Starting phenix.real_space_refine on Fri Mar 15 09:40:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nci_12267/03_2024/7nci_12267.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nci_12267/03_2024/7nci_12267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nci_12267/03_2024/7nci_12267.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nci_12267/03_2024/7nci_12267.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nci_12267/03_2024/7nci_12267.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nci_12267/03_2024/7nci_12267.pdb" } resolution = 3.55 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= 0.001 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: 4 Type Number sf(0) Gaussians C 3408 2.51 5 N 972 2.21 5 O 1116 1.98 5 H 5796 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11292 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 941 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain breaks: 1 Chain: "B" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 941 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain breaks: 1 Chain: "C" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 941 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain breaks: 1 Chain: "D" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 941 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain breaks: 1 Chain: "E" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 941 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain breaks: 1 Chain: "F" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 941 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain breaks: 1 Chain: "G" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 941 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain breaks: 1 Chain: "H" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 941 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain breaks: 1 Chain: "I" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 941 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain breaks: 1 Chain: "J" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 941 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain breaks: 1 Chain: "K" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 941 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain breaks: 1 Chain: "L" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 941 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain breaks: 1 Time building chain proxies: 5.19, per 1000 atoms: 0.46 Number of scatterers: 11292 At special positions: 0 Unit cell: (119.9, 95.7, 56.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 1116 8.00 N 972 7.00 C 3408 6.00 H 5796 1.00 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: 8.58 Conformation dependent library (CDL) restraints added in 1.2 seconds 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1368 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 21 removed outlier: 7.195A pdb=" N ALA A 18 " --> pdb=" O ALA B 19 " (cutoff:3.500A) removed outlier: 9.452A pdb=" N LYS B 21 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N GLU A 20 " --> pdb=" O LYS B 21 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA C 19 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS C 21 " --> pdb=" O GLU B 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 41 removed outlier: 5.672A pdb=" N TYR A 39 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N TYR B 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N TYR C 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY D 41 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N TYR E 39 " --> pdb=" O VAL F 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 55 removed outlier: 4.650A pdb=" N VAL A 49 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N GLY B 51 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N GLY A 51 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ALA B 53 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ALA A 53 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL B 55 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL A 55 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 9.220A pdb=" N VAL B 49 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 10.372A pdb=" N VAL C 52 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLY B 51 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N THR C 54 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA B 53 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY D 51 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL C 52 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ALA D 53 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N THR C 54 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL D 55 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 9.025A pdb=" N HIS D 50 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ALA E 53 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 9.108A pdb=" N VAL D 52 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 10.794A pdb=" N VAL E 55 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 9.009A pdb=" N THR D 54 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N HIS E 50 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ALA F 53 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 9.024A pdb=" N VAL E 52 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 10.619A pdb=" N VAL F 55 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N THR E 54 " --> pdb=" O VAL F 55 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 63 through 64 removed outlier: 7.057A pdb=" N VAL A 63 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL B 63 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N VAL C 66 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL D 66 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL E 63 " --> pdb=" O THR F 64 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 85 through 88 removed outlier: 6.399A pdb=" N GLY B 86 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLY C 86 " --> pdb=" O SER D 87 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N ALA D 89 " --> pdb=" O GLY C 86 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE C 88 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY D 86 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N ALA E 89 " --> pdb=" O GLY D 86 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE D 88 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLY E 86 " --> pdb=" O SER F 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 18 through 21 removed outlier: 3.790A pdb=" N ALA E 19 " --> pdb=" O ALA D 18 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS E 21 " --> pdb=" O GLU D 20 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA F 17 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS F 21 " --> pdb=" O GLU E 20 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 18 through 21 removed outlier: 7.012A pdb=" N ALA G 18 " --> pdb=" O ALA H 19 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N LYS H 21 " --> pdb=" O ALA G 18 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N GLU G 20 " --> pdb=" O LYS H 21 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA I 19 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS I 21 " --> pdb=" O GLU H 20 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA J 19 " --> pdb=" O ALA I 18 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU I 20 " --> pdb=" O ALA J 19 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS J 21 " --> pdb=" O GLU I 20 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA K 19 " --> pdb=" O ALA J 18 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS K 21 " --> pdb=" O GLU J 20 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA L 19 " --> pdb=" O ALA K 18 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU K 20 " --> pdb=" O ALA L 19 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS L 21 " --> pdb=" O GLU K 20 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 39 through 41 removed outlier: 5.540A pdb=" N TYR G 39 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N TYR H 39 " --> pdb=" O VAL I 40 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N TYR I 39 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N TYR J 39 " --> pdb=" O VAL K 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 49 through 55 removed outlier: 9.310A pdb=" N VAL G 49 " --> pdb=" O HIS H 50 " (cutoff:3.500A) removed outlier: 10.589A pdb=" N VAL H 52 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLY G 51 " --> pdb=" O VAL H 52 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N THR H 54 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA G 53 " --> pdb=" O THR H 54 " (cutoff:3.500A) removed outlier: 9.070A pdb=" N HIS H 50 " --> pdb=" O GLY I 51 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ALA I 53 " --> pdb=" O HIS H 50 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N VAL H 52 " --> pdb=" O ALA I 53 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N VAL I 55 " --> pdb=" O VAL H 52 " (cutoff:3.500A) removed outlier: 8.940A pdb=" N THR H 54 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N HIS I 50 " --> pdb=" O GLY J 51 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ALA J 53 " --> pdb=" O HIS I 50 " (cutoff:3.500A) removed outlier: 9.026A pdb=" N VAL I 52 " --> pdb=" O ALA J 53 " (cutoff:3.500A) removed outlier: 10.661A pdb=" N VAL J 55 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 8.932A pdb=" N THR I 54 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 9.182A pdb=" N HIS J 50 " --> pdb=" O GLY K 51 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ALA K 53 " --> pdb=" O HIS J 50 " (cutoff:3.500A) removed outlier: 9.085A pdb=" N VAL J 52 " --> pdb=" O ALA K 53 " (cutoff:3.500A) removed outlier: 10.710A pdb=" N VAL K 55 " --> pdb=" O VAL J 52 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N THR J 54 " --> pdb=" O VAL K 55 " (cutoff:3.500A) removed outlier: 9.203A pdb=" N HIS K 50 " --> pdb=" O GLY L 51 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ALA L 53 " --> pdb=" O HIS K 50 " (cutoff:3.500A) removed outlier: 9.215A pdb=" N VAL K 52 " --> pdb=" O ALA L 53 " (cutoff:3.500A) removed outlier: 10.709A pdb=" N VAL L 55 " --> pdb=" O VAL K 52 " (cutoff:3.500A) removed outlier: 8.950A pdb=" N THR K 54 " --> pdb=" O VAL L 55 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 63 through 66 removed outlier: 3.579A pdb=" N VAL H 66 " --> pdb=" O ASN G 65 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N VAL I 63 " --> pdb=" O THR J 64 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL J 63 " --> pdb=" O THR K 64 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N VAL K 63 " --> pdb=" O THR L 64 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 86 through 90 removed outlier: 6.516A pdb=" N GLY G 86 " --> pdb=" O SER H 87 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N ALA H 89 " --> pdb=" O GLY G 86 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE G 88 " --> pdb=" O ALA H 89 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLY H 86 " --> pdb=" O SER I 87 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLY I 86 " --> pdb=" O SER J 87 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLY J 86 " --> pdb=" O SER K 87 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N ALA K 89 " --> pdb=" O GLY J 86 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE J 88 " --> pdb=" O ALA K 89 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLY K 86 " --> pdb=" O SER L 87 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N ALA L 89 " --> pdb=" O GLY K 86 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE K 88 " --> pdb=" O ALA L 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 18 hydrogen bonds defined for protein. 51 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: 3.53 Time building geometry restraints manager: 8.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 0.97: 1817 0.97 - 1.12: 3979 1.12 - 1.28: 984 1.28 - 1.43: 1075 1.43 - 1.59: 3437 Bond restraints: 11292 Sorted by residual: bond pdb=" N VAL G 40 " pdb=" CA VAL G 40 " ideal model delta sigma weight residual 1.460 1.501 -0.041 1.44e-02 4.82e+03 8.11e+00 bond pdb=" N VAL J 40 " pdb=" CA VAL J 40 " ideal model delta sigma weight residual 1.461 1.501 -0.040 1.44e-02 4.82e+03 7.85e+00 bond pdb=" CA ILE A 88 " pdb=" CB ILE A 88 " ideal model delta sigma weight residual 1.548 1.587 -0.040 1.46e-02 4.69e+03 7.35e+00 bond pdb=" N VAL B 40 " pdb=" CA VAL B 40 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.44e-02 4.82e+03 5.53e+00 bond pdb=" N VAL A 40 " pdb=" CA VAL A 40 " ideal model delta sigma weight residual 1.460 1.490 -0.030 1.35e-02 5.49e+03 4.93e+00 ... (remaining 11287 not shown) Histogram of bond angle deviations from ideal: 73.18 - 84.57: 6 84.57 - 95.96: 0 95.96 - 107.35: 1333 107.35 - 118.74: 15344 118.74 - 130.13: 3849 Bond angle restraints: 20532 Sorted by residual: angle pdb=" N THR C 44 " pdb=" CA THR C 44 " pdb=" HA THR C 44 " ideal model delta sigma weight residual 110.00 73.18 36.82 3.00e+00 1.11e-01 1.51e+02 angle pdb=" C THR I 44 " pdb=" CA THR I 44 " pdb=" HA THR I 44 " ideal model delta sigma weight residual 109.00 73.72 35.28 3.00e+00 1.11e-01 1.38e+02 angle pdb=" C THR C 44 " pdb=" CA THR C 44 " pdb=" HA THR C 44 " ideal model delta sigma weight residual 109.00 74.54 34.46 3.00e+00 1.11e-01 1.32e+02 angle pdb=" N THR I 44 " pdb=" CA THR I 44 " pdb=" HA THR I 44 " ideal model delta sigma weight residual 110.00 75.68 34.32 3.00e+00 1.11e-01 1.31e+02 angle pdb=" CB THR I 44 " pdb=" CA THR I 44 " pdb=" HA THR I 44 " ideal model delta sigma weight residual 109.00 80.08 28.92 3.00e+00 1.11e-01 9.29e+01 ... (remaining 20527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 4359 17.86 - 35.72: 362 35.72 - 53.58: 141 53.58 - 71.44: 272 71.44 - 89.30: 26 Dihedral angle restraints: 5160 sinusoidal: 2904 harmonic: 2256 Sorted by residual: dihedral pdb=" C THR I 44 " pdb=" N THR I 44 " pdb=" CA THR I 44 " pdb=" CB THR I 44 " ideal model delta harmonic sigma weight residual -122.00 -136.89 14.89 0 2.50e+00 1.60e-01 3.55e+01 dihedral pdb=" CA VAL E 74 " pdb=" C VAL E 74 " pdb=" N THR E 75 " pdb=" CA THR E 75 " ideal model delta harmonic sigma weight residual 180.00 150.91 29.09 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA SER A 87 " pdb=" C SER A 87 " pdb=" N ILE A 88 " pdb=" CA ILE A 88 " ideal model delta harmonic sigma weight residual 180.00 151.03 28.97 0 5.00e+00 4.00e-02 3.36e+01 ... (remaining 5157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 740 0.107 - 0.213: 208 0.213 - 0.320: 34 0.320 - 0.427: 0 0.427 - 0.533: 2 Chirality restraints: 984 Sorted by residual: chirality pdb=" CA THR I 44 " pdb=" N THR I 44 " pdb=" C THR I 44 " pdb=" CB THR I 44 " both_signs ideal model delta sigma weight residual False 2.53 1.99 0.53 2.00e-01 2.50e+01 7.11e+00 chirality pdb=" CA THR C 44 " pdb=" N THR C 44 " pdb=" C THR C 44 " pdb=" CB THR C 44 " both_signs ideal model delta sigma weight residual False 2.53 2.05 0.48 2.00e-01 2.50e+01 5.77e+00 chirality pdb=" CB VAL J 40 " pdb=" CA VAL J 40 " pdb=" CG1 VAL J 40 " pdb=" CG2 VAL J 40 " both_signs ideal model delta sigma weight residual False -2.63 -2.91 0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 981 not shown) Planarity restraints: 1716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR L 39 " 0.077 2.00e-02 2.50e+03 3.32e-02 3.32e+01 pdb=" CG TYR L 39 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR L 39 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR L 39 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR L 39 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR L 39 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR L 39 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR L 39 " 0.021 2.00e-02 2.50e+03 pdb=" HD1 TYR L 39 " -0.038 2.00e-02 2.50e+03 pdb=" HD2 TYR L 39 " -0.021 2.00e-02 2.50e+03 pdb=" HE1 TYR L 39 " 0.025 2.00e-02 2.50e+03 pdb=" HE2 TYR L 39 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 39 " -0.025 2.00e-02 2.50e+03 3.16e-02 2.99e+01 pdb=" CG TYR B 39 " 0.076 2.00e-02 2.50e+03 pdb=" CD1 TYR B 39 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR B 39 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR B 39 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR B 39 " 0.020 2.00e-02 2.50e+03 pdb=" CZ TYR B 39 " 0.012 2.00e-02 2.50e+03 pdb=" OH TYR B 39 " -0.017 2.00e-02 2.50e+03 pdb=" HD1 TYR B 39 " -0.030 2.00e-02 2.50e+03 pdb=" HD2 TYR B 39 " -0.040 2.00e-02 2.50e+03 pdb=" HE1 TYR B 39 " -0.009 2.00e-02 2.50e+03 pdb=" HE2 TYR B 39 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 39 " 0.004 2.00e-02 2.50e+03 2.79e-02 2.33e+01 pdb=" CG TYR K 39 " -0.072 2.00e-02 2.50e+03 pdb=" CD1 TYR K 39 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR K 39 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR K 39 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR K 39 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR K 39 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR K 39 " -0.004 2.00e-02 2.50e+03 pdb=" HD1 TYR K 39 " 0.027 2.00e-02 2.50e+03 pdb=" HD2 TYR K 39 " 0.047 2.00e-02 2.50e+03 pdb=" HE1 TYR K 39 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 TYR K 39 " 0.009 2.00e-02 2.50e+03 ... (remaining 1713 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.22: 665 2.22 - 2.79: 22320 2.79 - 3.36: 26919 3.36 - 3.93: 34152 3.93 - 4.50: 52195 Nonbonded interactions: 136251 Sorted by model distance: nonbonded pdb=" H THR C 44 " pdb=" HA THR C 44 " model vdw 1.651 1.816 nonbonded pdb=" HG1 THR C 44 " pdb=" O THR D 44 " model vdw 1.680 1.850 nonbonded pdb=" HG1 THR I 44 " pdb=" O THR J 44 " model vdw 1.691 1.850 nonbonded pdb=" H THR I 44 " pdb=" HA THR I 44 " model vdw 1.692 1.816 nonbonded pdb=" HG1 THR H 44 " pdb=" O THR I 44 " model vdw 1.695 1.850 ... (remaining 136246 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' selection = chain 'K' selection = chain 'L' } 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 group one per residue 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: 0.830 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: 0.190 Extract box with map and model: 4.030 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 37.750 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6186 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 : 0.012 0.068 5496 Z= 0.789 Angle : 1.574 9.424 7416 Z= 0.948 Chirality : 0.101 0.533 984 Planarity : 0.005 0.034 924 Dihedral : 15.566 89.302 1848 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 0.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Cbeta Deviations : 0.29 % 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 (0.16), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.13), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.026 0.011 HIS L 50 TYR 0.061 0.017 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.4252 time to fit residues: 111.7116 Evaluate side-chains 111 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 HIS ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6371 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5496 Z= 0.237 Angle : 0.663 5.934 7416 Z= 0.385 Chirality : 0.053 0.385 984 Planarity : 0.002 0.009 924 Dihedral : 8.309 23.572 804 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 3.33 % Allowed : 19.63 % Favored : 77.04 % Cbeta Deviations : 0.29 % 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: -4.18 (0.16), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.13), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 50 TYR 0.020 0.003 TYR L 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 132 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 15 residues processed: 136 average time/residue: 0.3732 time to fit residues: 67.0033 Evaluate side-chains 129 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 114 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 65 ASN Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 65 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain K residue 39 TYR Chi-restraints excluded: chain K residue 65 ASN Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 46 GLU Chi-restraints excluded: chain L residue 65 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 HIS ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6466 moved from start: 0.5269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5496 Z= 0.247 Angle : 0.613 6.080 7416 Z= 0.354 Chirality : 0.054 0.393 984 Planarity : 0.002 0.011 924 Dihedral : 7.423 21.754 804 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.94 % Favored : 89.06 % Rotamer: Outliers : 7.22 % Allowed : 21.30 % Favored : 71.48 % Cbeta Deviations : 0.29 % 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 (0.21), residues: 768 helix: None (None), residues: 0 sheet: -1.73 (0.43), residues: 120 loop : -3.15 (0.16), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 50 TYR 0.017 0.002 TYR L 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 120 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 GLU cc_start: 0.6934 (pp20) cc_final: 0.6619 (pp20) outliers start: 39 outliers final: 33 residues processed: 136 average time/residue: 0.3744 time to fit residues: 65.7318 Evaluate side-chains 144 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 111 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 65 ASN Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 65 ASN Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 65 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 65 ASN Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 46 GLU Chi-restraints excluded: chain L residue 65 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 69 optimal weight: 0.0770 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 18 optimal weight: 7.9990 overall best weight: 1.5344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6538 moved from start: 0.5786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5496 Z= 0.271 Angle : 0.595 6.135 7416 Z= 0.346 Chirality : 0.054 0.390 984 Planarity : 0.002 0.008 924 Dihedral : 7.351 22.438 804 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.89 % Favored : 87.11 % Rotamer: Outliers : 8.33 % Allowed : 22.96 % Favored : 68.70 % Cbeta Deviations : 0.29 % 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: -4.28 (0.19), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.25 (0.15), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS G 50 TYR 0.015 0.002 TYR L 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 112 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 GLU cc_start: 0.7193 (pp20) cc_final: 0.6698 (pp20) REVERT: L 79 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7466 (mm-40) outliers start: 45 outliers final: 37 residues processed: 132 average time/residue: 0.3222 time to fit residues: 56.9739 Evaluate side-chains 147 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 109 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 65 ASN Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 65 ASN Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 65 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 65 ASN Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 46 GLU Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 0.2980 chunk 62 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6553 moved from start: 0.6154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5496 Z= 0.246 Angle : 0.565 6.003 7416 Z= 0.330 Chirality : 0.053 0.387 984 Planarity : 0.002 0.010 924 Dihedral : 7.076 22.715 804 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 19.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.19 % Favored : 85.81 % Rotamer: Outliers : 9.26 % Allowed : 23.33 % Favored : 67.41 % Cbeta Deviations : 0.29 % 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: -4.34 (0.20), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.30 (0.15), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS F 50 TYR 0.012 0.002 TYR J 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 109 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 42 residues processed: 130 average time/residue: 0.3168 time to fit residues: 55.2107 Evaluate side-chains 151 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 109 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 65 ASN Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 65 ASN Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 65 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 65 ASN Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 46 GLU Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 69 optimal weight: 0.0010 chunk 57 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 67 optimal weight: 0.4980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6455 moved from start: 0.6338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5496 Z= 0.157 Angle : 0.482 5.623 7416 Z= 0.282 Chirality : 0.053 0.374 984 Planarity : 0.001 0.006 924 Dihedral : 6.242 20.419 804 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.81 % Favored : 89.19 % Rotamer: Outliers : 4.81 % Allowed : 27.59 % Favored : 67.59 % Cbeta Deviations : 0.29 % 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: -4.24 (0.19), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.15), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 50 TYR 0.008 0.001 TYR J 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 119 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 GLU cc_start: 0.7122 (pp20) cc_final: 0.6599 (pp20) outliers start: 26 outliers final: 25 residues processed: 130 average time/residue: 0.3335 time to fit residues: 57.4078 Evaluate side-chains 133 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 108 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 65 ASN Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 65 ASN Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 38 optimal weight: 0.0980 chunk 69 optimal weight: 0.4980 chunk 43 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 32 optimal weight: 0.0270 chunk 27 optimal weight: 3.9990 chunk 41 optimal weight: 0.1980 overall best weight: 0.3638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6378 moved from start: 0.6656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5496 Z= 0.147 Angle : 0.454 5.254 7416 Z= 0.264 Chirality : 0.053 0.373 984 Planarity : 0.001 0.007 924 Dihedral : 5.443 17.659 804 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 4.63 % Allowed : 27.78 % Favored : 67.59 % Cbeta Deviations : 0.29 % 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: -3.80 (0.22), residues: 768 helix: None (None), residues: 0 sheet: -1.79 (0.44), residues: 120 loop : -2.97 (0.17), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS L 50 TYR 0.008 0.001 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 120 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 22 residues processed: 130 average time/residue: 0.3404 time to fit residues: 58.0478 Evaluate side-chains 131 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 109 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 65 ASN Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 65 ASN Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 65 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6518 moved from start: 0.6793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5496 Z= 0.236 Angle : 0.515 5.465 7416 Z= 0.302 Chirality : 0.053 0.387 984 Planarity : 0.002 0.009 924 Dihedral : 6.143 19.799 804 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 6.30 % Allowed : 25.93 % Favored : 67.78 % Cbeta Deviations : 0.29 % 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: -4.31 (0.20), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.28 (0.15), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 50 TYR 0.009 0.001 TYR J 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 101 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 31 residues processed: 116 average time/residue: 0.3924 time to fit residues: 60.7449 Evaluate side-chains 131 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 100 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 65 ASN Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 65 ASN Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 65 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 65 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 6.9990 chunk 38 optimal weight: 0.0770 chunk 28 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6548 moved from start: 0.6973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5496 Z= 0.233 Angle : 0.527 5.576 7416 Z= 0.308 Chirality : 0.053 0.390 984 Planarity : 0.002 0.007 924 Dihedral : 6.348 20.094 804 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 21.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.67 % Favored : 86.33 % Rotamer: Outliers : 5.93 % Allowed : 26.30 % Favored : 67.78 % Cbeta Deviations : 0.29 % 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: -4.36 (0.20), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.31 (0.15), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 50 TYR 0.011 0.001 TYR J 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 100 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 32 residues processed: 111 average time/residue: 0.3306 time to fit residues: 48.6926 Evaluate side-chains 131 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 99 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 65 ASN Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 65 ASN Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 65 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 65 ASN Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 65 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 0.0970 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 57 optimal weight: 0.1980 chunk 5 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 moved from start: 0.7136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5496 Z= 0.253 Angle : 0.541 5.602 7416 Z= 0.316 Chirality : 0.054 0.389 984 Planarity : 0.002 0.009 924 Dihedral : 6.560 19.962 804 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 23.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.45 % Favored : 85.55 % Rotamer: Outliers : 6.67 % Allowed : 25.93 % Favored : 67.41 % Cbeta Deviations : 0.29 % 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: -4.45 (0.20), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.16), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 50 TYR 0.013 0.001 TYR J 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 99 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 77 VAL cc_start: 0.4550 (OUTLIER) cc_final: 0.4269 (m) outliers start: 36 outliers final: 35 residues processed: 113 average time/residue: 0.3323 time to fit residues: 50.5783 Evaluate side-chains 134 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 98 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 65 ASN Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 65 ASN Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 65 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 65 ASN Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5322 r_free = 0.5322 target = 0.241694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5070 r_free = 0.5070 target = 0.185436 restraints weight = 26064.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.5162 r_free = 0.5162 target = 0.195025 restraints weight = 13350.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.5228 r_free = 0.5228 target = 0.202041 restraints weight = 8058.845| |-----------------------------------------------------------------------------| r_work (final): 0.5138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5990 moved from start: 0.7241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5496 Z= 0.228 Angle : 0.518 5.550 7416 Z= 0.302 Chirality : 0.053 0.387 984 Planarity : 0.002 0.007 924 Dihedral : 6.412 20.646 804 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 22.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.32 % Favored : 85.68 % Rotamer: Outliers : 6.48 % Allowed : 26.67 % Favored : 66.85 % Cbeta Deviations : 0.29 % 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: -4.47 (0.20), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.15), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 50 TYR 0.012 0.001 TYR J 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3453.23 seconds wall clock time: 61 minutes 8.14 seconds (3668.14 seconds total)