Starting phenix.real_space_refine on Wed Feb 4 02:21:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zmy_60262/02_2026/8zmy_60262.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zmy_60262/02_2026/8zmy_60262.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zmy_60262/02_2026/8zmy_60262.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zmy_60262/02_2026/8zmy_60262.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zmy_60262/02_2026/8zmy_60262.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zmy_60262/02_2026/8zmy_60262.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Br 15 7.06 5 S 39 5.16 5 C 5463 2.51 5 N 1446 2.21 5 O 1674 1.98 5 F 15 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8652 Number of models: 1 Model: "" Number of chains: 19 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: "B" 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: 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: "D" 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: "E" 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: "F" 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: "G" 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: "H" 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: "I" 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: "J" 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: "K" 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: "L" 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} Time building chain proxies: 2.02, per 1000 atoms: 0.23 Number of scatterers: 8652 At special positions: 0 Unit cell: (139.44, 116.2, 47.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Br 15 34.99 S 39 16.00 F 15 9.00 O 1674 8.00 N 1446 7.00 C 5463 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 254.7 milliseconds 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2016 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 45.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 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: 0.93 Time building geometry restraints manager: 0.99 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: 4.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 8.330 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.073 8718 Z= 0.469 Angle : 0.908 10.476 11703 Z= 0.401 Chirality : 0.052 0.170 1380 Planarity : 0.001 0.013 1452 Dihedral : 15.078 89.073 3102 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 29.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.52 (0.16), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.44 (0.12), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.002 TYR B 39 PHE 0.005 0.001 PHE E 4 HIS 0.003 0.002 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00981 ( 8718) covalent geometry : angle 0.90843 (11703) hydrogen bonds : bond 0.21390 ( 166) hydrogen bonds : angle 8.29770 ( 498) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.303 Fit side-chains REVERT: A 20 GLU cc_start: 0.7021 (tp30) cc_final: 0.6792 (pt0) REVERT: B 83 GLU cc_start: 0.7598 (tt0) cc_final: 0.7197 (tm-30) REVERT: C 83 GLU cc_start: 0.7399 (tt0) cc_final: 0.7007 (tm-30) REVERT: D 20 GLU cc_start: 0.7372 (tp30) cc_final: 0.6983 (pt0) REVERT: E 35 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7556 (tt0) REVERT: G 83 GLU cc_start: 0.7188 (tt0) cc_final: 0.6812 (tm-30) REVERT: I 1 MET cc_start: 0.8025 (ttm) cc_final: 0.7740 (ttm) REVERT: L 1 MET cc_start: 0.8255 (ttm) cc_final: 0.7943 (ttm) REVERT: L 28 GLU cc_start: 0.7335 (mt-10) cc_final: 0.7055 (mp0) REVERT: L 96 LYS cc_start: 0.6597 (ttmm) cc_final: 0.5402 (pptt) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.5807 time to fit residues: 148.2634 Evaluate side-chains 151 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN B 50 HIS B 62 GLN B 79 GLN C 62 GLN C 79 GLN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 HIS ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 62 GLN G 79 GLN H 62 GLN I 62 GLN ** J 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 50 HIS ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.136868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.119766 restraints weight = 7264.787| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 1.57 r_work: 0.3750 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.5633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8718 Z= 0.212 Angle : 0.836 14.495 11703 Z= 0.388 Chirality : 0.052 0.131 1380 Planarity : 0.003 0.017 1452 Dihedral : 11.149 88.791 1350 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 5.51 % Allowed : 18.87 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.68 (0.19), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.14), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.001 TYR I 39 PHE 0.016 0.003 PHE I 4 HIS 0.004 0.001 HIS L 50 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 8718) covalent geometry : angle 0.83644 (11703) hydrogen bonds : bond 0.03384 ( 166) hydrogen bonds : angle 4.73846 ( 498) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 158 time to evaluate : 0.322 Fit side-chains REVERT: A 20 GLU cc_start: 0.8310 (tp30) cc_final: 0.7447 (pt0) REVERT: A 60 LYS cc_start: 0.8856 (ttpp) cc_final: 0.7428 (pmtt) REVERT: B 35 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8051 (tt0) REVERT: B 83 GLU cc_start: 0.7898 (tt0) cc_final: 0.7583 (tm-30) REVERT: C 13 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8360 (mt-10) REVERT: C 35 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8136 (tt0) REVERT: C 83 GLU cc_start: 0.7979 (tt0) cc_final: 0.7400 (tm-30) REVERT: E 46 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8483 (mt-10) REVERT: F 13 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8529 (mt-10) REVERT: G 13 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8145 (mt-10) REVERT: G 35 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8091 (tt0) REVERT: G 83 GLU cc_start: 0.7932 (tt0) cc_final: 0.7388 (tm-30) REVERT: H 2 ASP cc_start: 0.8186 (m-30) cc_final: 0.7925 (m-30) REVERT: H 13 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8069 (mt-10) REVERT: H 35 GLU cc_start: 0.8408 (mt-10) cc_final: 0.7838 (tt0) REVERT: I 13 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8372 (mt-10) REVERT: I 21 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.7154 (mmpt) REVERT: I 35 GLU cc_start: 0.8452 (mt-10) cc_final: 0.7998 (tm-30) REVERT: I 96 LYS cc_start: 0.7767 (ttmm) cc_final: 0.6318 (mptp) REVERT: J 46 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8503 (mt-10) REVERT: J 61 GLU cc_start: 0.8342 (tt0) cc_final: 0.8104 (tt0) REVERT: K 28 GLU cc_start: 0.8272 (mt-10) cc_final: 0.8021 (mt-10) REVERT: L 21 LYS cc_start: 0.8938 (mttm) cc_final: 0.8733 (mttt) REVERT: L 96 LYS cc_start: 0.7603 (ttmm) cc_final: 0.6048 (pptt) outliers start: 45 outliers final: 21 residues processed: 189 average time/residue: 0.7059 time to fit residues: 139.3515 Evaluate side-chains 170 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain I residue 21 LYS Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 87 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 106 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 90 optimal weight: 0.7980 chunk 27 optimal weight: 9.9990 chunk 46 optimal weight: 0.7980 chunk 94 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 50 HIS H 50 HIS I 50 HIS ** J 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.130302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.114145 restraints weight = 7399.237| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 1.56 r_work: 0.3677 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3543 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.5883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 8718 Z= 0.203 Angle : 0.766 12.967 11703 Z= 0.352 Chirality : 0.051 0.137 1380 Planarity : 0.002 0.009 1452 Dihedral : 10.571 84.427 1350 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.53 % Allowed : 21.45 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.31 (0.21), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR H 39 PHE 0.010 0.002 PHE I 4 HIS 0.006 0.002 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 8718) covalent geometry : angle 0.76591 (11703) hydrogen bonds : bond 0.03340 ( 166) hydrogen bonds : angle 4.74978 ( 498) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 151 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8405 (tp30) cc_final: 0.7620 (mp0) REVERT: A 60 LYS cc_start: 0.8814 (ttpp) cc_final: 0.7286 (pmtt) REVERT: B 57 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7622 (tt0) REVERT: B 83 GLU cc_start: 0.7954 (tt0) cc_final: 0.7587 (tm-30) REVERT: C 13 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8160 (mt-10) REVERT: C 35 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8036 (tt0) REVERT: C 83 GLU cc_start: 0.8043 (tt0) cc_final: 0.7418 (tm-30) REVERT: F 13 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8394 (mt-10) REVERT: G 5 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.7863 (mpp) REVERT: G 83 GLU cc_start: 0.7999 (tt0) cc_final: 0.7404 (tm-30) REVERT: H 5 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.7958 (mpp) REVERT: I 96 LYS cc_start: 0.8039 (ttmm) cc_final: 0.6501 (mptp) REVERT: J 61 GLU cc_start: 0.8287 (tt0) cc_final: 0.7986 (tt0) REVERT: K 46 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8554 (mt-10) REVERT: L 96 LYS cc_start: 0.7835 (ttmm) cc_final: 0.6169 (pptt) outliers start: 37 outliers final: 23 residues processed: 172 average time/residue: 0.6929 time to fit residues: 124.6325 Evaluate side-chains 171 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain G residue 5 MET Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 5 MET Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 87 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 43 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 90 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN F 79 GLN J 79 GLN K 79 GLN L 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.124549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.108853 restraints weight = 7384.369| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 1.52 r_work: 0.3602 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.6436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.048 8718 Z= 0.416 Angle : 0.961 13.445 11703 Z= 0.452 Chirality : 0.055 0.156 1380 Planarity : 0.003 0.014 1452 Dihedral : 11.863 88.683 1350 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 6.25 % Allowed : 19.73 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.29 (0.21), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR D 39 PHE 0.015 0.003 PHE C 4 HIS 0.005 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00942 ( 8718) covalent geometry : angle 0.96051 (11703) hydrogen bonds : bond 0.03954 ( 166) hydrogen bonds : angle 5.23259 ( 498) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 150 time to evaluate : 0.243 Fit side-chains REVERT: A 20 GLU cc_start: 0.8636 (tp30) cc_final: 0.7711 (pt0) REVERT: A 35 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8098 (tt0) REVERT: A 57 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7874 (tt0) REVERT: A 60 LYS cc_start: 0.8840 (ttpp) cc_final: 0.7273 (pmtt) REVERT: A 97 LYS cc_start: 0.7351 (ptpt) cc_final: 0.5991 (pmtt) REVERT: B 28 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7821 (mt-10) REVERT: B 57 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7709 (tt0) REVERT: B 83 GLU cc_start: 0.7989 (tt0) cc_final: 0.7658 (tm-30) REVERT: B 96 LYS cc_start: 0.7676 (ttmm) cc_final: 0.6743 (tptp) REVERT: C 13 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8340 (mt-10) REVERT: C 57 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7806 (tt0) REVERT: C 83 GLU cc_start: 0.8007 (tt0) cc_final: 0.7492 (tm-30) REVERT: C 97 LYS cc_start: 0.6237 (tptt) cc_final: 0.5757 (mtpp) REVERT: D 35 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7815 (mt-10) REVERT: G 5 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.7959 (mpp) REVERT: G 83 GLU cc_start: 0.8071 (tt0) cc_final: 0.7547 (tm-30) REVERT: H 5 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.7962 (mpp) REVERT: H 20 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8027 (tm-30) REVERT: I 96 LYS cc_start: 0.8180 (ttmm) cc_final: 0.6478 (mptp) REVERT: J 61 GLU cc_start: 0.8379 (tt0) cc_final: 0.8124 (tt0) outliers start: 51 outliers final: 29 residues processed: 179 average time/residue: 0.6821 time to fit residues: 127.6246 Evaluate side-chains 180 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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 75 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 5 MET Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 5 MET Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 87 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 26 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.129885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.114058 restraints weight = 7281.540| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 1.54 r_work: 0.3680 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.6425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8718 Z= 0.147 Angle : 0.752 12.768 11703 Z= 0.339 Chirality : 0.050 0.141 1380 Planarity : 0.002 0.009 1452 Dihedral : 10.663 83.834 1350 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.29 % Allowed : 22.79 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.07 (0.22), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR D 39 PHE 0.012 0.002 PHE I 4 HIS 0.003 0.001 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 8718) covalent geometry : angle 0.75200 (11703) hydrogen bonds : bond 0.02586 ( 166) hydrogen bonds : angle 4.83588 ( 498) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 0.345 Fit side-chains REVERT: A 20 GLU cc_start: 0.8572 (tp30) cc_final: 0.7681 (mp0) REVERT: A 57 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7772 (tt0) REVERT: A 60 LYS cc_start: 0.8796 (ttpp) cc_final: 0.7272 (pmtt) REVERT: A 64 THR cc_start: 0.8783 (OUTLIER) cc_final: 0.8453 (m) REVERT: A 97 LYS cc_start: 0.7463 (ptpt) cc_final: 0.6039 (pmtt) REVERT: B 28 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7839 (mt-10) REVERT: B 57 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7618 (tt0) REVERT: B 83 GLU cc_start: 0.7860 (tt0) cc_final: 0.7545 (tm-30) REVERT: C 13 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8353 (mt-10) REVERT: C 57 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7738 (tt0) REVERT: C 83 GLU cc_start: 0.7922 (tt0) cc_final: 0.7358 (tm-30) REVERT: C 97 LYS cc_start: 0.6222 (tptt) cc_final: 0.5754 (mtpp) REVERT: D 35 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7689 (mt-10) REVERT: G 5 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.8044 (mpp) REVERT: G 13 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8206 (mt-10) REVERT: G 83 GLU cc_start: 0.7946 (tt0) cc_final: 0.7383 (tm-30) REVERT: H 5 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.8134 (mpp) REVERT: H 13 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8418 (mt-10) REVERT: I 96 LYS cc_start: 0.8150 (ttmm) cc_final: 0.6484 (mptp) REVERT: J 61 GLU cc_start: 0.8296 (tt0) cc_final: 0.8082 (tt0) outliers start: 35 outliers final: 16 residues processed: 159 average time/residue: 0.6678 time to fit residues: 111.1947 Evaluate side-chains 158 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain G residue 5 MET Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 5 MET Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 87 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 102 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.123133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.107532 restraints weight = 7139.940| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 1.50 r_work: 0.3587 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.6576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.042 8718 Z= 0.360 Angle : 0.918 13.437 11703 Z= 0.425 Chirality : 0.053 0.149 1380 Planarity : 0.003 0.013 1452 Dihedral : 11.108 88.874 1350 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 5.51 % Allowed : 21.94 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.17 (0.21), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.002 TYR D 39 PHE 0.014 0.003 PHE C 4 HIS 0.004 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00817 ( 8718) covalent geometry : angle 0.91821 (11703) hydrogen bonds : bond 0.03690 ( 166) hydrogen bonds : angle 5.08778 ( 498) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 142 time to evaluate : 0.237 Fit side-chains REVERT: A 20 GLU cc_start: 0.8623 (tp30) cc_final: 0.7747 (mp0) REVERT: A 35 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8090 (tt0) REVERT: A 57 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7857 (tt0) REVERT: A 60 LYS cc_start: 0.8799 (ttpp) cc_final: 0.7315 (ptpp) REVERT: A 72 THR cc_start: 0.9057 (m) cc_final: 0.8720 (p) REVERT: A 97 LYS cc_start: 0.7457 (ptpt) cc_final: 0.6184 (pmtt) REVERT: B 5 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.7499 (mpp) REVERT: B 28 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7858 (mt-10) REVERT: B 57 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7641 (tt0) REVERT: B 83 GLU cc_start: 0.7953 (tt0) cc_final: 0.7580 (tm-30) REVERT: C 13 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8409 (mt-10) REVERT: C 57 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7822 (tt0) REVERT: C 83 GLU cc_start: 0.8028 (tt0) cc_final: 0.7429 (tm-30) REVERT: C 97 LYS cc_start: 0.6244 (tptt) cc_final: 0.5732 (mtpp) REVERT: D 35 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7821 (mt-10) REVERT: F 61 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8181 (tt0) REVERT: G 5 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.7960 (mpp) REVERT: G 13 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8272 (mt-10) REVERT: G 83 GLU cc_start: 0.8038 (tt0) cc_final: 0.7487 (tm-30) REVERT: H 5 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.7989 (mpp) REVERT: H 20 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.7773 (tm-30) REVERT: H 57 GLU cc_start: 0.8058 (mp0) cc_final: 0.7387 (mp0) REVERT: I 21 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.7379 (mmtt) outliers start: 45 outliers final: 27 residues processed: 170 average time/residue: 0.7098 time to fit residues: 125.8327 Evaluate side-chains 177 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 5 MET Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain 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 44 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 5 MET Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain I residue 21 LYS Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 87 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 74 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 34 optimal weight: 0.0030 chunk 25 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 overall best weight: 2.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.131380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.115401 restraints weight = 7382.880| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 1.55 r_work: 0.3677 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.6591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8718 Z= 0.139 Angle : 0.748 12.889 11703 Z= 0.334 Chirality : 0.050 0.140 1380 Planarity : 0.002 0.009 1452 Dihedral : 10.038 86.142 1350 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.29 % Allowed : 24.02 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.01 (0.22), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR A 39 PHE 0.013 0.002 PHE I 4 HIS 0.003 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 8718) covalent geometry : angle 0.74764 (11703) hydrogen bonds : bond 0.02462 ( 166) hydrogen bonds : angle 4.71167 ( 498) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 0.321 Fit side-chains REVERT: A 20 GLU cc_start: 0.8557 (tp30) cc_final: 0.7719 (mp0) REVERT: A 60 LYS cc_start: 0.8745 (ttpp) cc_final: 0.7221 (pmtt) REVERT: A 64 THR cc_start: 0.8765 (OUTLIER) cc_final: 0.8522 (m) REVERT: A 97 LYS cc_start: 0.7453 (ptpt) cc_final: 0.6311 (pptt) REVERT: B 6 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8657 (ttpt) REVERT: B 28 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7839 (mt-10) REVERT: B 83 GLU cc_start: 0.7842 (tt0) cc_final: 0.7511 (tm-30) REVERT: C 13 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8369 (mt-10) REVERT: C 57 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7769 (tt0) REVERT: C 83 GLU cc_start: 0.7902 (tt0) cc_final: 0.7322 (tm-30) REVERT: C 97 LYS cc_start: 0.6324 (tptt) cc_final: 0.5831 (mtpp) REVERT: D 20 GLU cc_start: 0.8909 (mm-30) cc_final: 0.7813 (mp0) REVERT: D 35 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7681 (mt-10) REVERT: E 35 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7937 (tt0) REVERT: G 5 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.7979 (mpp) REVERT: G 13 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8189 (mt-10) REVERT: G 83 GLU cc_start: 0.7907 (tt0) cc_final: 0.7331 (tm-30) REVERT: H 5 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8224 (mpp) REVERT: H 13 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8502 (mt-10) REVERT: I 21 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.7269 (mmpt) REVERT: I 96 LYS cc_start: 0.8137 (ttmm) cc_final: 0.6483 (mptp) REVERT: J 5 MET cc_start: 0.8675 (mmp) cc_final: 0.8415 (mmt) outliers start: 35 outliers final: 24 residues processed: 161 average time/residue: 0.6697 time to fit residues: 112.9018 Evaluate side-chains 166 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 0.192 ------------------------------------------------------------------------------- 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 6 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain G residue 5 MET Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 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 I residue 21 LYS 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 10 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 8 optimal weight: 8.9990 chunk 44 optimal weight: 9.9990 chunk 94 optimal weight: 8.9990 chunk 68 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 4 optimal weight: 0.3980 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.129552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.113410 restraints weight = 7312.735| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 1.55 r_work: 0.3665 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3536 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.6630 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= 0.164 Angle : 0.754 12.664 11703 Z= 0.339 Chirality : 0.050 0.140 1380 Planarity : 0.002 0.009 1452 Dihedral : 9.965 86.767 1350 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.78 % Allowed : 23.53 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.95 (0.22), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR A 39 PHE 0.011 0.002 PHE I 4 HIS 0.003 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 8718) covalent geometry : angle 0.75441 (11703) hydrogen bonds : bond 0.02630 ( 166) hydrogen bonds : angle 4.66321 ( 498) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 141 time to evaluate : 0.322 Fit side-chains REVERT: A 20 GLU cc_start: 0.8546 (tp30) cc_final: 0.7663 (mp0) REVERT: A 35 GLU cc_start: 0.8312 (mt-10) cc_final: 0.7983 (tt0) REVERT: A 60 LYS cc_start: 0.8740 (ttpp) cc_final: 0.7271 (ptpp) REVERT: A 64 THR cc_start: 0.8777 (OUTLIER) cc_final: 0.8525 (m) REVERT: A 97 LYS cc_start: 0.7467 (ptpt) cc_final: 0.6364 (pptt) REVERT: B 28 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7855 (mt-10) REVERT: B 83 GLU cc_start: 0.7841 (tt0) cc_final: 0.7518 (tm-30) REVERT: C 13 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8371 (mt-10) REVERT: C 57 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7783 (tt0) REVERT: C 83 GLU cc_start: 0.7950 (tt0) cc_final: 0.7379 (tm-30) REVERT: C 97 LYS cc_start: 0.6296 (tptt) cc_final: 0.5791 (mtpp) REVERT: D 20 GLU cc_start: 0.8924 (mm-30) cc_final: 0.7813 (mp0) REVERT: D 35 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7698 (mt-10) REVERT: G 5 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.7999 (mpp) REVERT: G 13 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8204 (mt-10) REVERT: G 83 GLU cc_start: 0.7966 (tt0) cc_final: 0.7432 (tm-30) REVERT: H 5 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8110 (mpp) REVERT: I 21 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.7309 (mmtt) REVERT: I 96 LYS cc_start: 0.8183 (ttmm) cc_final: 0.6549 (mptp) outliers start: 39 outliers final: 27 residues processed: 165 average time/residue: 0.6511 time to fit residues: 112.1778 Evaluate side-chains 173 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain G residue 5 MET Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 5 MET Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain I residue 21 LYS Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain 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 39 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 35 optimal weight: 0.8980 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.124088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.108495 restraints weight = 7105.894| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 1.49 r_work: 0.3605 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3478 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.6674 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= 0.304 Angle : 0.877 13.117 11703 Z= 0.403 Chirality : 0.052 0.150 1380 Planarity : 0.003 0.012 1452 Dihedral : 10.425 86.474 1350 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 5.27 % Allowed : 23.04 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 TYR 0.007 0.002 TYR A 39 PHE 0.012 0.003 PHE I 4 HIS 0.003 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00689 ( 8718) covalent geometry : angle 0.87743 (11703) hydrogen bonds : bond 0.03429 ( 166) hydrogen bonds : angle 4.92873 ( 498) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 140 time to evaluate : 0.274 Fit side-chains REVERT: A 20 GLU cc_start: 0.8603 (tp30) cc_final: 0.7725 (mp0) REVERT: A 28 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7766 (mt-10) REVERT: A 35 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8032 (tt0) REVERT: A 60 LYS cc_start: 0.8748 (ttpp) cc_final: 0.7237 (ptpp) REVERT: A 97 LYS cc_start: 0.7544 (ptpt) cc_final: 0.6459 (pptt) REVERT: B 5 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.7556 (mpp) REVERT: B 28 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7872 (mt-10) REVERT: B 83 GLU cc_start: 0.7849 (tt0) cc_final: 0.7526 (tm-30) REVERT: C 13 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8480 (mt-10) REVERT: C 57 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7819 (tt0) REVERT: C 83 GLU cc_start: 0.8000 (tt0) cc_final: 0.7395 (tm-30) REVERT: C 97 LYS cc_start: 0.6236 (tptt) cc_final: 0.5701 (mtpp) REVERT: D 35 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7771 (mt-10) REVERT: G 5 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.7901 (mpp) REVERT: G 13 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8243 (mt-10) REVERT: G 83 GLU cc_start: 0.7996 (tt0) cc_final: 0.7449 (tm-30) REVERT: H 5 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8062 (mpp) REVERT: I 6 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8753 (ttpt) REVERT: L 5 MET cc_start: 0.8447 (mmm) cc_final: 0.8169 (mmt) outliers start: 43 outliers final: 31 residues processed: 167 average time/residue: 0.5962 time to fit residues: 104.2614 Evaluate side-chains 176 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 140 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 5 MET Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 5 MET Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 5 MET Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain I residue 6 LYS Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain 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 46 GLU Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 48 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 97 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.124409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.108796 restraints weight = 7087.445| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 1.49 r_work: 0.3611 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.6705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 8718 Z= 0.285 Angle : 0.870 13.176 11703 Z= 0.398 Chirality : 0.052 0.150 1380 Planarity : 0.002 0.012 1452 Dihedral : 10.247 86.875 1350 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 4.53 % Allowed : 23.90 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 TYR 0.006 0.002 TYR A 39 PHE 0.012 0.003 PHE G 4 HIS 0.003 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00646 ( 8718) covalent geometry : angle 0.86965 (11703) hydrogen bonds : bond 0.03362 ( 166) hydrogen bonds : angle 4.95447 ( 498) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 0.240 Fit side-chains REVERT: A 20 GLU cc_start: 0.8602 (tp30) cc_final: 0.7721 (mp0) REVERT: A 28 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7821 (mt-10) REVERT: A 35 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8012 (tt0) REVERT: A 60 LYS cc_start: 0.8737 (ttpp) cc_final: 0.8359 (ttmp) REVERT: B 5 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.7536 (mpp) REVERT: B 28 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7891 (mt-10) REVERT: B 83 GLU cc_start: 0.7856 (tt0) cc_final: 0.7524 (tm-30) REVERT: C 13 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8470 (mt-10) REVERT: C 57 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7819 (tt0) REVERT: C 83 GLU cc_start: 0.7996 (tt0) cc_final: 0.7405 (tm-30) REVERT: C 97 LYS cc_start: 0.6327 (tptt) cc_final: 0.5728 (mtpp) REVERT: D 35 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7771 (mt-10) REVERT: G 5 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.7943 (mpp) REVERT: G 13 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8211 (mt-10) REVERT: G 83 GLU cc_start: 0.7970 (tt0) cc_final: 0.7432 (tm-30) REVERT: H 5 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8066 (mpp) REVERT: L 5 MET cc_start: 0.8427 (mmm) cc_final: 0.8181 (mmt) outliers start: 37 outliers final: 30 residues processed: 162 average time/residue: 0.6534 time to fit residues: 110.7752 Evaluate side-chains 172 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 5 MET Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 5 MET Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 5 MET Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 81 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 46 GLU Chi-restraints excluded: chain L residue 64 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 56 optimal weight: 10.0000 chunk 71 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.132138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.116367 restraints weight = 7141.410| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 1.51 r_work: 0.3703 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.6717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8718 Z= 0.124 Angle : 0.735 12.577 11703 Z= 0.327 Chirality : 0.050 0.137 1380 Planarity : 0.002 0.009 1452 Dihedral : 9.505 87.214 1350 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.31 % Allowed : 25.12 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.87 (0.22), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR A 39 PHE 0.011 0.002 PHE I 4 HIS 0.003 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8718) covalent geometry : angle 0.73499 (11703) hydrogen bonds : bond 0.02361 ( 166) hydrogen bonds : angle 4.60019 ( 498) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2660.17 seconds wall clock time: 46 minutes 13.01 seconds (2773.01 seconds total)