41 outliers final: 27 residues processed: 165 average time/residue: 1.6711 time to fit residues: 288.5744 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 : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 44 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 44 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 5 MET Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain J residue 5 MET 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 K residue 44 THR Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 87 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 79 GLN L 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.6570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 8718 Z= 0.406 Angle : 0.856 13.042 11703 Z= 0.391 Chirality : 0.052 0.147 1380 Planarity : 0.002 0.013 1452 Dihedral : 11.057 84.344 1350 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 5.51 % Allowed : 21.45 % Favored : 73.04 % 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: -3.11 (0.22), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 50 PHE 0.013 0.003 PHE I 4 TYR 0.008 0.001 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 188 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 143 time to evaluate : 1.072 Fit side-chains REVERT: A 20 GLU cc_start: 0.8357 (tp30) cc_final: 0.7414 (mp0) REVERT: A 35 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7528 (tt0) REVERT: A 57 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7527 (tt0) REVERT: A 60 LYS cc_start: 0.8648 (ttpp) cc_final: 0.7239 (ptpp) REVERT: A 97 LYS cc_start: 0.7475 (ptpt) cc_final: 0.6235 (pmtt) REVERT: B 57 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7310 (tt0) REVERT: B 83 GLU cc_start: 0.7421 (tt0) cc_final: 0.7129 (tm-30) REVERT: C 13 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8182 (mt-10) REVERT: C 57 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7452 (tt0) REVERT: C 83 GLU cc_start: 0.7313 (tt0) cc_final: 0.6750 (tm-30) REVERT: C 97 LYS cc_start: 0.6338 (tptt) cc_final: 0.5883 (mtpp) REVERT: D 20 GLU cc_start: 0.8565 (mm-30) cc_final: 0.7416 (mp0) REVERT: D 35 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7307 (mt-10) REVERT: F 32 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8382 (mptt) REVERT: G 5 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7557 (mpp) REVERT: G 13 GLU cc_start: 0.8395 (mt-10) cc_final: 0.7826 (mt-10) REVERT: G 83 GLU cc_start: 0.7400 (tt0) cc_final: 0.6841 (tm-30) REVERT: H 5 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7491 (mpp) REVERT: H 13 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8152 (mt-10) REVERT: I 83 GLU cc_start: 0.8027 (pt0) cc_final: 0.7808 (pt0) REVERT: J 5 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.7971 (mmt) REVERT: J 61 GLU cc_start: 0.8079 (tt0) cc_final: 0.7861 (tt0) REVERT: K 46 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8321 (mt-10) outliers start: 45 outliers final: 32 residues processed: 169 average time/residue: 1.7224 time to fit residues: 306.2482 Evaluate side-chains 179 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 142 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 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 32 LYS Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 5 MET Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 5 MET Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain J residue 5 MET 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 K residue 44 THR Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 87 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 104 optimal weight: 0.9990 chunk 65 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.6598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 8718 Z= 0.263 Angle : 0.775 12.737 11703 Z= 0.349 Chirality : 0.051 0.143 1380 Planarity : 0.002 0.012 1452 Dihedral : 10.459 87.797 1350 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.66 % Allowed : 22.55 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.99 (0.22), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 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 177 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 139 time to evaluate : 1.021 Fit side-chains REVERT: A 20 GLU cc_start: 0.8309 (tp30) cc_final: 0.7442 (mp0) REVERT: A 35 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7485 (tt0) REVERT: A 57 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7497 (tt0) REVERT: A 60 LYS cc_start: 0.8604 (ttpp) cc_final: 0.7166 (pmtt) REVERT: B 57 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7319 (tt0) REVERT: B 83 GLU cc_start: 0.7350 (tt0) cc_final: 0.7066 (tm-30) REVERT: C 13 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8079 (mt-10) REVERT: C 57 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7457 (tt0) REVERT: C 83 GLU cc_start: 0.7296 (tt0) cc_final: 0.6736 (tm-30) REVERT: C 97 LYS cc_start: 0.6289 (tptt) cc_final: 0.5800 (mtpp) REVERT: D 20 GLU cc_start: 0.8560 (mm-30) cc_final: 0.7441 (mp0) REVERT: D 35 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7267 (tt0) REVERT: G 5 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7513 (mpp) REVERT: G 13 GLU cc_start: 0.8414 (mt-10) cc_final: 0.7870 (mt-10) REVERT: G 83 GLU cc_start: 0.7290 (tt0) cc_final: 0.6745 (tm-30) REVERT: H 5 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.7466 (mpp) REVERT: H 13 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8181 (mt-10) REVERT: I 83 GLU cc_start: 0.8027 (pt0) cc_final: 0.7808 (pt0) REVERT: J 5 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8095 (mmt) REVERT: J 61 GLU cc_start: 0.8007 (tt0) cc_final: 0.7794 (tt0) REVERT: J 64 THR cc_start: 0.8827 (OUTLIER) cc_final: 0.8625 (p) REVERT: K 46 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8261 (mt-10) outliers start: 38 outliers final: 27 residues processed: 162 average time/residue: 1.6768 time to fit residues: 284.5497 Evaluate side-chains 171 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 0.993 ------------------------------------------------------------------------------- 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 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 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 58 LYS Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain J residue 5 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 70 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 94 optimal weight: 9.9990 chunk 99 optimal weight: 0.6980 overall best weight: 5.7388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.6647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.034 8718 Z= 0.442 Angle : 0.867 13.079 11703 Z= 0.398 Chirality : 0.052 0.147 1380 Planarity : 0.002 0.013 1452 Dihedral : 10.779 86.785 1350 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 5.27 % Allowed : 22.06 % 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: -3.02 (0.22), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 50 PHE 0.012 0.003 PHE G 4 TYR 0.007 0.002 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 184 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 141 time to evaluate : 0.936 Fit side-chains REVERT: A 20 GLU cc_start: 0.8357 (tp30) cc_final: 0.7406 (mp0) REVERT: A 35 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7547 (tt0) REVERT: A 60 LYS cc_start: 0.8634 (ttpp) cc_final: 0.7229 (ptpp) REVERT: B 57 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7290 (tt0) REVERT: B 83 GLU cc_start: 0.7393 (tt0) cc_final: 0.7111 (tm-30) REVERT: C 5 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.7528 (mpp) REVERT: C 13 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8178 (mt-10) REVERT: C 57 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7485 (tt0) REVERT: C 83 GLU cc_start: 0.7368 (tt0) cc_final: 0.6825 (tm-30) REVERT: C 97 LYS cc_start: 0.6350 (tptt) cc_final: 0.5804 (mtpp) REVERT: D 20 GLU cc_start: 0.8572 (mm-30) cc_final: 0.7412 (mp0) REVERT: D 35 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7309 (mt-10) REVERT: F 61 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7908 (tt0) REVERT: G 5 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7635 (mpp) REVERT: G 13 GLU cc_start: 0.8449 (mt-10) cc_final: 0.7885 (mt-10) REVERT: G 83 GLU cc_start: 0.7395 (tt0) cc_final: 0.6844 (tm-30) REVERT: H 5 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7448 (mpp) REVERT: H 13 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8245 (mt-10) REVERT: J 5 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.8318 (mmt) REVERT: K 46 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8279 (mt-10) outliers start: 43 outliers final: 28 residues processed: 165 average time/residue: 1.8218 time to fit residues: 313.9545 Evaluate side-chains 175 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 1.033 ------------------------------------------------------------------------------- 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 5 MET Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain 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 54 THR Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain J residue 5 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 7.9990 chunk 97 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 58 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.6668 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= 0.143 Angle : 0.702 12.363 11703 Z= 0.312 Chirality : 0.050 0.136 1380 Planarity : 0.002 0.010 1452 Dihedral : 9.854 84.706 1350 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.92 % Allowed : 23.65 % 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: -2.83 (0.23), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 50 PHE 0.010 0.002 PHE I 4 TYR 0.006 0.001 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 165 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.840 Fit side-chains REVERT: A 20 GLU cc_start: 0.8346 (tp30) cc_final: 0.7535 (mt-10) REVERT: A 60 LYS cc_start: 0.8569 (ttpp) cc_final: 0.7180 (ptpp) REVERT: B 83 GLU cc_start: 0.7302 (tt0) cc_final: 0.7028 (tm-30) REVERT: C 13 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8049 (mt-10) REVERT: C 83 GLU cc_start: 0.7206 (tt0) cc_final: 0.6586 (tm-30) REVERT: C 97 LYS cc_start: 0.6327 (tptt) cc_final: 0.5839 (mtpp) REVERT: D 20 GLU cc_start: 0.8542 (mm-30) cc_final: 0.7416 (mp0) REVERT: G 13 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7784 (mt-10) REVERT: G 83 GLU cc_start: 0.7233 (tt0) cc_final: 0.6726 (tm-30) REVERT: H 5 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.7505 (mpp) REVERT: H 13 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8043 (mt-10) REVERT: I 21 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.7050 (mmtt) REVERT: J 61 GLU cc_start: 0.8131 (tt0) cc_final: 0.7916 (tt0) outliers start: 32 outliers final: 17 residues processed: 148 average time/residue: 1.7528 time to fit residues: 271.1297 Evaluate side-chains 150 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 75 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 64 THR 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 I residue 21 LYS 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 87 SER Chi-restraints excluded: chain K residue 44 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 102 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 99 optimal weight: 0.1980 chunk 85 optimal weight: 10.0000 chunk 8 optimal weight: 0.0970 chunk 66 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 overall best weight: 3.6584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.6656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 8718 Z= 0.297 Angle : 0.779 12.677 11703 Z= 0.353 Chirality : 0.050 0.142 1380 Planarity : 0.002 0.017 1452 Dihedral : 10.000 86.489 1350 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.19 % Allowed : 24.39 % 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: -2.82 (0.22), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 50 PHE 0.012 0.002 PHE G 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 166 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.858 Fit side-chains REVERT: A 20 GLU cc_start: 0.8310 (tp30) cc_final: 0.7398 (mp0) REVERT: A 35 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7489 (tt0) REVERT: A 60 LYS cc_start: 0.8605 (ttpp) cc_final: 0.7170 (ptpp) REVERT: B 5 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.6905 (mpp) REVERT: B 83 GLU cc_start: 0.7330 (tt0) cc_final: 0.7063 (tm-30) REVERT: C 13 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8092 (mt-10) REVERT: C 83 GLU cc_start: 0.7298 (tt0) cc_final: 0.6754 (tm-30) REVERT: C 97 LYS cc_start: 0.6424 (tptt) cc_final: 0.5913 (mtpp) REVERT: D 20 GLU cc_start: 0.8546 (mm-30) cc_final: 0.7450 (mp0) REVERT: F 64 THR cc_start: 0.8758 (OUTLIER) cc_final: 0.8456 (m) REVERT: G 13 GLU cc_start: 0.8426 (mt-10) cc_final: 0.7822 (mt-10) REVERT: G 83 GLU cc_start: 0.7368 (tt0) cc_final: 0.6817 (tm-30) REVERT: H 5 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.7496 (mpp) REVERT: H 13 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8180 (mt-10) outliers start: 26 outliers final: 20 residues processed: 156 average time/residue: 1.7383 time to fit residues: 283.7586 Evaluate side-chains 162 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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 75 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 F residue 59 THR Chi-restraints excluded: chain F residue 64 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 54 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 HIS H 50 HIS ** H 62 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 = 0.3946 r_free = 0.3946 target = 0.123721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.108467 restraints weight = 6962.371| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 1.45 r_work: 0.3587 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.6727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.051 8718 Z= 0.653 Angle : 0.987 13.606 11703 Z= 0.463 Chirality : 0.056 0.157 1380 Planarity : 0.003 0.018 1452 Dihedral : 10.583 87.068 1350 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 3.55 % Allowed : 24.39 % Favored : 72.06 % 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: -2.98 (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 0.013 0.003 PHE K 94 TYR 0.008 0.002 TYR G 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4506.32 seconds wall clock time: 81 minutes 15.86 seconds (4875.86 seconds total)