Starting phenix.real_space_refine (version: dev) on Mon Feb 20 03:35:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nci_12267/02_2023/7nci_12267.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nci_12267/02_2023/7nci_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_12267/02_2023/7nci_12267.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nci_12267/02_2023/7nci_12267.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nci_12267/02_2023/7nci_12267.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nci_12267/02_2023/7nci_12267.pdb" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 5.28, per 1000 atoms: 0.47 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: 9.03 Conformation dependent library (CDL) restraints added in 1.0 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: 0.32 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: 3.65 Time building geometry restraints manager: 9.13 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: 3611 17.86 - 35.72: 306 35.72 - 53.58: 47 53.58 - 71.44: 222 71.44 - 89.30: 26 Dihedral angle restraints: 4212 sinusoidal: 1956 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 4209 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 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. 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: 0.170 Extract box with map and model: 4.380 Check model and map are aligned: 0.160 Process input model: 36.240 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.120 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5901 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 % 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 *********************** 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 : 0.803 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: 0.4285 time to fit residues: 112.2967 Evaluate side-chains 111 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.737 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8829 ------------------------------------------------------------------------------- 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: 0.8980 chunk 54 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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: 0.6072 moved from start: 0.4458 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= 0.239 Angle : 0.652 5.871 7416 Z= 0.379 Chirality : 0.053 0.387 984 Planarity : 0.002 0.010 924 Dihedral : 8.346 23.401 804 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer Outliers : 2.41 % 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: -4.13 (0.16), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.14 (0.12), residues: 768 *********************** 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 145 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 132 time to evaluate : 0.911 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: 13 outliers final: 11 residues processed: 136 average time/residue: 0.3767 time to fit residues: 66.7883 Evaluate side-chains 124 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 113 time to evaluate : 0.867 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1439 time to fit residues: 3.8118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 65 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6125 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 5496 Z= 0.215 Angle : 0.584 5.829 7416 Z= 0.339 Chirality : 0.054 0.388 984 Planarity : 0.002 0.008 924 Dihedral : 7.227 20.743 804 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer Outliers : 3.89 % 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: -3.85 (0.21), residues: 768 helix: None (None), residues: 0 sheet: -1.55 (0.43), residues: 120 loop : -3.08 (0.16), residues: 648 *********************** 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 142 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 121 time to evaluate : 0.839 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: 21 outliers final: 18 residues processed: 129 average time/residue: 0.3999 time to fit residues: 66.4923 Evaluate side-chains 129 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 111 time to evaluate : 0.904 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1252 time to fit residues: 5.0339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 33 optimal weight: 0.0040 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6132 moved from start: 0.5579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 5496 Z= 0.195 Angle : 0.532 5.785 7416 Z= 0.309 Chirality : 0.053 0.386 984 Planarity : 0.002 0.007 924 Dihedral : 6.667 19.529 804 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.16 % Favored : 89.84 % Rotamer Outliers : 2.41 % 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: -3.72 (0.22), residues: 768 helix: None (None), residues: 0 sheet: -1.61 (0.44), residues: 120 loop : -2.95 (0.17), residues: 648 *********************** 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 130 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 117 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 125 average time/residue: 0.3496 time to fit residues: 57.8380 Evaluate side-chains 122 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 113 time to evaluate : 0.764 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1206 time to fit residues: 2.9175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 1 optimal weight: 0.2980 chunk 51 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 HIS ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6259 moved from start: 0.6025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 5496 Z= 0.296 Angle : 0.600 6.210 7416 Z= 0.349 Chirality : 0.054 0.396 984 Planarity : 0.002 0.009 924 Dihedral : 7.185 22.119 804 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 20.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.24 % Favored : 87.76 % Rotamer Outliers : 5.74 % 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 (0.20), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.15), residues: 768 *********************** 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 140 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 109 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 24 residues processed: 118 average time/residue: 0.3595 time to fit residues: 55.1649 Evaluate side-chains 128 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 104 time to evaluate : 0.804 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 24 outliers final: 1 residues processed: 24 average time/residue: 0.1293 time to fit residues: 6.6311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 0.0030 chunk 17 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6212 moved from start: 0.6252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 5496 Z= 0.208 Angle : 0.525 5.847 7416 Z= 0.307 Chirality : 0.053 0.384 984 Planarity : 0.002 0.007 924 Dihedral : 6.705 21.991 804 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.72 % Favored : 88.28 % Rotamer Outliers : 2.22 % 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: -4.20 (0.20), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.15), residues: 768 *********************** 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 125 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 113 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 121 average time/residue: 0.3258 time to fit residues: 52.8646 Evaluate side-chains 117 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 0.856 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.1882 time to fit residues: 3.3073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 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: 0.6334 moved from start: 0.6672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 5496 Z= 0.332 Angle : 0.628 6.283 7416 Z= 0.366 Chirality : 0.054 0.397 984 Planarity : 0.003 0.011 924 Dihedral : 7.411 23.449 804 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 26.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.58 % Favored : 85.42 % Rotamer Outliers : 5.93 % 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: -4.44 (0.20), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.38 (0.15), residues: 768 *********************** 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 136 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 104 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 30 residues processed: 116 average time/residue: 0.3406 time to fit residues: 52.6408 Evaluate side-chains 129 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 99 time to evaluate : 0.867 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 2 residues processed: 30 average time/residue: 0.1249 time to fit residues: 8.0597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 0.3980 chunk 54 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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** ** E 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: 0.6239 moved from start: 0.6771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 5496 Z= 0.186 Angle : 0.512 5.890 7416 Z= 0.299 Chirality : 0.053 0.379 984 Planarity : 0.002 0.006 924 Dihedral : 6.608 22.556 804 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.72 % Favored : 88.28 % Rotamer Outliers : 1.11 % 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 *********************** 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 110 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 104 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 109 average time/residue: 0.3718 time to fit residues: 53.3048 Evaluate side-chains 105 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 99 time to evaluate : 0.869 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.1284 time to fit residues: 2.2906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 0.7980 chunk 38 optimal weight: 0.1980 chunk 28 optimal weight: 0.1980 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 68 optimal weight: 0.0370 chunk 41 optimal weight: 2.9990 overall best weight: 0.4460 ------------------------------------------------------------------------------- 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** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6150 moved from start: 0.6919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 5496 Z= 0.141 Angle : 0.459 5.435 7416 Z= 0.267 Chirality : 0.053 0.373 984 Planarity : 0.001 0.006 924 Dihedral : 5.756 19.068 804 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.94 % Favored : 89.06 % Rotamer Outliers : 1.30 % 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: -4.19 (0.20), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.15), residues: 768 *********************** 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 116 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 109 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 111 average time/residue: 0.3584 time to fit residues: 52.2997 Evaluate side-chains 110 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 104 time to evaluate : 0.815 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.1244 time to fit residues: 2.3385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 0.0370 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 57 optimal weight: 0.5980 chunk 5 optimal weight: 0.0370 chunk 44 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6170 moved from start: 0.7050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 5496 Z= 0.159 Angle : 0.460 5.511 7416 Z= 0.268 Chirality : 0.053 0.380 984 Planarity : 0.001 0.006 924 Dihedral : 5.673 19.579 804 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer Outliers : 0.74 % 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: -4.14 (0.20), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.16), residues: 768 ********************** 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 110 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 106 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 107 average time/residue: 0.3844 time to fit residues: 54.1245 Evaluate side-chains 105 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 101 time to evaluate : 0.833 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.1339 time to fit residues: 2.2241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 15 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 41 optimal weight: 0.0270 overall best weight: 1.3244 ------------------------------------------------------------------------------- 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** ** E 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5282 r_free = 0.5282 target = 0.245720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.5053 r_free = 0.5053 target = 0.184236 restraints weight = 25804.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.5131 r_free = 0.5131 target = 0.193097 restraints weight = 12971.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.5191 r_free = 0.5191 target = 0.199657 restraints weight = 7774.619| |-----------------------------------------------------------------------------| r_work (final): 0.5122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6213 moved from start: 0.7173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 5496 Z= 0.235 Angle : 0.518 5.749 7416 Z= 0.301 Chirality : 0.053 0.390 984 Planarity : 0.002 0.008 924 Dihedral : 6.186 20.820 804 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 18.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.54 % Favored : 86.46 % Rotamer Outliers : 1.30 % 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: -4.29 (0.21), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.16), residues: 768 =============================================================================== Job complete usr+sys time: 3432.13 seconds wall clock time: 61 minutes 35.08 seconds (3695.08 seconds total)