Starting phenix.real_space_refine on Sun Mar 10 22:06:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xyo_10650/03_2024/6xyo_10650.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xyo_10650/03_2024/6xyo_10650.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xyo_10650/03_2024/6xyo_10650.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xyo_10650/03_2024/6xyo_10650.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xyo_10650/03_2024/6xyo_10650.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xyo_10650/03_2024/6xyo_10650.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 3 Type Number sf(0) Gaussians C 3410 2.51 5 N 965 2.21 5 O 1115 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 57": "OE1" <-> "OE2" Residue "B ASP 98": "OD1" <-> "OD2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "D ASP 98": "OD1" <-> "OD2" Residue "E GLU 57": "OE1" <-> "OE2" Residue "F ASP 98": "OD1" <-> "OD2" Residue "G GLU 57": "OE1" <-> "OE2" Residue "H ASP 98": "OD1" <-> "OD2" Residue "I GLU 57": "OE1" <-> "OE2" Residue "J ASP 98": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5490 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 549 Classifications: {'peptide': 81} Link IDs: {'TRANS': 80} Chain: "B" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 549 Classifications: {'peptide': 79} Link IDs: {'TRANS': 78} Chain: "C" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 549 Classifications: {'peptide': 81} Link IDs: {'TRANS': 80} Chain: "D" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 549 Classifications: {'peptide': 79} Link IDs: {'TRANS': 78} Chain: "E" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 549 Classifications: {'peptide': 81} Link IDs: {'TRANS': 80} Chain: "F" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 549 Classifications: {'peptide': 79} Link IDs: {'TRANS': 78} Chain: "G" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 549 Classifications: {'peptide': 81} Link IDs: {'TRANS': 80} Chain: "H" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 549 Classifications: {'peptide': 79} Link IDs: {'TRANS': 78} Chain: "I" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 549 Classifications: {'peptide': 81} Link IDs: {'TRANS': 80} Chain: "J" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 549 Classifications: {'peptide': 79} Link IDs: {'TRANS': 78} Time building chain proxies: 3.16, per 1000 atoms: 0.58 Number of scatterers: 5490 At special positions: 0 Unit cell: (108.599, 88.703, 45.595, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1115 8.00 N 965 7.00 C 3410 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 1.1 seconds 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1350 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 15 sheets defined 0.0% alpha, 59.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 15 through 20 removed outlier: 6.214A pdb=" N VAL C 16 " --> pdb=" O ALA E 17 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N ALA E 19 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ALA C 18 " --> pdb=" O ALA E 19 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL A 15 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N ALA E 18 " --> pdb=" O VAL A 15 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA A 17 " --> pdb=" O ALA E 18 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N GLU E 20 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ALA A 19 " --> pdb=" O GLU E 20 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N VAL G 15 " --> pdb=" O VAL I 16 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ALA I 18 " --> pdb=" O VAL G 15 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA G 17 " --> pdb=" O ALA I 18 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N GLU I 20 " --> pdb=" O ALA G 17 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA G 19 " --> pdb=" O GLU I 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 24 through 30 removed outlier: 6.620A pdb=" N GLY A 25 " --> pdb=" O VAL E 26 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N GLU E 28 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ALA A 27 " --> pdb=" O GLU E 28 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ALA E 30 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA A 29 " --> pdb=" O ALA E 30 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLY G 25 " --> pdb=" O VAL I 26 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N GLU I 28 " --> pdb=" O GLY G 25 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA G 27 " --> pdb=" O GLU I 28 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ALA I 30 " --> pdb=" O ALA G 27 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ALA G 29 " --> pdb=" O ALA I 30 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 38 through 40 removed outlier: 6.451A pdb=" N TYR A 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TYR G 39 " --> pdb=" O VAL I 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 56 removed outlier: 6.710A pdb=" N THR C 44 " --> pdb=" O LYS E 43 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LYS E 45 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLU C 46 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLY E 47 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL C 52 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA E 53 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR C 54 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL E 55 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ALA C 56 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N LYS A 43 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 9.868A pdb=" N GLU E 46 " --> pdb=" O LYS A 43 " (cutoff:3.500A) removed outlier: 8.941A pdb=" N LYS A 45 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N VAL E 48 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLY A 47 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N HIS E 50 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL A 49 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL E 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N GLY A 51 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 9.696A pdb=" N THR E 54 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N ALA A 53 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 10.066A pdb=" N ALA E 56 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 9.240A pdb=" N VAL A 55 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LYS A 43 " --> pdb=" O THR I 44 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N GLU I 46 " --> pdb=" O LYS A 43 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LYS A 45 " --> pdb=" O GLU I 46 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N VAL I 48 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N GLY A 47 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N HIS I 50 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N VAL A 49 " --> pdb=" O HIS I 50 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N VAL I 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLY A 51 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N THR I 54 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ALA A 53 " --> pdb=" O THR I 54 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL G 48 " --> pdb=" O GLY I 47 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL I 49 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N HIS G 50 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLY I 51 " --> pdb=" O HIS G 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 59 through 66 removed outlier: 6.252A pdb=" N LYS C 60 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N VAL E 63 " --> pdb=" O LYS C 60 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLN C 62 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ASN E 65 " --> pdb=" O GLN C 62 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N THR C 64 " --> pdb=" O ASN E 65 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR A 59 " --> pdb=" O LYS E 60 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N GLN E 62 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLU A 61 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N THR E 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL A 63 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL E 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASN A 65 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR G 59 " --> pdb=" O LYS I 60 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N GLN I 62 " --> pdb=" O THR G 59 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLU G 61 " --> pdb=" O GLN I 62 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N THR I 64 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL G 63 " --> pdb=" O THR I 64 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N VAL I 66 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASN G 65 " --> pdb=" O VAL I 66 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 69 through 71 removed outlier: 6.401A pdb=" N ALA A 69 " --> pdb=" O VAL I 70 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 74 through 81 removed outlier: 6.294A pdb=" N VAL A 74 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N VAL E 77 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ALA A 76 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N GLN E 79 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ALA A 78 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N THR E 81 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LYS A 80 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL G 74 " --> pdb=" O THR I 75 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL I 77 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ALA G 76 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N GLN I 79 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ALA G 78 " --> pdb=" O GLN I 79 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N THR I 81 " --> pdb=" O ALA G 78 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LYS G 80 " --> pdb=" O THR I 81 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 89 through 90 removed outlier: 6.589A pdb=" N ALA C 89 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ALA A 89 " --> pdb=" O ALA I 90 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 23 through 32 removed outlier: 6.910A pdb=" N GLN D 24 " --> pdb=" O LYS F 23 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLY F 25 " --> pdb=" O GLN D 24 " (cutoff:3.500A) removed outlier: 9.257A pdb=" N LYS B 23 " --> pdb=" O GLN F 24 " (cutoff:3.500A) removed outlier: 9.044A pdb=" N VAL F 26 " --> pdb=" O LYS B 23 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLY B 25 " --> pdb=" O VAL F 26 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N GLU F 28 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ALA B 27 " --> pdb=" O GLU F 28 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA F 30 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA B 29 " --> pdb=" O ALA F 30 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N LYS F 32 " --> pdb=" O ALA B 29 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLY B 31 " --> pdb=" O LYS F 32 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLN B 24 " --> pdb=" O LYS J 23 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLY J 25 " --> pdb=" O GLN B 24 " (cutoff:3.500A) removed outlier: 9.220A pdb=" N LYS H 23 " --> pdb=" O GLN J 24 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N VAL J 26 " --> pdb=" O LYS H 23 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLY H 25 " --> pdb=" O VAL J 26 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N GLU J 28 " --> pdb=" O GLY H 25 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ALA H 27 " --> pdb=" O GLU J 28 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ALA J 30 " --> pdb=" O ALA H 27 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ALA H 29 " --> pdb=" O ALA J 30 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N LYS J 32 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLY H 31 " --> pdb=" O LYS J 32 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 35 through 57 removed outlier: 6.775A pdb=" N GLY D 36 " --> pdb=" O GLU F 35 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL F 37 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU D 38 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N TYR F 39 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL D 40 " --> pdb=" O TYR F 39 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY F 41 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N SER D 42 " --> pdb=" O GLY F 41 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LYS F 43 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N THR D 44 " --> pdb=" O LYS F 43 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LYS F 45 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLU D 46 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLY F 47 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL D 52 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ALA F 53 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR D 54 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL F 55 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ALA D 56 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLU F 57 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N GLU B 35 " --> pdb=" O GLY F 36 " (cutoff:3.500A) removed outlier: 9.243A pdb=" N LEU F 38 " --> pdb=" O GLU B 35 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N VAL B 37 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 10.307A pdb=" N VAL F 40 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 9.149A pdb=" N TYR B 39 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 10.380A pdb=" N SER F 42 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N GLY B 41 " --> pdb=" O SER F 42 " (cutoff:3.500A) removed outlier: 10.197A pdb=" N THR F 44 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 8.781A pdb=" N LYS B 43 " --> pdb=" O THR F 44 " (cutoff:3.500A) removed outlier: 10.167A pdb=" N GLU F 46 " --> pdb=" O LYS B 43 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N LYS B 45 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N VAL F 48 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLY B 47 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N HIS F 50 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL B 49 " --> pdb=" O HIS F 50 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL F 52 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N GLY B 51 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 9.572A pdb=" N THR F 54 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 8.864A pdb=" N ALA B 53 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 10.358A pdb=" N ALA F 56 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 9.009A pdb=" N VAL B 55 " --> pdb=" O ALA F 56 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLY B 36 " --> pdb=" O GLU J 35 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL J 37 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU B 38 " --> pdb=" O VAL J 37 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N TYR J 39 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL B 40 " --> pdb=" O TYR J 39 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLY J 41 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N SER B 42 " --> pdb=" O GLY J 41 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LYS J 43 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR B 44 " --> pdb=" O LYS J 43 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LYS J 45 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLU B 46 " --> pdb=" O LYS J 45 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLY J 47 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL B 52 " --> pdb=" O GLY J 51 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ALA J 53 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR B 54 " --> pdb=" O ALA J 53 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL J 55 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA B 56 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLU J 57 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N GLU H 35 " --> pdb=" O GLY J 36 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N LEU J 38 " --> pdb=" O GLU H 35 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N VAL H 37 " --> pdb=" O LEU J 38 " (cutoff:3.500A) removed outlier: 10.282A pdb=" N VAL J 40 " --> pdb=" O VAL H 37 " (cutoff:3.500A) removed outlier: 9.118A pdb=" N TYR H 39 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 10.356A pdb=" N SER J 42 " --> pdb=" O TYR H 39 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N GLY H 41 " --> pdb=" O SER J 42 " (cutoff:3.500A) removed outlier: 10.175A pdb=" N THR J 44 " --> pdb=" O GLY H 41 " (cutoff:3.500A) removed outlier: 8.755A pdb=" N LYS H 43 " --> pdb=" O THR J 44 " (cutoff:3.500A) removed outlier: 10.150A pdb=" N GLU J 46 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 9.136A pdb=" N LYS H 45 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N VAL J 48 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLY H 47 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N HIS J 50 " --> pdb=" O GLY H 47 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL H 49 " --> pdb=" O HIS J 50 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL J 52 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N GLY H 51 " --> pdb=" O VAL J 52 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N THR J 54 " --> pdb=" O GLY H 51 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N ALA H 53 " --> pdb=" O THR J 54 " (cutoff:3.500A) removed outlier: 10.360A pdb=" N ALA J 56 " --> pdb=" O ALA H 53 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N VAL H 55 " --> pdb=" O ALA J 56 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 60 through 66 removed outlier: 6.496A pdb=" N LYS D 60 " --> pdb=" O GLU F 61 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N VAL F 63 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLN D 62 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ASN F 65 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N THR D 64 " --> pdb=" O ASN F 65 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LYS B 60 " --> pdb=" O GLU J 61 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N VAL J 63 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLN B 62 " --> pdb=" O VAL J 63 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ASN J 65 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR B 64 " --> pdb=" O ASN J 65 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 69 through 71 removed outlier: 6.366A pdb=" N ALA D 69 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ALA B 69 " --> pdb=" O VAL J 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 74 through 82 removed outlier: 6.364A pdb=" N VAL B 74 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N VAL F 77 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ALA B 76 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N GLN F 79 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ALA B 78 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N THR F 81 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LYS B 80 " --> pdb=" O THR F 81 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL H 74 " --> pdb=" O THR J 75 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL J 77 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ALA H 76 " --> pdb=" O VAL J 77 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N GLN J 79 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ALA H 78 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N THR J 81 " --> pdb=" O ALA H 78 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LYS H 80 " --> pdb=" O THR J 81 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 88 through 92 removed outlier: 6.838A pdb=" N ALA F 89 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ALA B 89 " --> pdb=" O ALA F 90 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N THR F 92 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA B 91 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA J 89 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ALA H 89 " --> pdb=" O ALA J 90 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N THR J 92 " --> pdb=" O ALA H 89 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA H 91 " --> pdb=" O THR J 92 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 95 through 96 removed outlier: 6.381A pdb=" N VAL D 95 " --> pdb=" O LYS F 96 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL B 95 " --> pdb=" O LYS J 96 " (cutoff:3.500A) 124 hydrogen bonds defined for protein. 372 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.50 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 985 1.28 - 1.35: 855 1.35 - 1.41: 178 1.41 - 1.48: 885 1.48 - 1.54: 2607 Bond restraints: 5510 Sorted by residual: bond pdb=" N THR A 59 " pdb=" CA THR A 59 " ideal model delta sigma weight residual 1.459 1.494 -0.036 1.22e-02 6.72e+03 8.50e+00 bond pdb=" N THR E 59 " pdb=" CA THR E 59 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.22e-02 6.72e+03 8.45e+00 bond pdb=" N VAL G 63 " pdb=" CA VAL G 63 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.19e-02 7.06e+03 7.98e+00 bond pdb=" N VAL I 63 " pdb=" CA VAL I 63 " ideal model delta sigma weight residual 1.458 1.492 -0.033 1.19e-02 7.06e+03 7.84e+00 bond pdb=" N THR I 59 " pdb=" CA THR I 59 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.22e-02 6.72e+03 7.71e+00 ... (remaining 5505 not shown) Histogram of bond angle deviations from ideal: 105.86 - 110.94: 2224 110.94 - 116.02: 1574 116.02 - 121.10: 1938 121.10 - 126.18: 1674 126.18 - 131.26: 15 Bond angle restraints: 7425 Sorted by residual: angle pdb=" CA LEU A 38 " pdb=" CB LEU A 38 " pdb=" CG LEU A 38 " ideal model delta sigma weight residual 116.30 126.26 -9.96 3.50e+00 8.16e-02 8.10e+00 angle pdb=" CA LEU C 38 " pdb=" CB LEU C 38 " pdb=" CG LEU C 38 " ideal model delta sigma weight residual 116.30 126.26 -9.96 3.50e+00 8.16e-02 8.10e+00 angle pdb=" CA LEU G 38 " pdb=" CB LEU G 38 " pdb=" CG LEU G 38 " ideal model delta sigma weight residual 116.30 126.24 -9.94 3.50e+00 8.16e-02 8.07e+00 angle pdb=" CA LEU E 38 " pdb=" CB LEU E 38 " pdb=" CG LEU E 38 " ideal model delta sigma weight residual 116.30 126.23 -9.93 3.50e+00 8.16e-02 8.05e+00 angle pdb=" CA LEU I 38 " pdb=" CB LEU I 38 " pdb=" CG LEU I 38 " ideal model delta sigma weight residual 116.30 126.23 -9.93 3.50e+00 8.16e-02 8.05e+00 ... (remaining 7420 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.16: 2739 11.16 - 22.33: 356 22.33 - 33.49: 105 33.49 - 44.66: 25 44.66 - 55.82: 30 Dihedral angle restraints: 3255 sinusoidal: 1105 harmonic: 2150 Sorted by residual: dihedral pdb=" CA THR G 22 " pdb=" C THR G 22 " pdb=" N LYS G 23 " pdb=" CA LYS G 23 " ideal model delta harmonic sigma weight residual 180.00 162.23 17.77 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA THR A 22 " pdb=" C THR A 22 " pdb=" N LYS A 23 " pdb=" CA LYS A 23 " ideal model delta harmonic sigma weight residual 180.00 162.24 17.76 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA THR E 22 " pdb=" C THR E 22 " pdb=" N LYS E 23 " pdb=" CA LYS E 23 " ideal model delta harmonic sigma weight residual 180.00 162.24 17.76 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 3252 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 687 0.060 - 0.121: 226 0.121 - 0.181: 29 0.181 - 0.241: 4 0.241 - 0.302: 4 Chirality restraints: 950 Sorted by residual: chirality pdb=" CA GLU G 61 " pdb=" N GLU G 61 " pdb=" C GLU G 61 " pdb=" CB GLU G 61 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA GLU E 61 " pdb=" N GLU E 61 " pdb=" C GLU E 61 " pdb=" CB GLU E 61 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CA GLU A 61 " pdb=" N GLU A 61 " pdb=" C GLU A 61 " pdb=" CB GLU A 61 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 947 not shown) Planarity restraints: 935 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL G 63 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.91e+00 pdb=" C VAL G 63 " 0.038 2.00e-02 2.50e+03 pdb=" O VAL G 63 " -0.014 2.00e-02 2.50e+03 pdb=" N THR G 64 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 60 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.10e+00 pdb=" C LYS E 60 " -0.030 2.00e-02 2.50e+03 pdb=" O LYS E 60 " 0.011 2.00e-02 2.50e+03 pdb=" N GLU E 61 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 60 " 0.008 2.00e-02 2.50e+03 1.73e-02 3.01e+00 pdb=" C LYS A 60 " -0.030 2.00e-02 2.50e+03 pdb=" O LYS A 60 " 0.011 2.00e-02 2.50e+03 pdb=" N GLU A 61 " 0.010 2.00e-02 2.50e+03 ... (remaining 932 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1509 2.82 - 3.34: 4095 3.34 - 3.86: 9579 3.86 - 4.38: 10881 4.38 - 4.90: 20127 Nonbonded interactions: 46191 Sorted by model distance: nonbonded pdb=" NZ LYS G 80 " pdb=" OE1 GLU I 46 " model vdw 2.300 2.520 nonbonded pdb=" NZ LYS A 80 " pdb=" OE1 GLU E 46 " model vdw 2.326 2.520 nonbonded pdb=" OE1 GLU C 46 " pdb=" NZ LYS E 80 " model vdw 2.326 2.520 nonbonded pdb=" OE1 GLU A 46 " pdb=" NZ LYS I 80 " model vdw 2.337 2.520 nonbonded pdb=" NZ LYS D 58 " pdb=" OE2 GLU E 35 " model vdw 2.376 2.520 ... (remaining 46186 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 21 through 94) selection = (chain 'B' and resid 21 through 94) selection = (chain 'C' and resid 21 through 94) selection = (chain 'D' and resid 21 through 94) selection = (chain 'E' and resid 21 through 94) selection = (chain 'F' and resid 21 through 94) selection = (chain 'G' and resid 21 through 94) selection = (chain 'H' and resid 21 through 94) selection = (chain 'I' and resid 21 through 94) selection = (chain 'J' and resid 21 through 94) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 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: 0.000 Extract box with map and model: 6.760 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 18.160 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 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 : 0.008 0.036 5510 Z= 0.539 Angle : 0.739 9.960 7425 Z= 0.419 Chirality : 0.062 0.302 950 Planarity : 0.003 0.022 935 Dihedral : 12.927 55.821 1905 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.93 % Allowed : 1.85 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.24), residues: 780 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS I 50 PHE 0.006 0.002 PHE H 94 TYR 0.010 0.002 TYR G 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 193 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.6711 (OUTLIER) cc_final: 0.6153 (mm-30) REVERT: A 60 LYS cc_start: 0.8651 (tttt) cc_final: 0.8346 (tttm) REVERT: A 62 GLN cc_start: 0.7805 (tt0) cc_final: 0.7583 (mt0) REVERT: B 32 LYS cc_start: 0.8181 (tttm) cc_final: 0.7712 (tmtm) REVERT: B 61 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7892 (tm-30) REVERT: B 75 THR cc_start: 0.8531 (m) cc_final: 0.8307 (t) REVERT: C 28 GLU cc_start: 0.6678 (OUTLIER) cc_final: 0.5902 (mm-30) REVERT: C 80 LYS cc_start: 0.8909 (tptm) cc_final: 0.7807 (ttmt) REVERT: D 32 LYS cc_start: 0.8161 (tttm) cc_final: 0.7615 (tmtm) REVERT: D 97 LYS cc_start: 0.8905 (mttt) cc_final: 0.7574 (mmpt) REVERT: E 28 GLU cc_start: 0.6737 (OUTLIER) cc_final: 0.6190 (mm-30) REVERT: E 35 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7884 (mm-30) REVERT: E 46 GLU cc_start: 0.8288 (mt-10) cc_final: 0.8035 (mt-10) REVERT: E 60 LYS cc_start: 0.8627 (tttt) cc_final: 0.8287 (tppp) REVERT: E 62 GLN cc_start: 0.7866 (tt0) cc_final: 0.7586 (mt0) REVERT: F 32 LYS cc_start: 0.8156 (tttm) cc_final: 0.7748 (tmtm) REVERT: G 28 GLU cc_start: 0.6542 (OUTLIER) cc_final: 0.6154 (mm-30) REVERT: G 60 LYS cc_start: 0.8834 (tttt) cc_final: 0.8577 (ttpp) REVERT: H 32 LYS cc_start: 0.8434 (tttm) cc_final: 0.8069 (tttm) REVERT: I 28 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.6137 (mm-30) REVERT: I 60 LYS cc_start: 0.8677 (tttt) cc_final: 0.8132 (tttm) REVERT: I 62 GLN cc_start: 0.7792 (tt0) cc_final: 0.7527 (mt0) REVERT: J 32 LYS cc_start: 0.8250 (tttm) cc_final: 0.7659 (tmtm) outliers start: 5 outliers final: 0 residues processed: 198 average time/residue: 1.5461 time to fit residues: 315.6293 Evaluate side-chains 178 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 173 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain I residue 28 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 38 optimal weight: 20.0000 chunk 30 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 chunk 22 optimal weight: 8.9990 chunk 35 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 68 optimal weight: 20.0000 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 79 GLN B 50 HIS ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN C 79 GLN D 50 HIS ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 GLN E 62 GLN E 79 GLN F 50 HIS ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 GLN G 62 GLN G 79 GLN ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 62 GLN I 79 GLN J 50 HIS ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 5510 Z= 0.407 Angle : 0.554 7.846 7425 Z= 0.304 Chirality : 0.051 0.122 950 Planarity : 0.002 0.010 935 Dihedral : 6.531 44.758 815 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.96 % Allowed : 10.93 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.27), residues: 780 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 50 PHE 0.007 0.002 PHE J 94 TYR 0.010 0.002 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 190 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 32 LYS cc_start: 0.8104 (tttm) cc_final: 0.7770 (tttm) REVERT: B 61 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7903 (tm-30) REVERT: C 80 LYS cc_start: 0.8797 (tptm) cc_final: 0.7526 (ttmt) REVERT: D 32 LYS cc_start: 0.8015 (tttm) cc_final: 0.7562 (tmtm) REVERT: D 97 LYS cc_start: 0.8923 (mttt) cc_final: 0.7614 (mmpt) REVERT: E 35 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7859 (mm-30) REVERT: E 46 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7936 (mt-10) REVERT: E 60 LYS cc_start: 0.8624 (tttt) cc_final: 0.8277 (tppp) REVERT: E 62 GLN cc_start: 0.7960 (tt0) cc_final: 0.7476 (mt0) REVERT: F 32 LYS cc_start: 0.8104 (tttm) cc_final: 0.7597 (tmtm) REVERT: F 96 LYS cc_start: 0.8733 (tttm) cc_final: 0.8519 (tttm) REVERT: G 60 LYS cc_start: 0.8842 (tttt) cc_final: 0.8575 (tttp) REVERT: H 32 LYS cc_start: 0.8247 (tttm) cc_final: 0.7967 (tttm) REVERT: J 32 LYS cc_start: 0.8208 (tttm) cc_final: 0.7626 (tmtm) outliers start: 16 outliers final: 13 residues processed: 193 average time/residue: 1.5333 time to fit residues: 305.3297 Evaluate side-chains 193 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 180 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 20.0000 chunk 21 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 67 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN C 79 GLN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 GLN ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 GLN ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 5510 Z= 0.409 Angle : 0.547 7.562 7425 Z= 0.300 Chirality : 0.051 0.127 950 Planarity : 0.002 0.011 935 Dihedral : 5.272 16.206 800 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.26 % Allowed : 14.81 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.27), residues: 780 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS G 50 PHE 0.007 0.002 PHE J 94 TYR 0.011 0.002 TYR I 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 180 time to evaluate : 0.618 Fit side-chains REVERT: A 62 GLN cc_start: 0.7891 (tt0) cc_final: 0.7457 (mt0) REVERT: B 32 LYS cc_start: 0.8082 (tttm) cc_final: 0.7769 (tttm) REVERT: C 80 LYS cc_start: 0.8852 (tptm) cc_final: 0.7630 (ttmt) REVERT: D 32 LYS cc_start: 0.8011 (tttm) cc_final: 0.7540 (tmtm) REVERT: D 97 LYS cc_start: 0.8938 (mttt) cc_final: 0.7612 (mmpt) REVERT: E 46 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7932 (mt-10) REVERT: E 60 LYS cc_start: 0.8604 (tttt) cc_final: 0.8202 (tttm) REVERT: E 62 GLN cc_start: 0.7977 (tt0) cc_final: 0.7507 (mt0) REVERT: F 32 LYS cc_start: 0.8092 (tttm) cc_final: 0.7578 (tmtm) REVERT: H 32 LYS cc_start: 0.8227 (tttm) cc_final: 0.7870 (tttm) REVERT: J 32 LYS cc_start: 0.8157 (tttm) cc_final: 0.7580 (tmtm) outliers start: 23 outliers final: 16 residues processed: 184 average time/residue: 1.5386 time to fit residues: 291.8044 Evaluate side-chains 193 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 177 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 20.0000 chunk 51 optimal weight: 0.9990 chunk 35 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 64 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 overall best weight: 6.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN C 79 GLN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 GLN G 62 GLN ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 GLN ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 5510 Z= 0.480 Angle : 0.578 7.671 7425 Z= 0.317 Chirality : 0.052 0.127 950 Planarity : 0.002 0.011 935 Dihedral : 5.384 16.736 800 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.26 % Allowed : 17.78 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.28), residues: 780 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS G 50 PHE 0.007 0.002 PHE J 94 TYR 0.011 0.002 TYR I 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 179 time to evaluate : 0.613 Fit side-chains REVERT: A 62 GLN cc_start: 0.7927 (tt0) cc_final: 0.7480 (mt0) REVERT: B 32 LYS cc_start: 0.8107 (tttm) cc_final: 0.7797 (tttm) REVERT: B 57 GLU cc_start: 0.8262 (tt0) cc_final: 0.8045 (tt0) REVERT: B 61 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7890 (tm-30) REVERT: C 58 LYS cc_start: 0.8569 (tppt) cc_final: 0.7786 (mmmt) REVERT: C 80 LYS cc_start: 0.8849 (tptm) cc_final: 0.7703 (ttmt) REVERT: D 32 LYS cc_start: 0.8015 (tttm) cc_final: 0.7528 (tmtm) REVERT: D 97 LYS cc_start: 0.8937 (mttt) cc_final: 0.7606 (mmpt) REVERT: E 35 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7841 (mm-30) REVERT: E 46 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7928 (mt-10) REVERT: E 60 LYS cc_start: 0.8556 (tttt) cc_final: 0.8355 (tttm) REVERT: F 32 LYS cc_start: 0.8089 (tttm) cc_final: 0.7549 (tmtm) REVERT: H 32 LYS cc_start: 0.8219 (tttm) cc_final: 0.7836 (tttm) REVERT: I 62 GLN cc_start: 0.8082 (tt0) cc_final: 0.7480 (mt0) REVERT: J 28 GLU cc_start: 0.7338 (tt0) cc_final: 0.7098 (mt-10) REVERT: J 32 LYS cc_start: 0.8140 (tttm) cc_final: 0.7672 (tmtm) outliers start: 23 outliers final: 18 residues processed: 185 average time/residue: 1.4916 time to fit residues: 284.6682 Evaluate side-chains 198 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 180 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 23 LYS Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 GLN E 62 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 GLN G 62 GLN ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 GLN ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.036 5510 Z= 0.490 Angle : 0.584 7.792 7425 Z= 0.321 Chirality : 0.052 0.126 950 Planarity : 0.002 0.011 935 Dihedral : 5.424 16.909 800 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.26 % Allowed : 19.44 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.28), residues: 780 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.55 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS G 50 PHE 0.007 0.002 PHE J 94 TYR 0.011 0.002 TYR I 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 181 time to evaluate : 0.580 Fit side-chains REVERT: A 62 GLN cc_start: 0.7940 (tt0) cc_final: 0.7485 (mt0) REVERT: B 32 LYS cc_start: 0.8108 (tttm) cc_final: 0.7840 (tttm) REVERT: C 58 LYS cc_start: 0.8600 (tppt) cc_final: 0.7814 (mmmt) REVERT: C 80 LYS cc_start: 0.8866 (tptm) cc_final: 0.7707 (ttmt) REVERT: D 32 LYS cc_start: 0.8012 (tttm) cc_final: 0.7554 (tmtm) REVERT: D 97 LYS cc_start: 0.8946 (mttt) cc_final: 0.7626 (mmpt) REVERT: E 46 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7884 (mt-10) REVERT: E 60 LYS cc_start: 0.8562 (tttt) cc_final: 0.8347 (tttm) REVERT: F 32 LYS cc_start: 0.8086 (tttm) cc_final: 0.7550 (tmtm) REVERT: H 32 LYS cc_start: 0.8218 (tttm) cc_final: 0.7820 (tttm) REVERT: I 62 GLN cc_start: 0.8083 (tt0) cc_final: 0.7505 (mt0) REVERT: J 28 GLU cc_start: 0.7332 (tt0) cc_final: 0.7092 (mt-10) REVERT: J 32 LYS cc_start: 0.8116 (tttm) cc_final: 0.7660 (tmtm) outliers start: 23 outliers final: 19 residues processed: 185 average time/residue: 1.5615 time to fit residues: 297.8983 Evaluate side-chains 198 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 179 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 23 LYS Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 60 optimal weight: 20.0000 chunk 33 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 69 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 GLN E 62 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 GLN G 62 GLN ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 GLN ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 5510 Z= 0.319 Angle : 0.502 7.236 7425 Z= 0.276 Chirality : 0.050 0.123 950 Planarity : 0.002 0.011 935 Dihedral : 5.144 16.146 800 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.63 % Allowed : 19.44 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.28), residues: 780 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS G 50 PHE 0.007 0.001 PHE J 94 TYR 0.010 0.002 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 180 time to evaluate : 0.560 Fit side-chains REVERT: A 62 GLN cc_start: 0.7886 (tt0) cc_final: 0.7447 (mt0) REVERT: B 32 LYS cc_start: 0.8092 (tttm) cc_final: 0.7792 (tttm) REVERT: B 57 GLU cc_start: 0.8203 (tt0) cc_final: 0.7984 (tm-30) REVERT: C 58 LYS cc_start: 0.8601 (tppt) cc_final: 0.7810 (mmmt) REVERT: C 80 LYS cc_start: 0.8824 (tptm) cc_final: 0.7622 (ttmt) REVERT: D 32 LYS cc_start: 0.8022 (tttm) cc_final: 0.7654 (tmtm) REVERT: D 97 LYS cc_start: 0.8936 (mttt) cc_final: 0.7600 (mmpt) REVERT: E 46 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7939 (mt-10) REVERT: E 60 LYS cc_start: 0.8560 (tttt) cc_final: 0.8353 (tttm) REVERT: F 32 LYS cc_start: 0.8072 (tttm) cc_final: 0.7645 (tmtm) REVERT: H 32 LYS cc_start: 0.8201 (tttm) cc_final: 0.7809 (tttm) REVERT: I 58 LYS cc_start: 0.8378 (tppt) cc_final: 0.7648 (mtpt) REVERT: I 62 GLN cc_start: 0.8058 (tt0) cc_final: 0.7483 (mt0) REVERT: J 32 LYS cc_start: 0.8154 (tttm) cc_final: 0.7698 (tmtm) outliers start: 25 outliers final: 21 residues processed: 184 average time/residue: 1.6566 time to fit residues: 313.8455 Evaluate side-chains 199 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 178 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 23 LYS Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 20.0000 chunk 41 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 43 optimal weight: 0.8980 overall best weight: 6.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN D 24 GLN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 GLN E 62 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 GLN G 62 GLN ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 GLN ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.037 5510 Z= 0.530 Angle : 0.604 8.117 7425 Z= 0.331 Chirality : 0.053 0.128 950 Planarity : 0.002 0.010 935 Dihedral : 5.461 17.117 800 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.44 % Allowed : 21.11 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.28), residues: 780 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS G 50 PHE 0.007 0.002 PHE J 94 TYR 0.011 0.002 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 183 time to evaluate : 0.624 Fit side-chains REVERT: A 62 GLN cc_start: 0.7919 (tt0) cc_final: 0.7369 (mt0) REVERT: B 32 LYS cc_start: 0.8116 (tttm) cc_final: 0.7849 (tttm) REVERT: B 57 GLU cc_start: 0.8246 (tt0) cc_final: 0.7996 (tm-30) REVERT: B 61 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7888 (tm-30) REVERT: C 58 LYS cc_start: 0.8584 (tppt) cc_final: 0.7803 (mmmt) REVERT: C 80 LYS cc_start: 0.8843 (tptm) cc_final: 0.7728 (ttmt) REVERT: D 32 LYS cc_start: 0.8013 (tttm) cc_final: 0.7631 (tmtm) REVERT: D 97 LYS cc_start: 0.8946 (mttt) cc_final: 0.7622 (mmpt) REVERT: E 35 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7906 (mm-30) REVERT: E 60 LYS cc_start: 0.8574 (tttt) cc_final: 0.8347 (tttm) REVERT: F 32 LYS cc_start: 0.8073 (tttm) cc_final: 0.7641 (tmtm) REVERT: H 32 LYS cc_start: 0.8260 (tttm) cc_final: 0.7835 (tttm) REVERT: I 58 LYS cc_start: 0.8384 (tppt) cc_final: 0.7657 (mtpt) REVERT: I 62 GLN cc_start: 0.8109 (tt0) cc_final: 0.7548 (mt0) REVERT: J 28 GLU cc_start: 0.7323 (tt0) cc_final: 0.7082 (mt-10) REVERT: J 32 LYS cc_start: 0.8110 (tttm) cc_final: 0.7656 (tmtm) outliers start: 24 outliers final: 18 residues processed: 187 average time/residue: 1.6110 time to fit residues: 310.4140 Evaluate side-chains 201 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 183 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 49 optimal weight: 20.0000 chunk 35 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 65 optimal weight: 8.9990 chunk 69 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN D 24 GLN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 GLN G 62 GLN ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 GLN ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 5510 Z= 0.333 Angle : 0.510 6.806 7425 Z= 0.281 Chirality : 0.051 0.124 950 Planarity : 0.002 0.010 935 Dihedral : 5.171 16.314 800 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.89 % Allowed : 22.41 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.28), residues: 780 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS G 50 PHE 0.007 0.002 PHE J 94 TYR 0.010 0.002 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 182 time to evaluate : 0.532 Fit side-chains REVERT: A 62 GLN cc_start: 0.7904 (tt0) cc_final: 0.7363 (mt0) REVERT: B 32 LYS cc_start: 0.8105 (tttm) cc_final: 0.7804 (tttm) REVERT: B 57 GLU cc_start: 0.8205 (tt0) cc_final: 0.7975 (tm-30) REVERT: B 61 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7827 (tm-30) REVERT: C 58 LYS cc_start: 0.8588 (tppt) cc_final: 0.7798 (mmmt) REVERT: C 80 LYS cc_start: 0.8817 (tptm) cc_final: 0.7635 (ttmt) REVERT: D 32 LYS cc_start: 0.8020 (tttm) cc_final: 0.7661 (tmtm) REVERT: D 97 LYS cc_start: 0.8931 (mttt) cc_final: 0.7599 (mmpt) REVERT: E 60 LYS cc_start: 0.8593 (tttt) cc_final: 0.8371 (tttm) REVERT: F 32 LYS cc_start: 0.8052 (tttm) cc_final: 0.7623 (tmtm) REVERT: H 32 LYS cc_start: 0.8220 (tttm) cc_final: 0.7812 (tttm) REVERT: I 58 LYS cc_start: 0.8413 (tppt) cc_final: 0.7684 (mtpt) REVERT: I 62 GLN cc_start: 0.8075 (tt0) cc_final: 0.7515 (mt0) REVERT: J 28 GLU cc_start: 0.7313 (tt0) cc_final: 0.7074 (mt-10) REVERT: J 32 LYS cc_start: 0.8144 (tttm) cc_final: 0.7683 (tmtm) outliers start: 21 outliers final: 20 residues processed: 185 average time/residue: 1.5028 time to fit residues: 286.8310 Evaluate side-chains 200 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 180 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN D 24 GLN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 GLN G 62 GLN ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 GLN ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.033 5510 Z= 0.459 Angle : 0.573 7.689 7425 Z= 0.315 Chirality : 0.052 0.124 950 Planarity : 0.002 0.010 935 Dihedral : 5.362 16.989 800 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.26 % Allowed : 22.59 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.28), residues: 780 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS G 50 PHE 0.007 0.002 PHE J 94 TYR 0.011 0.002 TYR I 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 179 time to evaluate : 0.639 Fit side-chains REVERT: A 62 GLN cc_start: 0.7958 (tt0) cc_final: 0.7395 (mt0) REVERT: B 32 LYS cc_start: 0.8114 (tttm) cc_final: 0.7805 (tttm) REVERT: B 57 GLU cc_start: 0.8227 (tt0) cc_final: 0.7986 (tm-30) REVERT: C 58 LYS cc_start: 0.8580 (tppt) cc_final: 0.7826 (mmmt) REVERT: C 80 LYS cc_start: 0.8834 (tptm) cc_final: 0.7717 (ttmt) REVERT: D 32 LYS cc_start: 0.8037 (tttm) cc_final: 0.7670 (tmtm) REVERT: D 97 LYS cc_start: 0.8946 (mttt) cc_final: 0.7639 (mmpt) REVERT: E 46 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7882 (mt-10) REVERT: E 60 LYS cc_start: 0.8596 (tttt) cc_final: 0.8368 (tttm) REVERT: F 32 LYS cc_start: 0.8059 (tttm) cc_final: 0.7622 (tmtm) REVERT: H 32 LYS cc_start: 0.8257 (tttm) cc_final: 0.7840 (tttm) REVERT: I 58 LYS cc_start: 0.8418 (tppt) cc_final: 0.7696 (mtpt) REVERT: I 62 GLN cc_start: 0.8097 (tt0) cc_final: 0.7538 (mt0) REVERT: J 32 LYS cc_start: 0.8126 (tttm) cc_final: 0.7678 (tmtm) outliers start: 23 outliers final: 20 residues processed: 182 average time/residue: 1.5587 time to fit residues: 292.4874 Evaluate side-chains 199 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 179 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 5.9990 chunk 49 optimal weight: 20.0000 chunk 74 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 chunk 59 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 GLN G 62 GLN ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 GLN ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 5510 Z= 0.278 Angle : 0.486 6.474 7425 Z= 0.268 Chirality : 0.050 0.121 950 Planarity : 0.002 0.011 935 Dihedral : 5.058 15.976 800 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.70 % Allowed : 23.89 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.28), residues: 780 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS G 50 PHE 0.007 0.001 PHE J 94 TYR 0.009 0.001 TYR E 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 178 time to evaluate : 0.534 Fit side-chains REVERT: A 62 GLN cc_start: 0.7929 (tt0) cc_final: 0.7401 (mt0) REVERT: B 32 LYS cc_start: 0.8085 (tttm) cc_final: 0.7787 (tttm) REVERT: B 61 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7799 (tm-30) REVERT: C 58 LYS cc_start: 0.8591 (tppt) cc_final: 0.7831 (mmmt) REVERT: C 80 LYS cc_start: 0.8829 (tptm) cc_final: 0.7641 (ttmt) REVERT: D 32 LYS cc_start: 0.8013 (tttm) cc_final: 0.7583 (tmtm) REVERT: D 97 LYS cc_start: 0.8935 (mttt) cc_final: 0.7577 (mmpt) REVERT: E 60 LYS cc_start: 0.8670 (tttt) cc_final: 0.8458 (tttm) REVERT: F 32 LYS cc_start: 0.8041 (tttm) cc_final: 0.7621 (tmtm) REVERT: H 32 LYS cc_start: 0.8206 (tttm) cc_final: 0.7801 (tttm) REVERT: I 58 LYS cc_start: 0.8439 (tppt) cc_final: 0.7710 (mtpt) REVERT: I 62 GLN cc_start: 0.8062 (tt0) cc_final: 0.7507 (mt0) REVERT: J 28 GLU cc_start: 0.7310 (tt0) cc_final: 0.7084 (mt-10) REVERT: J 32 LYS cc_start: 0.8166 (tttm) cc_final: 0.7594 (tmtm) outliers start: 20 outliers final: 20 residues processed: 180 average time/residue: 1.5246 time to fit residues: 283.0574 Evaluate side-chains 197 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 177 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 0.0000 chunk 8 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 7 optimal weight: 30.0000 chunk 10 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN D 24 GLN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 GLN G 62 GLN ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 GLN ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.136398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.106390 restraints weight = 5468.108| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.32 r_work: 0.3413 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.036 5510 Z= 0.517 Angle : 0.602 8.278 7425 Z= 0.330 Chirality : 0.053 0.125 950 Planarity : 0.002 0.010 935 Dihedral : 5.435 17.175 800 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.44 % Allowed : 23.15 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.28), residues: 780 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS G 50 PHE 0.007 0.002 PHE J 94 TYR 0.011 0.002 TYR I 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4086.41 seconds wall clock time: 72 minutes 20.56 seconds (4340.56 seconds total)