Starting phenix.real_space_refine on Tue Feb 13 07:32:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osl_20185/02_2024/6osl_20185.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osl_20185/02_2024/6osl_20185.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osl_20185/02_2024/6osl_20185.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osl_20185/02_2024/6osl_20185.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osl_20185/02_2024/6osl_20185.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osl_20185/02_2024/6osl_20185.pdb" } resolution = 3.0 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= 0.008 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 2540 2.51 5 N 710 2.21 5 O 810 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 GLU 57": "OE1" <-> "OE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "E GLU 57": "OE1" <-> "OE2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "G GLU 57": "OE1" <-> "OE2" Residue "H GLU 57": "OE1" <-> "OE2" Residue "I GLU 57": "OE1" <-> "OE2" Residue "J GLU 57": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4060 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 406 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "B" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 406 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "C" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 406 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "D" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 406 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "E" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 406 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "F" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 406 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "G" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 406 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "H" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 406 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "I" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 406 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "J" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 406 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Time building chain proxies: 2.47, per 1000 atoms: 0.61 Number of scatterers: 4060 At special positions: 0 Unit cell: (98.58, 83.74, 42.4, 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 810 8.00 N 710 7.00 C 2540 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: 1.58 Conformation dependent library (CDL) restraints added in 1.0 seconds 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1000 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 49.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 41 removed outlier: 6.706A pdb=" N VAL A 40 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL C 40 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL E 40 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL G 40 " --> pdb=" O GLY I 41 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 49 removed outlier: 7.313A pdb=" N GLU C 46 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N GLY A 47 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL C 48 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLU E 46 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLY C 47 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N GLU E 46 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N VAL G 49 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 9.311A pdb=" N VAL E 48 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLU I 46 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY G 47 " --> pdb=" O GLU I 46 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 57 removed outlier: 6.527A pdb=" N VAL E 52 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N VAL G 55 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N THR E 54 " --> pdb=" O VAL G 55 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N GLU G 57 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA E 56 " --> pdb=" O GLU G 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 61 through 65 Processing sheet with id=AA5, first strand: chain 'A' and resid 69 through 75 removed outlier: 9.171A pdb=" N ALA A 69 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 10.579A pdb=" N THR C 72 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 9.250A pdb=" N VAL A 71 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 9.490A pdb=" N VAL C 74 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N GLY A 73 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N ALA C 69 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 10.407A pdb=" N THR E 72 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 9.038A pdb=" N VAL C 71 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 9.296A pdb=" N VAL E 74 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLY C 73 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N ALA E 69 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 10.419A pdb=" N THR G 72 " --> pdb=" O ALA E 69 " (cutoff:3.500A) removed outlier: 9.049A pdb=" N VAL E 71 " --> pdb=" O THR G 72 " (cutoff:3.500A) removed outlier: 9.310A pdb=" N VAL G 74 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N GLY E 73 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ALA G 76 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N THR E 75 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N ALA G 78 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA C 78 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N THR E 81 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LYS C 80 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ALA A 78 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N THR C 81 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LYS A 80 " --> pdb=" O THR C 81 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 69 through 75 removed outlier: 9.171A pdb=" N ALA A 69 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 10.579A pdb=" N THR C 72 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 9.250A pdb=" N VAL A 71 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 9.490A pdb=" N VAL C 74 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N GLY A 73 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N ALA C 69 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 10.407A pdb=" N THR E 72 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 9.038A pdb=" N VAL C 71 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 9.296A pdb=" N VAL E 74 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLY C 73 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N ALA E 69 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 10.419A pdb=" N THR G 72 " --> pdb=" O ALA E 69 " (cutoff:3.500A) removed outlier: 9.049A pdb=" N VAL E 71 " --> pdb=" O THR G 72 " (cutoff:3.500A) removed outlier: 9.310A pdb=" N VAL G 74 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N GLY E 73 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ALA G 76 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N THR E 75 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N ALA G 78 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N ALA G 69 " --> pdb=" O VAL I 70 " (cutoff:3.500A) removed outlier: 10.417A pdb=" N THR I 72 " --> pdb=" O ALA G 69 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N VAL G 71 " --> pdb=" O THR I 72 " (cutoff:3.500A) removed outlier: 9.293A pdb=" N VAL I 74 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLY G 73 " --> pdb=" O VAL I 74 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ALA I 76 " --> pdb=" O GLY G 73 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N THR G 75 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ALA I 78 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N VAL G 77 " --> pdb=" O ALA I 78 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N LYS I 80 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 9.141A pdb=" N GLN G 79 " --> pdb=" O LYS I 80 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 86 through 88 Processing sheet with id=AA8, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AA9, first strand: chain 'B' and resid 45 through 49 removed outlier: 8.313A pdb=" N GLU B 46 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N VAL D 49 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 9.207A pdb=" N VAL B 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLU F 46 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLY D 47 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N GLU F 46 " --> pdb=" O GLY H 47 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N VAL H 49 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 9.272A pdb=" N VAL F 48 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLU J 46 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLY H 47 " --> pdb=" O GLU J 46 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 52 through 57 removed outlier: 6.498A pdb=" N VAL B 52 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N VAL D 55 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N THR B 54 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N GLU D 57 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ALA B 56 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL F 52 " --> pdb=" O ALA H 53 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N VAL H 55 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR F 54 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N GLU H 57 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ALA F 56 " --> pdb=" O GLU H 57 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 62 through 65 Processing sheet with id=AB3, first strand: chain 'B' and resid 69 through 75 removed outlier: 8.967A pdb=" N ALA B 69 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 10.432A pdb=" N THR D 72 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 9.064A pdb=" N VAL B 71 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 9.307A pdb=" N VAL D 74 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLY B 73 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N ALA D 69 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 10.385A pdb=" N THR F 72 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N VAL D 71 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 9.272A pdb=" N VAL F 74 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLY D 73 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 8.907A pdb=" N ALA F 69 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 10.388A pdb=" N THR H 72 " --> pdb=" O ALA F 69 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N VAL F 71 " --> pdb=" O THR H 72 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N VAL H 74 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N GLY F 73 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N ALA H 69 " --> pdb=" O VAL J 70 " (cutoff:3.500A) removed outlier: 10.396A pdb=" N THR J 72 " --> pdb=" O ALA H 69 " (cutoff:3.500A) removed outlier: 9.038A pdb=" N VAL H 71 " --> pdb=" O THR J 72 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N VAL J 74 " --> pdb=" O VAL H 71 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY H 73 " --> pdb=" O VAL J 74 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 78 through 81 removed outlier: 6.809A pdb=" N ALA D 78 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N THR F 81 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LYS D 80 " --> pdb=" O THR F 81 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA F 78 " --> pdb=" O GLN H 79 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N THR H 81 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LYS F 80 " --> pdb=" O THR H 81 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ALA H 78 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N THR J 81 " --> pdb=" O ALA H 78 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LYS H 80 " --> pdb=" O THR J 81 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 86 through 88 Processing sheet with id=AB6, first strand: chain 'B' and resid 91 through 92 Processing sheet with id=AB7, first strand: chain 'D' and resid 40 through 41 removed outlier: 6.522A pdb=" N VAL D 40 " --> pdb=" O GLY F 41 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL F 40 " --> pdb=" O GLY H 41 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL H 40 " --> pdb=" O GLY J 41 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 95 hydrogen bonds defined for protein. 279 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: 1.07 Time building geometry restraints manager: 1.68 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: 700 1.28 - 1.35: 630 1.35 - 1.42: 180 1.42 - 1.48: 701 1.48 - 1.55: 1869 Bond restraints: 4080 Sorted by residual: bond pdb=" CB GLU I 57 " pdb=" CG GLU I 57 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.19e+00 bond pdb=" CB GLU H 57 " pdb=" CG GLU H 57 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.18e+00 bond pdb=" CB GLU D 57 " pdb=" CG GLU D 57 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.18e+00 bond pdb=" CB GLU C 57 " pdb=" CG GLU C 57 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.16e+00 bond pdb=" CB GLU B 57 " pdb=" CG GLU B 57 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.14e+00 ... (remaining 4075 not shown) Histogram of bond angle deviations from ideal: 106.12 - 111.05: 1822 111.05 - 115.99: 1053 115.99 - 120.92: 1341 120.92 - 125.85: 1284 125.85 - 130.79: 10 Bond angle restraints: 5510 Sorted by residual: angle pdb=" C VAL J 49 " pdb=" N HIS J 50 " pdb=" CA HIS J 50 " ideal model delta sigma weight residual 122.46 113.24 9.22 1.80e+00 3.09e-01 2.62e+01 angle pdb=" C VAL H 49 " pdb=" N HIS H 50 " pdb=" CA HIS H 50 " ideal model delta sigma weight residual 122.46 113.27 9.19 1.80e+00 3.09e-01 2.61e+01 angle pdb=" C VAL B 49 " pdb=" N HIS B 50 " pdb=" CA HIS B 50 " ideal model delta sigma weight residual 122.46 113.27 9.19 1.80e+00 3.09e-01 2.60e+01 angle pdb=" C VAL D 49 " pdb=" N HIS D 50 " pdb=" CA HIS D 50 " ideal model delta sigma weight residual 122.46 113.27 9.19 1.80e+00 3.09e-01 2.60e+01 angle pdb=" C VAL I 49 " pdb=" N HIS I 50 " pdb=" CA HIS I 50 " ideal model delta sigma weight residual 122.46 113.28 9.18 1.80e+00 3.09e-01 2.60e+01 ... (remaining 5505 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.33: 2200 16.33 - 32.65: 159 32.65 - 48.97: 11 48.97 - 65.29: 0 65.29 - 81.62: 10 Dihedral angle restraints: 2380 sinusoidal: 790 harmonic: 1590 Sorted by residual: dihedral pdb=" CA THR D 75 " pdb=" C THR D 75 " pdb=" N ALA D 76 " pdb=" CA ALA D 76 " ideal model delta harmonic sigma weight residual 180.00 164.48 15.52 0 5.00e+00 4.00e-02 9.63e+00 dihedral pdb=" CA THR J 75 " pdb=" C THR J 75 " pdb=" N ALA J 76 " pdb=" CA ALA J 76 " ideal model delta harmonic sigma weight residual 180.00 164.48 15.52 0 5.00e+00 4.00e-02 9.63e+00 dihedral pdb=" CA THR G 75 " pdb=" C THR G 75 " pdb=" N ALA G 76 " pdb=" CA ALA G 76 " ideal model delta harmonic sigma weight residual 180.00 164.48 15.52 0 5.00e+00 4.00e-02 9.63e+00 ... (remaining 2377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 490 0.062 - 0.123: 187 0.123 - 0.185: 33 0.185 - 0.246: 0 0.246 - 0.308: 10 Chirality restraints: 720 Sorted by residual: chirality pdb=" CA HIS A 50 " pdb=" N HIS A 50 " pdb=" C HIS A 50 " pdb=" CB HIS A 50 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CA HIS B 50 " pdb=" N HIS B 50 " pdb=" C HIS B 50 " pdb=" CB HIS B 50 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CA HIS E 50 " pdb=" N HIS E 50 " pdb=" C HIS E 50 " pdb=" CB HIS E 50 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 717 not shown) Planarity restraints: 680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS H 50 " 0.020 2.00e-02 2.50e+03 1.81e-02 4.90e+00 pdb=" CG HIS H 50 " -0.038 2.00e-02 2.50e+03 pdb=" ND1 HIS H 50 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 HIS H 50 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS H 50 " 0.005 2.00e-02 2.50e+03 pdb=" NE2 HIS H 50 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS F 50 " 0.020 2.00e-02 2.50e+03 1.79e-02 4.82e+00 pdb=" CG HIS F 50 " -0.038 2.00e-02 2.50e+03 pdb=" ND1 HIS F 50 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 HIS F 50 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS F 50 " 0.005 2.00e-02 2.50e+03 pdb=" NE2 HIS F 50 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 50 " 0.019 2.00e-02 2.50e+03 1.79e-02 4.80e+00 pdb=" CG HIS B 50 " -0.038 2.00e-02 2.50e+03 pdb=" ND1 HIS B 50 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 HIS B 50 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS B 50 " 0.005 2.00e-02 2.50e+03 pdb=" NE2 HIS B 50 " 0.006 2.00e-02 2.50e+03 ... (remaining 677 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1390 2.83 - 3.34: 3595 3.34 - 3.86: 6312 3.86 - 4.38: 6929 4.38 - 4.90: 14282 Nonbonded interactions: 32508 Sorted by model distance: nonbonded pdb=" O HIS B 50 " pdb=" O GLY D 51 " model vdw 2.308 3.040 nonbonded pdb=" O HIS E 50 " pdb=" O GLY G 51 " model vdw 2.367 3.040 nonbonded pdb=" O HIS F 50 " pdb=" O GLY H 51 " model vdw 2.385 3.040 nonbonded pdb=" O HIS C 50 " pdb=" O GLY E 51 " model vdw 2.392 3.040 nonbonded pdb=" O HIS G 50 " pdb=" O GLY I 51 " model vdw 2.397 3.040 ... (remaining 32503 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.880 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 15.620 Find NCS groups from input model: 0.280 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:11.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.044 4080 Z= 0.699 Angle : 1.064 9.216 5510 Z= 0.629 Chirality : 0.074 0.308 720 Planarity : 0.004 0.018 680 Dihedral : 13.469 81.616 1380 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 2.44 % Allowed : 16.83 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.40 (0.22), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.17), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.010 HIS B 50 PHE 0.003 0.001 PHE B 94 TYR 0.006 0.002 TYR H 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 0.463 Fit side-chains REVERT: A 57 GLU cc_start: 0.8300 (pt0) cc_final: 0.8062 (pt0) REVERT: B 57 GLU cc_start: 0.8476 (pt0) cc_final: 0.8251 (pt0) REVERT: B 60 LYS cc_start: 0.8175 (mttt) cc_final: 0.7827 (mtpt) REVERT: B 94 PHE cc_start: 0.7459 (p90) cc_final: 0.6872 (p90) REVERT: B 96 LYS cc_start: 0.6521 (ttmt) cc_final: 0.5825 (tttm) REVERT: C 45 LYS cc_start: 0.7280 (pttt) cc_final: 0.6868 (ptmt) REVERT: C 57 GLU cc_start: 0.8071 (pt0) cc_final: 0.7845 (pt0) REVERT: C 60 LYS cc_start: 0.8111 (mttt) cc_final: 0.7853 (mttp) REVERT: C 94 PHE cc_start: 0.7878 (p90) cc_final: 0.7667 (p90) REVERT: C 96 LYS cc_start: 0.6006 (ttmt) cc_final: 0.5290 (tttm) REVERT: D 45 LYS cc_start: 0.7180 (pttt) cc_final: 0.6720 (ptpt) REVERT: D 60 LYS cc_start: 0.8216 (mttt) cc_final: 0.7880 (mttp) REVERT: D 96 LYS cc_start: 0.5686 (ttmt) cc_final: 0.5187 (tttm) REVERT: E 60 LYS cc_start: 0.8442 (mttt) cc_final: 0.7882 (mtpt) REVERT: E 94 PHE cc_start: 0.7846 (p90) cc_final: 0.7544 (p90) REVERT: E 96 LYS cc_start: 0.5451 (ttmt) cc_final: 0.4832 (tttp) REVERT: F 60 LYS cc_start: 0.8252 (mttt) cc_final: 0.7744 (mtpt) REVERT: F 94 PHE cc_start: 0.7570 (p90) cc_final: 0.7072 (p90) REVERT: F 96 LYS cc_start: 0.5874 (ttmt) cc_final: 0.5444 (tttp) REVERT: G 96 LYS cc_start: 0.4790 (ttmt) cc_final: 0.4355 (tttm) REVERT: H 60 LYS cc_start: 0.7935 (mttt) cc_final: 0.7581 (mttp) REVERT: H 96 LYS cc_start: 0.4792 (ttmt) cc_final: 0.4338 (tttm) REVERT: I 60 LYS cc_start: 0.8096 (mttt) cc_final: 0.7402 (tttm) REVERT: I 94 PHE cc_start: 0.7633 (p90) cc_final: 0.5078 (m-80) REVERT: I 96 LYS cc_start: 0.5840 (ttmt) cc_final: 0.5302 (tttp) REVERT: J 60 LYS cc_start: 0.7840 (mttt) cc_final: 0.7306 (tttm) REVERT: J 94 PHE cc_start: 0.7679 (p90) cc_final: 0.5194 (t80) REVERT: J 96 LYS cc_start: 0.5533 (ttmt) cc_final: 0.5071 (tttm) outliers start: 10 outliers final: 0 residues processed: 96 average time/residue: 1.1871 time to fit residues: 117.6775 Evaluate side-chains 68 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 4080 Z= 0.314 Angle : 0.766 8.333 5510 Z= 0.456 Chirality : 0.061 0.256 720 Planarity : 0.003 0.018 680 Dihedral : 5.613 17.365 590 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 6.59 % Allowed : 19.51 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.97 (0.24), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.19), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.009 HIS C 50 PHE 0.006 0.002 PHE F 94 TYR 0.004 0.001 TYR G 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 80 time to evaluate : 0.437 Fit side-chains REVERT: A 57 GLU cc_start: 0.8035 (pt0) cc_final: 0.7698 (pt0) REVERT: A 60 LYS cc_start: 0.8402 (mttt) cc_final: 0.7974 (mttp) REVERT: A 96 LYS cc_start: 0.6047 (ttmt) cc_final: 0.5461 (tttp) REVERT: B 45 LYS cc_start: 0.7129 (pttt) cc_final: 0.6739 (ptpt) REVERT: B 60 LYS cc_start: 0.8122 (mttt) cc_final: 0.7788 (mtpt) REVERT: B 96 LYS cc_start: 0.6436 (ttmt) cc_final: 0.5801 (tttm) REVERT: C 45 LYS cc_start: 0.6899 (pttt) cc_final: 0.6567 (ptmt) REVERT: C 60 LYS cc_start: 0.8108 (mttt) cc_final: 0.7816 (mttp) REVERT: C 96 LYS cc_start: 0.5816 (ttmt) cc_final: 0.5162 (tttm) REVERT: D 60 LYS cc_start: 0.8205 (mttt) cc_final: 0.7940 (mttp) REVERT: D 94 PHE cc_start: 0.7624 (p90) cc_final: 0.7172 (p90) REVERT: D 96 LYS cc_start: 0.5637 (ttmt) cc_final: 0.5114 (tttm) REVERT: E 57 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8122 (pt0) REVERT: E 60 LYS cc_start: 0.8273 (mttt) cc_final: 0.7776 (mtpt) REVERT: E 94 PHE cc_start: 0.7647 (p90) cc_final: 0.7338 (p90) REVERT: E 96 LYS cc_start: 0.5416 (ttmt) cc_final: 0.4747 (tttp) REVERT: F 60 LYS cc_start: 0.8267 (mttt) cc_final: 0.7742 (mtpt) REVERT: F 94 PHE cc_start: 0.7537 (p90) cc_final: 0.7133 (p90) REVERT: F 96 LYS cc_start: 0.5822 (ttmt) cc_final: 0.5216 (tttp) REVERT: G 96 LYS cc_start: 0.4863 (ttmt) cc_final: 0.4448 (tttm) REVERT: H 60 LYS cc_start: 0.7831 (mttt) cc_final: 0.7468 (mttp) REVERT: H 96 LYS cc_start: 0.5314 (ttmt) cc_final: 0.4856 (tttp) REVERT: I 60 LYS cc_start: 0.8081 (mttt) cc_final: 0.7456 (tttm) REVERT: I 94 PHE cc_start: 0.7651 (p90) cc_final: 0.5249 (m-80) REVERT: I 96 LYS cc_start: 0.5628 (ttmt) cc_final: 0.5051 (tttp) REVERT: J 60 LYS cc_start: 0.7831 (mttt) cc_final: 0.7368 (tttm) REVERT: J 94 PHE cc_start: 0.7724 (p90) cc_final: 0.5438 (t80) REVERT: J 96 LYS cc_start: 0.5328 (ttmt) cc_final: 0.4917 (tttm) outliers start: 27 outliers final: 16 residues processed: 87 average time/residue: 1.1678 time to fit residues: 104.9748 Evaluate side-chains 88 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 71 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 20.0000 chunk 14 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4080 Z= 0.278 Angle : 0.709 7.998 5510 Z= 0.424 Chirality : 0.059 0.253 720 Planarity : 0.003 0.017 680 Dihedral : 5.266 14.802 590 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 12.68 % Allowed : 15.61 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.26), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.20), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.008 HIS H 50 PHE 0.019 0.002 PHE C 94 TYR 0.004 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 80 time to evaluate : 0.406 Fit side-chains REVERT: A 60 LYS cc_start: 0.8321 (mttt) cc_final: 0.7899 (mttp) REVERT: A 96 LYS cc_start: 0.6123 (ttmt) cc_final: 0.5542 (tttp) REVERT: B 45 LYS cc_start: 0.7072 (pttt) cc_final: 0.6732 (ptpt) REVERT: B 60 LYS cc_start: 0.8057 (mttt) cc_final: 0.7674 (mtpt) REVERT: B 96 LYS cc_start: 0.6509 (ttmt) cc_final: 0.5854 (tttm) REVERT: C 45 LYS cc_start: 0.6725 (pttt) cc_final: 0.6401 (ptmt) REVERT: C 60 LYS cc_start: 0.8027 (mttt) cc_final: 0.7725 (mttp) REVERT: C 96 LYS cc_start: 0.5746 (ttmt) cc_final: 0.5175 (tttm) REVERT: D 60 LYS cc_start: 0.8115 (mttt) cc_final: 0.7844 (mttp) REVERT: D 94 PHE cc_start: 0.7503 (p90) cc_final: 0.7173 (p90) REVERT: D 96 LYS cc_start: 0.5705 (ttmt) cc_final: 0.5190 (tttm) REVERT: E 57 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8219 (pt0) REVERT: E 60 LYS cc_start: 0.8193 (mttt) cc_final: 0.7684 (mtpt) REVERT: E 94 PHE cc_start: 0.7643 (p90) cc_final: 0.7346 (p90) REVERT: E 96 LYS cc_start: 0.5409 (ttmt) cc_final: 0.4741 (tttp) REVERT: F 45 LYS cc_start: 0.7608 (OUTLIER) cc_final: 0.7053 (ptpt) REVERT: F 60 LYS cc_start: 0.8138 (mttt) cc_final: 0.7618 (mtpt) REVERT: F 94 PHE cc_start: 0.7533 (p90) cc_final: 0.7259 (p90) REVERT: F 96 LYS cc_start: 0.5723 (ttmt) cc_final: 0.5136 (tttp) REVERT: G 96 LYS cc_start: 0.4866 (ttmt) cc_final: 0.4440 (tttm) REVERT: H 60 LYS cc_start: 0.7861 (mttt) cc_final: 0.7474 (mttp) REVERT: H 96 LYS cc_start: 0.5282 (ttmt) cc_final: 0.4818 (tttp) REVERT: I 60 LYS cc_start: 0.8037 (mttt) cc_final: 0.7426 (tttm) REVERT: I 94 PHE cc_start: 0.7639 (p90) cc_final: 0.5207 (m-80) REVERT: I 96 LYS cc_start: 0.5631 (ttmt) cc_final: 0.5040 (tttp) REVERT: J 57 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7855 (pt0) REVERT: J 60 LYS cc_start: 0.7829 (mttt) cc_final: 0.7361 (tttm) REVERT: J 94 PHE cc_start: 0.7641 (p90) cc_final: 0.5430 (t80) REVERT: J 96 LYS cc_start: 0.5316 (ttmt) cc_final: 0.4901 (tttm) outliers start: 52 outliers final: 38 residues processed: 106 average time/residue: 0.9597 time to fit residues: 105.6802 Evaluate side-chains 109 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 68 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 21 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 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 : 0.005 0.036 4080 Z= 0.332 Angle : 0.755 8.232 5510 Z= 0.451 Chirality : 0.061 0.268 720 Planarity : 0.003 0.017 680 Dihedral : 5.436 15.278 590 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 11.95 % Allowed : 17.07 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.26), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.20), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.009 HIS C 50 PHE 0.011 0.002 PHE C 94 TYR 0.006 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 71 time to evaluate : 0.469 Fit side-chains REVERT: A 60 LYS cc_start: 0.8257 (mttt) cc_final: 0.7850 (mttp) REVERT: A 96 LYS cc_start: 0.6419 (ttmt) cc_final: 0.5828 (tttp) REVERT: B 45 LYS cc_start: 0.7093 (pttt) cc_final: 0.6751 (ptpt) REVERT: B 60 LYS cc_start: 0.8022 (mttt) cc_final: 0.7652 (mtpt) REVERT: B 96 LYS cc_start: 0.6520 (ttmt) cc_final: 0.5853 (tttm) REVERT: C 45 LYS cc_start: 0.6653 (pttt) cc_final: 0.6340 (ptmt) REVERT: C 60 LYS cc_start: 0.8023 (mttt) cc_final: 0.7717 (mttp) REVERT: C 96 LYS cc_start: 0.5793 (ttmt) cc_final: 0.5256 (tttm) REVERT: D 60 LYS cc_start: 0.8031 (mttt) cc_final: 0.7731 (mttp) REVERT: D 94 PHE cc_start: 0.7540 (p90) cc_final: 0.7228 (p90) REVERT: D 96 LYS cc_start: 0.5648 (ttmt) cc_final: 0.5211 (tttm) REVERT: E 60 LYS cc_start: 0.8189 (mttt) cc_final: 0.7659 (mtpt) REVERT: E 96 LYS cc_start: 0.5367 (ttmt) cc_final: 0.4776 (tttp) REVERT: F 45 LYS cc_start: 0.7526 (OUTLIER) cc_final: 0.6975 (ptpt) REVERT: F 60 LYS cc_start: 0.8123 (mttt) cc_final: 0.7589 (mtpt) REVERT: F 94 PHE cc_start: 0.7558 (p90) cc_final: 0.7268 (p90) REVERT: F 96 LYS cc_start: 0.5800 (ttmt) cc_final: 0.5236 (tttp) REVERT: G 96 LYS cc_start: 0.4846 (ttmt) cc_final: 0.4413 (tttm) REVERT: H 60 LYS cc_start: 0.7874 (mttt) cc_final: 0.7485 (mttp) REVERT: H 96 LYS cc_start: 0.5304 (ttmt) cc_final: 0.4845 (tttp) REVERT: I 60 LYS cc_start: 0.8085 (mttt) cc_final: 0.7457 (tttm) REVERT: I 94 PHE cc_start: 0.7679 (p90) cc_final: 0.5192 (m-80) REVERT: I 96 LYS cc_start: 0.5559 (ttmt) cc_final: 0.4983 (tttp) REVERT: J 57 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7957 (pt0) REVERT: J 60 LYS cc_start: 0.7852 (mttt) cc_final: 0.7398 (tttm) REVERT: J 94 PHE cc_start: 0.7483 (p90) cc_final: 0.5347 (t80) REVERT: J 96 LYS cc_start: 0.5287 (ttmt) cc_final: 0.4802 (tmtm) outliers start: 49 outliers final: 42 residues processed: 97 average time/residue: 0.9978 time to fit residues: 100.4502 Evaluate side-chains 113 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 69 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 4080 Z= 0.189 Angle : 0.616 6.379 5510 Z= 0.370 Chirality : 0.056 0.223 720 Planarity : 0.003 0.015 680 Dihedral : 4.843 16.219 590 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 10.24 % Allowed : 20.00 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.27), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.21), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.007 HIS H 50 PHE 0.010 0.002 PHE C 94 TYR 0.003 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 79 time to evaluate : 0.454 Fit side-chains REVERT: A 60 LYS cc_start: 0.8250 (mttt) cc_final: 0.7828 (mttp) REVERT: A 96 LYS cc_start: 0.6409 (ttmt) cc_final: 0.5787 (tttp) REVERT: B 60 LYS cc_start: 0.7984 (mttt) cc_final: 0.7582 (mtpt) REVERT: B 96 LYS cc_start: 0.6565 (ttmt) cc_final: 0.5887 (tttm) REVERT: C 45 LYS cc_start: 0.6596 (pttt) cc_final: 0.6297 (ptmt) REVERT: C 60 LYS cc_start: 0.7977 (mttt) cc_final: 0.7688 (mttm) REVERT: C 96 LYS cc_start: 0.5637 (ttmt) cc_final: 0.5322 (tttm) REVERT: D 60 LYS cc_start: 0.7997 (mttt) cc_final: 0.7708 (mttp) REVERT: D 94 PHE cc_start: 0.7459 (p90) cc_final: 0.7180 (p90) REVERT: D 96 LYS cc_start: 0.5710 (ttmt) cc_final: 0.5195 (tttm) REVERT: E 94 PHE cc_start: 0.7604 (p90) cc_final: 0.7278 (p90) REVERT: E 96 LYS cc_start: 0.5481 (ttmt) cc_final: 0.4798 (tttp) REVERT: F 57 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8179 (pt0) REVERT: F 60 LYS cc_start: 0.8081 (mttt) cc_final: 0.7567 (mtpt) REVERT: F 94 PHE cc_start: 0.7600 (p90) cc_final: 0.7377 (p90) REVERT: F 96 LYS cc_start: 0.5750 (ttmt) cc_final: 0.5196 (tttp) REVERT: G 96 LYS cc_start: 0.4799 (ttmt) cc_final: 0.4379 (tttm) REVERT: H 60 LYS cc_start: 0.7726 (mttt) cc_final: 0.7378 (mttp) REVERT: H 96 LYS cc_start: 0.5274 (ttmt) cc_final: 0.4814 (tttm) REVERT: I 60 LYS cc_start: 0.8012 (mttt) cc_final: 0.7410 (tttm) REVERT: I 94 PHE cc_start: 0.7588 (p90) cc_final: 0.5170 (m-80) REVERT: I 96 LYS cc_start: 0.5617 (ttmt) cc_final: 0.5021 (tttp) REVERT: J 57 GLU cc_start: 0.8143 (pt0) cc_final: 0.7749 (pt0) REVERT: J 60 LYS cc_start: 0.7725 (mttt) cc_final: 0.7314 (tttp) REVERT: J 94 PHE cc_start: 0.7525 (p90) cc_final: 0.5375 (t80) REVERT: J 96 LYS cc_start: 0.5285 (ttmt) cc_final: 0.4877 (tttm) outliers start: 42 outliers final: 35 residues processed: 101 average time/residue: 0.8801 time to fit residues: 92.8453 Evaluate side-chains 106 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 70 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 20.0000 chunk 46 optimal weight: 6.9990 chunk 5 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 4080 Z= 0.471 Angle : 0.838 9.619 5510 Z= 0.499 Chirality : 0.064 0.299 720 Planarity : 0.004 0.022 680 Dihedral : 5.792 16.328 590 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.05 % Favored : 88.95 % Rotamer: Outliers : 12.93 % Allowed : 16.83 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.26), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.20), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.018 0.009 HIS C 50 PHE 0.006 0.001 PHE A 94 TYR 0.009 0.002 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 64 time to evaluate : 0.473 Fit side-chains REVERT: A 57 GLU cc_start: 0.8082 (pt0) cc_final: 0.7809 (pt0) REVERT: A 60 LYS cc_start: 0.8279 (mttt) cc_final: 0.7855 (mttp) REVERT: A 96 LYS cc_start: 0.6449 (ttmt) cc_final: 0.5800 (tttp) REVERT: B 60 LYS cc_start: 0.8006 (mttt) cc_final: 0.7644 (mtpt) REVERT: B 96 LYS cc_start: 0.6514 (ttmt) cc_final: 0.5860 (tttm) REVERT: C 45 LYS cc_start: 0.6786 (pttt) cc_final: 0.6433 (ptmt) REVERT: C 60 LYS cc_start: 0.8054 (mttt) cc_final: 0.7738 (mttp) REVERT: C 96 LYS cc_start: 0.5633 (ttmt) cc_final: 0.5334 (tttm) REVERT: D 60 LYS cc_start: 0.8049 (mttt) cc_final: 0.7814 (mttp) REVERT: D 96 LYS cc_start: 0.5714 (ttmt) cc_final: 0.5295 (tttm) REVERT: E 60 LYS cc_start: 0.8197 (mttt) cc_final: 0.7695 (mtpt) REVERT: E 96 LYS cc_start: 0.5319 (ttmt) cc_final: 0.4764 (tttp) REVERT: F 45 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7003 (ptpt) REVERT: F 57 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8304 (pt0) REVERT: F 60 LYS cc_start: 0.8122 (mttt) cc_final: 0.7598 (mtpt) REVERT: F 94 PHE cc_start: 0.7641 (p90) cc_final: 0.7323 (p90) REVERT: F 96 LYS cc_start: 0.5673 (ttmt) cc_final: 0.5166 (tttp) REVERT: G 96 LYS cc_start: 0.4844 (ttmt) cc_final: 0.4450 (tttm) REVERT: H 60 LYS cc_start: 0.7772 (mttt) cc_final: 0.7383 (mttp) REVERT: H 96 LYS cc_start: 0.5325 (ttmt) cc_final: 0.4828 (tttp) REVERT: I 60 LYS cc_start: 0.8105 (mttt) cc_final: 0.7512 (tttm) REVERT: I 94 PHE cc_start: 0.7782 (p90) cc_final: 0.5140 (m-80) REVERT: I 96 LYS cc_start: 0.5538 (ttmt) cc_final: 0.4989 (tttp) REVERT: J 57 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.8001 (pt0) REVERT: J 60 LYS cc_start: 0.7845 (mttt) cc_final: 0.7309 (tttm) REVERT: J 94 PHE cc_start: 0.7539 (p90) cc_final: 0.5366 (t80) REVERT: J 96 LYS cc_start: 0.5290 (ttmt) cc_final: 0.4774 (tmtm) outliers start: 53 outliers final: 40 residues processed: 97 average time/residue: 0.9258 time to fit residues: 93.3035 Evaluate side-chains 106 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 63 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 48 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 4080 Z= 0.455 Angle : 0.833 9.319 5510 Z= 0.495 Chirality : 0.063 0.298 720 Planarity : 0.004 0.022 680 Dihedral : 5.826 16.880 590 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 11.71 % Allowed : 18.29 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.26), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.20), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.009 HIS C 50 PHE 0.013 0.002 PHE D 94 TYR 0.009 0.002 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 67 time to evaluate : 0.473 Fit side-chains REVERT: A 57 GLU cc_start: 0.8079 (pt0) cc_final: 0.7807 (pt0) REVERT: A 60 LYS cc_start: 0.8254 (mttt) cc_final: 0.7846 (mttp) REVERT: A 96 LYS cc_start: 0.6436 (ttmt) cc_final: 0.5832 (tttp) REVERT: B 60 LYS cc_start: 0.8021 (mttt) cc_final: 0.7656 (mtpt) REVERT: B 96 LYS cc_start: 0.6516 (ttmt) cc_final: 0.5853 (tttm) REVERT: C 45 LYS cc_start: 0.7098 (pttt) cc_final: 0.6756 (ptmt) REVERT: C 60 LYS cc_start: 0.8064 (mttt) cc_final: 0.7749 (mttm) REVERT: C 96 LYS cc_start: 0.5636 (ttmt) cc_final: 0.5343 (tttm) REVERT: D 60 LYS cc_start: 0.8052 (mttt) cc_final: 0.7769 (mttp) REVERT: D 96 LYS cc_start: 0.5712 (ttmt) cc_final: 0.5309 (tttm) REVERT: E 60 LYS cc_start: 0.8207 (mttt) cc_final: 0.7699 (mtpt) REVERT: E 96 LYS cc_start: 0.5229 (ttmt) cc_final: 0.4715 (tttp) REVERT: F 45 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.7010 (ptpt) REVERT: F 57 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8310 (pt0) REVERT: F 60 LYS cc_start: 0.8127 (mttt) cc_final: 0.7605 (mtpt) REVERT: F 94 PHE cc_start: 0.7620 (p90) cc_final: 0.7304 (p90) REVERT: F 96 LYS cc_start: 0.5566 (ttmt) cc_final: 0.5097 (tttp) REVERT: G 96 LYS cc_start: 0.5018 (ttmt) cc_final: 0.4630 (tttm) REVERT: H 60 LYS cc_start: 0.7794 (mttt) cc_final: 0.7410 (mttp) REVERT: H 96 LYS cc_start: 0.5279 (ttmt) cc_final: 0.4799 (tttm) REVERT: I 57 GLU cc_start: 0.8138 (pt0) cc_final: 0.7913 (pt0) REVERT: I 60 LYS cc_start: 0.8178 (mttt) cc_final: 0.7534 (tttp) REVERT: I 94 PHE cc_start: 0.7675 (p90) cc_final: 0.5044 (m-80) REVERT: I 96 LYS cc_start: 0.5584 (ttmt) cc_final: 0.5049 (tttp) REVERT: J 57 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7998 (pt0) REVERT: J 60 LYS cc_start: 0.7903 (mttt) cc_final: 0.7326 (tttm) REVERT: J 94 PHE cc_start: 0.7537 (p90) cc_final: 0.5316 (t80) REVERT: J 96 LYS cc_start: 0.5242 (ttmt) cc_final: 0.4779 (tttm) outliers start: 48 outliers final: 42 residues processed: 97 average time/residue: 0.9820 time to fit residues: 99.0286 Evaluate side-chains 109 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 64 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 43 optimal weight: 0.0670 chunk 46 optimal weight: 1.9990 chunk 42 optimal weight: 0.1980 chunk 44 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 35 optimal weight: 20.0000 chunk 13 optimal weight: 6.9990 overall best weight: 3.0524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4080 Z= 0.239 Angle : 0.667 7.439 5510 Z= 0.399 Chirality : 0.057 0.248 720 Planarity : 0.003 0.019 680 Dihedral : 5.132 15.644 590 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 11.71 % Allowed : 19.27 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.27), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.21), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.008 HIS H 50 PHE 0.014 0.002 PHE D 94 TYR 0.004 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 72 time to evaluate : 0.458 Fit side-chains REVERT: A 60 LYS cc_start: 0.8261 (mttt) cc_final: 0.7843 (mttp) REVERT: A 96 LYS cc_start: 0.6402 (ttmt) cc_final: 0.5817 (tttp) REVERT: B 60 LYS cc_start: 0.7976 (mttt) cc_final: 0.7569 (mtpt) REVERT: B 96 LYS cc_start: 0.6560 (ttmt) cc_final: 0.5868 (tttm) REVERT: C 45 LYS cc_start: 0.6688 (pttt) cc_final: 0.6470 (ptmt) REVERT: C 60 LYS cc_start: 0.8010 (mttt) cc_final: 0.7727 (mttp) REVERT: C 96 LYS cc_start: 0.5634 (ttmt) cc_final: 0.5339 (tttm) REVERT: D 60 LYS cc_start: 0.8031 (mttt) cc_final: 0.7718 (mttp) REVERT: D 96 LYS cc_start: 0.5754 (ttmt) cc_final: 0.5326 (tttm) REVERT: E 96 LYS cc_start: 0.5339 (ttmt) cc_final: 0.4760 (tttp) REVERT: F 60 LYS cc_start: 0.8091 (mttt) cc_final: 0.7576 (mtpt) REVERT: F 94 PHE cc_start: 0.7629 (p90) cc_final: 0.7361 (p90) REVERT: F 96 LYS cc_start: 0.5501 (ttmt) cc_final: 0.4992 (tttp) REVERT: G 96 LYS cc_start: 0.4939 (ttmt) cc_final: 0.4548 (tttm) REVERT: H 60 LYS cc_start: 0.7692 (mttt) cc_final: 0.7332 (mttp) REVERT: H 96 LYS cc_start: 0.5325 (ttmt) cc_final: 0.4836 (tttp) REVERT: I 57 GLU cc_start: 0.8011 (pt0) cc_final: 0.7755 (pt0) REVERT: I 60 LYS cc_start: 0.8059 (mttt) cc_final: 0.7468 (tttm) REVERT: I 94 PHE cc_start: 0.7685 (p90) cc_final: 0.5097 (m-80) REVERT: I 96 LYS cc_start: 0.5452 (ttmt) cc_final: 0.4953 (tttp) REVERT: J 57 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7885 (pt0) REVERT: J 60 LYS cc_start: 0.7807 (mttt) cc_final: 0.7266 (tttm) REVERT: J 94 PHE cc_start: 0.7561 (p90) cc_final: 0.5311 (t80) REVERT: J 96 LYS cc_start: 0.5183 (ttmt) cc_final: 0.4765 (tttm) outliers start: 48 outliers final: 42 residues processed: 97 average time/residue: 0.8772 time to fit residues: 88.8111 Evaluate side-chains 111 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 68 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 29 optimal weight: 20.0000 chunk 47 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 4080 Z= 0.486 Angle : 0.857 9.805 5510 Z= 0.509 Chirality : 0.064 0.309 720 Planarity : 0.004 0.019 680 Dihedral : 5.879 16.809 590 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 11.46 % Allowed : 20.24 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.27), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.20), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.009 HIS C 50 PHE 0.011 0.002 PHE D 94 TYR 0.009 0.002 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 64 time to evaluate : 0.422 Fit side-chains REVERT: A 60 LYS cc_start: 0.8256 (mttt) cc_final: 0.7845 (mttp) REVERT: A 96 LYS cc_start: 0.6532 (ttmt) cc_final: 0.5928 (tttp) REVERT: B 60 LYS cc_start: 0.8010 (mttt) cc_final: 0.7638 (mtpt) REVERT: B 96 LYS cc_start: 0.6526 (ttmt) cc_final: 0.5870 (tttm) REVERT: C 45 LYS cc_start: 0.7105 (pttt) cc_final: 0.6578 (ptpt) REVERT: C 60 LYS cc_start: 0.8066 (mttt) cc_final: 0.7754 (mttm) REVERT: C 96 LYS cc_start: 0.5632 (ttmt) cc_final: 0.5340 (tttm) REVERT: D 60 LYS cc_start: 0.8051 (mttt) cc_final: 0.7764 (mttp) REVERT: D 94 PHE cc_start: 0.7562 (p90) cc_final: 0.7317 (p90) REVERT: D 96 LYS cc_start: 0.5724 (ttmt) cc_final: 0.5257 (tttm) REVERT: E 60 LYS cc_start: 0.8208 (mttt) cc_final: 0.7698 (mtpt) REVERT: E 96 LYS cc_start: 0.5280 (ttmt) cc_final: 0.4745 (tttp) REVERT: F 45 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.7009 (ptpt) REVERT: F 60 LYS cc_start: 0.8127 (mttt) cc_final: 0.7594 (mtpt) REVERT: F 94 PHE cc_start: 0.7700 (p90) cc_final: 0.7301 (p90) REVERT: F 96 LYS cc_start: 0.5514 (ttmt) cc_final: 0.5052 (tttp) REVERT: G 96 LYS cc_start: 0.4983 (ttmt) cc_final: 0.4580 (tttm) REVERT: H 60 LYS cc_start: 0.7764 (mttt) cc_final: 0.7366 (mttp) REVERT: H 96 LYS cc_start: 0.5269 (ttmt) cc_final: 0.4785 (tttm) REVERT: I 57 GLU cc_start: 0.8122 (pt0) cc_final: 0.7910 (pt0) REVERT: I 60 LYS cc_start: 0.8186 (mttt) cc_final: 0.7532 (tttm) REVERT: I 94 PHE cc_start: 0.7705 (p90) cc_final: 0.4974 (m-80) REVERT: I 96 LYS cc_start: 0.5498 (ttmt) cc_final: 0.5019 (tttp) REVERT: J 60 LYS cc_start: 0.7882 (mttt) cc_final: 0.7650 (mttm) REVERT: J 94 PHE cc_start: 0.7514 (p90) cc_final: 0.5336 (t80) REVERT: J 96 LYS cc_start: 0.5195 (ttmt) cc_final: 0.4749 (tttm) outliers start: 47 outliers final: 42 residues processed: 93 average time/residue: 0.9721 time to fit residues: 94.0037 Evaluate side-chains 106 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 63 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 5 optimal weight: 20.0000 chunk 11 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4080 Z= 0.195 Angle : 0.639 6.901 5510 Z= 0.383 Chirality : 0.056 0.239 720 Planarity : 0.003 0.017 680 Dihedral : 4.995 16.520 590 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 10.00 % Allowed : 22.20 % Favored : 67.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.28), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (0.21), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.007 HIS H 50 PHE 0.012 0.002 PHE E 94 TYR 0.003 0.001 TYR C 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 77 time to evaluate : 0.458 Fit side-chains REVERT: A 60 LYS cc_start: 0.8304 (mttt) cc_final: 0.7896 (mttp) REVERT: A 96 LYS cc_start: 0.6333 (ttmt) cc_final: 0.5761 (tttp) REVERT: B 60 LYS cc_start: 0.7984 (mttt) cc_final: 0.7562 (mtpt) REVERT: B 96 LYS cc_start: 0.6559 (ttmt) cc_final: 0.5870 (tttm) REVERT: C 60 LYS cc_start: 0.8009 (mttt) cc_final: 0.7722 (mttp) REVERT: C 96 LYS cc_start: 0.5631 (ttmt) cc_final: 0.5341 (tttm) REVERT: D 60 LYS cc_start: 0.8000 (mttt) cc_final: 0.7680 (mttp) REVERT: D 96 LYS cc_start: 0.5766 (ttmt) cc_final: 0.5248 (tttm) REVERT: E 60 LYS cc_start: 0.8154 (mttt) cc_final: 0.7643 (mtpt) REVERT: E 96 LYS cc_start: 0.5497 (ttmt) cc_final: 0.4848 (tttp) REVERT: F 60 LYS cc_start: 0.8093 (mttt) cc_final: 0.7581 (mtpt) REVERT: F 94 PHE cc_start: 0.7574 (p90) cc_final: 0.7351 (p90) REVERT: F 96 LYS cc_start: 0.5495 (ttmt) cc_final: 0.4992 (tttp) REVERT: G 96 LYS cc_start: 0.4899 (ttmt) cc_final: 0.4504 (tttm) REVERT: H 60 LYS cc_start: 0.7680 (mttt) cc_final: 0.7314 (mttp) REVERT: H 96 LYS cc_start: 0.5266 (ttmt) cc_final: 0.4803 (tttp) REVERT: I 57 GLU cc_start: 0.7971 (pt0) cc_final: 0.7710 (pt0) REVERT: I 60 LYS cc_start: 0.8009 (mttt) cc_final: 0.7432 (tttm) REVERT: I 94 PHE cc_start: 0.7654 (p90) cc_final: 0.5033 (m-80) REVERT: I 96 LYS cc_start: 0.5482 (ttmt) cc_final: 0.4970 (tttp) REVERT: J 60 LYS cc_start: 0.7827 (mttt) cc_final: 0.7265 (tttm) REVERT: J 94 PHE cc_start: 0.7638 (p90) cc_final: 0.5287 (t80) REVERT: J 96 LYS cc_start: 0.5256 (ttmt) cc_final: 0.4824 (tttm) outliers start: 41 outliers final: 41 residues processed: 100 average time/residue: 0.9148 time to fit residues: 95.4039 Evaluate side-chains 112 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 71 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 28 optimal weight: 0.2980 chunk 45 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 overall best weight: 4.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.202618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.173462 restraints weight = 4431.752| |-----------------------------------------------------------------------------| r_work (start): 0.4437 rms_B_bonded: 2.60 r_work: 0.4348 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.4236 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.4236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 4080 Z= 0.369 Angle : 0.771 8.762 5510 Z= 0.460 Chirality : 0.061 0.286 720 Planarity : 0.003 0.016 680 Dihedral : 5.535 19.169 590 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.35 % Favored : 89.65 % Rotamer: Outliers : 10.49 % Allowed : 21.22 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.27), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (0.21), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.008 HIS C 50 PHE 0.010 0.002 PHE E 94 TYR 0.006 0.001 TYR A 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1963.36 seconds wall clock time: 35 minutes 47.65 seconds (2147.65 seconds total)