Starting phenix.real_space_refine on Sun Mar 10 15:17:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uur_20900/03_2024/6uur_20900.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uur_20900/03_2024/6uur_20900.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uur_20900/03_2024/6uur_20900.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uur_20900/03_2024/6uur_20900.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uur_20900/03_2024/6uur_20900.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uur_20900/03_2024/6uur_20900.pdb" } resolution = 3.5 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= 1.000 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 S 40 5.16 5 C 1740 2.51 5 N 500 2.21 5 O 490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 144": "OD1" <-> "OD2" Residue "B TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 144": "OD1" <-> "OD2" Residue "C TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 144": "OD1" <-> "OD2" Residue "D TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 144": "OD1" <-> "OD2" Residue "E TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 144": "OD1" <-> "OD2" Residue "F TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 144": "OD1" <-> "OD2" Residue "G TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 144": "OD1" <-> "OD2" Residue "H TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 144": "OD1" <-> "OD2" Residue "I TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 144": "OD1" <-> "OD2" Residue "J TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 144": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2770 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 277 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "B" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 277 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "C" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 277 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "D" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 277 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "E" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 277 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "F" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 277 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "G" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 277 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "H" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 277 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "I" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 277 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "J" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 277 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Time building chain proxies: 1.94, per 1000 atoms: 0.70 Number of scatterers: 2770 At special positions: 0 Unit cell: (86.67, 58.85, 40.66, 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) S 40 16.00 O 490 8.00 N 500 7.00 C 1740 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 539.6 milliseconds 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 640 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 50.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'H' and resid 107 through 124 removed outlier: 6.498A pdb=" N THR D 107 " --> pdb=" O ASN H 108 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N LYS H 110 " --> pdb=" O THR D 107 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N MET D 109 " --> pdb=" O LYS H 110 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N MET H 112 " --> pdb=" O MET D 109 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N HIS D 111 " --> pdb=" O MET H 112 " (cutoff:3.500A) removed outlier: 10.439A pdb=" N GLY H 114 " --> pdb=" O HIS D 111 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ALA D 113 " --> pdb=" O GLY H 114 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ALA H 116 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA D 115 " --> pdb=" O ALA H 116 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ALA H 118 " --> pdb=" O ALA D 115 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA D 117 " --> pdb=" O ALA H 118 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N ALA H 120 " --> pdb=" O ALA D 117 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLY D 119 " --> pdb=" O ALA H 120 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N VAL H 122 " --> pdb=" O GLY D 119 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL D 121 " --> pdb=" O VAL H 122 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N GLY H 124 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLY D 123 " --> pdb=" O GLY H 124 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR A 107 " --> pdb=" O ASN D 108 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N LYS D 110 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N MET A 109 " --> pdb=" O LYS D 110 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N MET D 112 " --> pdb=" O MET A 109 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N HIS A 111 " --> pdb=" O MET D 112 " (cutoff:3.500A) removed outlier: 10.404A pdb=" N GLY D 114 " --> pdb=" O HIS A 111 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ALA A 113 " --> pdb=" O GLY D 114 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ALA D 116 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ALA A 115 " --> pdb=" O ALA D 116 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N ALA D 118 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA A 117 " --> pdb=" O ALA D 118 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N ALA D 120 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLY A 119 " --> pdb=" O ALA D 120 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N VAL D 122 " --> pdb=" O GLY A 119 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL A 121 " --> pdb=" O VAL D 122 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N GLY D 124 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLY A 123 " --> pdb=" O GLY D 124 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N MET A 112 " --> pdb=" O HIS E 111 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ALA E 113 " --> pdb=" O MET A 112 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLY A 114 " --> pdb=" O ALA E 113 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N MET E 112 " --> pdb=" O HIS I 111 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA I 113 " --> pdb=" O MET E 112 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLY E 114 " --> pdb=" O ALA I 113 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 134 through 135 removed outlier: 6.634A pdb=" N MET D 134 " --> pdb=" O SER H 135 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N MET A 134 " --> pdb=" O SER D 135 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 138 through 140 removed outlier: 6.152A pdb=" N ILE A 139 " --> pdb=" O HIS E 140 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE E 139 " --> pdb=" O HIS I 140 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 107 through 124 removed outlier: 6.854A pdb=" N MET C 112 " --> pdb=" O HIS G 111 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ALA G 113 " --> pdb=" O MET C 112 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLY C 114 " --> pdb=" O ALA G 113 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N MET B 112 " --> pdb=" O HIS C 111 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ALA C 113 " --> pdb=" O MET B 112 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLY B 114 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR B 107 " --> pdb=" O ASN F 108 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N LYS F 110 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N MET B 109 " --> pdb=" O LYS F 110 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N MET F 112 " --> pdb=" O MET B 109 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N HIS B 111 " --> pdb=" O MET F 112 " (cutoff:3.500A) removed outlier: 10.439A pdb=" N GLY F 114 " --> pdb=" O HIS B 111 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ALA B 113 " --> pdb=" O GLY F 114 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ALA F 116 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA B 115 " --> pdb=" O ALA F 116 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ALA F 118 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA B 117 " --> pdb=" O ALA F 118 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N ALA F 120 " --> pdb=" O ALA B 117 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLY B 119 " --> pdb=" O ALA F 120 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N VAL F 122 " --> pdb=" O GLY B 119 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL B 121 " --> pdb=" O VAL F 122 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N GLY F 124 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLY B 123 " --> pdb=" O GLY F 124 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N THR F 107 " --> pdb=" O ASN J 108 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N LYS J 110 " --> pdb=" O THR F 107 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N MET F 109 " --> pdb=" O LYS J 110 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N MET J 112 " --> pdb=" O MET F 109 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N HIS F 111 " --> pdb=" O MET J 112 " (cutoff:3.500A) removed outlier: 10.439A pdb=" N GLY J 114 " --> pdb=" O HIS F 111 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ALA F 113 " --> pdb=" O GLY J 114 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ALA J 116 " --> pdb=" O ALA F 113 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA F 115 " --> pdb=" O ALA J 116 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ALA J 118 " --> pdb=" O ALA F 115 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA F 117 " --> pdb=" O ALA J 118 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N ALA J 120 " --> pdb=" O ALA F 117 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLY F 119 " --> pdb=" O ALA J 120 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N VAL J 122 " --> pdb=" O GLY F 119 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL F 121 " --> pdb=" O VAL J 122 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N GLY J 124 " --> pdb=" O VAL F 121 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLY F 123 " --> pdb=" O GLY J 124 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 134 through 135 removed outlier: 6.632A pdb=" N MET B 134 " --> pdb=" O SER F 135 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N MET F 134 " --> pdb=" O SER J 135 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 138 through 140 removed outlier: 6.176A pdb=" N ILE C 139 " --> pdb=" O HIS G 140 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE B 139 " --> pdb=" O HIS C 140 " (cutoff:3.500A) 69 hydrogen bonds defined for protein. 204 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.67 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 900 1.35 - 1.46: 650 1.46 - 1.58: 1190 1.58 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 2820 Sorted by residual: bond pdb=" CB MET C 112 " pdb=" CG MET C 112 " ideal model delta sigma weight residual 1.520 1.496 0.024 3.00e-02 1.11e+03 6.30e-01 bond pdb=" CB MET F 112 " pdb=" CG MET F 112 " ideal model delta sigma weight residual 1.520 1.496 0.024 3.00e-02 1.11e+03 6.30e-01 bond pdb=" CB MET H 112 " pdb=" CG MET H 112 " ideal model delta sigma weight residual 1.520 1.496 0.024 3.00e-02 1.11e+03 6.28e-01 bond pdb=" CB MET B 112 " pdb=" CG MET B 112 " ideal model delta sigma weight residual 1.520 1.496 0.024 3.00e-02 1.11e+03 6.28e-01 bond pdb=" CB MET D 112 " pdb=" CG MET D 112 " ideal model delta sigma weight residual 1.520 1.496 0.024 3.00e-02 1.11e+03 6.26e-01 ... (remaining 2815 not shown) Histogram of bond angle deviations from ideal: 99.40 - 105.80: 66 105.80 - 112.19: 1394 112.19 - 118.59: 730 118.59 - 124.98: 1530 124.98 - 131.38: 40 Bond angle restraints: 3760 Sorted by residual: angle pdb=" CA LEU J 130 " pdb=" CB LEU J 130 " pdb=" CG LEU J 130 " ideal model delta sigma weight residual 116.30 122.72 -6.42 3.50e+00 8.16e-02 3.36e+00 angle pdb=" CA LEU H 130 " pdb=" CB LEU H 130 " pdb=" CG LEU H 130 " ideal model delta sigma weight residual 116.30 122.72 -6.42 3.50e+00 8.16e-02 3.36e+00 angle pdb=" CA LEU F 130 " pdb=" CB LEU F 130 " pdb=" CG LEU F 130 " ideal model delta sigma weight residual 116.30 122.71 -6.41 3.50e+00 8.16e-02 3.35e+00 angle pdb=" CA LEU C 130 " pdb=" CB LEU C 130 " pdb=" CG LEU C 130 " ideal model delta sigma weight residual 116.30 122.71 -6.41 3.50e+00 8.16e-02 3.35e+00 angle pdb=" CA LEU G 130 " pdb=" CB LEU G 130 " pdb=" CG LEU G 130 " ideal model delta sigma weight residual 116.30 122.70 -6.40 3.50e+00 8.16e-02 3.35e+00 ... (remaining 3755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.18: 1130 8.18 - 16.36: 200 16.36 - 24.54: 130 24.54 - 32.72: 110 32.72 - 40.90: 40 Dihedral angle restraints: 1610 sinusoidal: 560 harmonic: 1050 Sorted by residual: dihedral pdb=" CA MET F 109 " pdb=" C MET F 109 " pdb=" N LYS F 110 " pdb=" CA LYS F 110 " ideal model delta harmonic sigma weight residual -180.00 -164.95 -15.05 0 5.00e+00 4.00e-02 9.06e+00 dihedral pdb=" CA MET H 109 " pdb=" C MET H 109 " pdb=" N LYS H 110 " pdb=" CA LYS H 110 " ideal model delta harmonic sigma weight residual 180.00 -165.00 -15.00 0 5.00e+00 4.00e-02 9.00e+00 dihedral pdb=" CA MET C 109 " pdb=" C MET C 109 " pdb=" N LYS C 110 " pdb=" CA LYS C 110 " ideal model delta harmonic sigma weight residual -180.00 -165.00 -15.00 0 5.00e+00 4.00e-02 8.99e+00 ... (remaining 1607 not shown) Histogram of chiral volume deviations from ideal: 0.004 - 0.030: 206 0.030 - 0.056: 94 0.056 - 0.083: 34 0.083 - 0.109: 29 0.109 - 0.135: 27 Chirality restraints: 390 Sorted by residual: chirality pdb=" CA ILE E 139 " pdb=" N ILE E 139 " pdb=" C ILE E 139 " pdb=" CB ILE E 139 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA ILE J 139 " pdb=" N ILE J 139 " pdb=" C ILE J 139 " pdb=" CB ILE J 139 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA ILE B 139 " pdb=" N ILE B 139 " pdb=" C ILE B 139 " pdb=" CB ILE B 139 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.52e-01 ... (remaining 387 not shown) Planarity restraints: 480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE J 141 " -0.005 2.00e-02 2.50e+03 3.48e-03 2.12e-01 pdb=" CG PHE J 141 " 0.003 2.00e-02 2.50e+03 pdb=" CD1 PHE J 141 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE J 141 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE J 141 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE J 141 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE J 141 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 141 " 0.005 2.00e-02 2.50e+03 3.42e-03 2.04e-01 pdb=" CG PHE H 141 " -0.002 2.00e-02 2.50e+03 pdb=" CD1 PHE H 141 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE H 141 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE H 141 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE H 141 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE H 141 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 141 " -0.004 2.00e-02 2.50e+03 3.28e-03 1.88e-01 pdb=" CG PHE C 141 " 0.003 2.00e-02 2.50e+03 pdb=" CD1 PHE C 141 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE C 141 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 141 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 141 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 141 " -0.005 2.00e-02 2.50e+03 ... (remaining 477 not shown) Histogram of nonbonded interaction distances: 2.64 - 3.09: 1589 3.09 - 3.55: 2685 3.55 - 4.00: 4124 4.00 - 4.45: 5058 4.45 - 4.90: 9474 Nonbonded interactions: 22930 Sorted by model distance: nonbonded pdb=" N GLY J 126 " pdb=" O GLY J 126 " model vdw 2.644 2.496 nonbonded pdb=" N GLY I 126 " pdb=" O GLY I 126 " model vdw 2.644 2.496 nonbonded pdb=" N GLY B 126 " pdb=" O GLY B 126 " model vdw 2.644 2.496 nonbonded pdb=" N GLY F 126 " pdb=" O GLY F 126 " model vdw 2.644 2.496 nonbonded pdb=" N GLY E 126 " pdb=" O GLY E 126 " model vdw 2.644 2.496 ... (remaining 22925 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.170 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 12.830 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 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 : 0.004 0.024 2820 Z= 0.252 Angle : 0.760 6.416 3760 Z= 0.384 Chirality : 0.051 0.135 390 Planarity : 0.002 0.010 480 Dihedral : 15.648 40.900 970 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 15.20 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.46 (0.30), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.23), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS E 140 PHE 0.006 0.003 PHE J 141 TYR 0.005 0.001 TYR C 128 ARG 0.000 0.000 ARG C 136 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.7521 (t0) cc_final: 0.7187 (t0) REVERT: C 108 ASN cc_start: 0.7606 (t0) cc_final: 0.7250 (t0) REVERT: E 108 ASN cc_start: 0.7362 (t0) cc_final: 0.6505 (t0) REVERT: F 108 ASN cc_start: 0.7517 (t0) cc_final: 0.7177 (t0) REVERT: H 108 ASN cc_start: 0.7936 (t0) cc_final: 0.6878 (t0) REVERT: I 108 ASN cc_start: 0.7743 (t0) cc_final: 0.7099 (t0) REVERT: J 110 LYS cc_start: 0.7840 (mttt) cc_final: 0.7560 (mtpp) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1357 time to fit residues: 14.4645 Evaluate side-chains 79 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 ASN ** H 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 2820 Z= 0.357 Angle : 0.817 5.335 3760 Z= 0.408 Chirality : 0.047 0.130 390 Planarity : 0.003 0.011 480 Dihedral : 5.057 19.049 420 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 7.20 % Allowed : 16.80 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.36 (0.32), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.24), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 140 PHE 0.012 0.004 PHE G 141 TYR 0.007 0.001 TYR C 145 ARG 0.001 0.000 ARG I 136 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 78 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: D 108 ASN cc_start: 0.7712 (t0) cc_final: 0.6519 (t0) REVERT: F 108 ASN cc_start: 0.7309 (t0) cc_final: 0.7014 (t0) REVERT: J 112 MET cc_start: 0.7969 (mtm) cc_final: 0.7616 (mtm) outliers start: 18 outliers final: 12 residues processed: 88 average time/residue: 0.1324 time to fit residues: 14.1744 Evaluate side-chains 84 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 72 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain J residue 108 ASN Chi-restraints excluded: chain J residue 138 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 32 optimal weight: 0.0570 chunk 12 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 35 optimal weight: 0.0870 chunk 27 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 overall best weight: 2.4282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 2820 Z= 0.375 Angle : 0.834 6.840 3760 Z= 0.419 Chirality : 0.048 0.132 390 Planarity : 0.002 0.010 480 Dihedral : 4.906 18.505 420 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 7.20 % Allowed : 18.40 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.23 (0.32), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.21 (0.24), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS I 140 PHE 0.010 0.003 PHE G 141 TYR 0.006 0.001 TYR H 145 ARG 0.000 0.000 ARG C 136 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 74 time to evaluate : 0.289 Fit side-chains REVERT: D 108 ASN cc_start: 0.7956 (t0) cc_final: 0.7302 (t0) REVERT: F 108 ASN cc_start: 0.7562 (t0) cc_final: 0.7350 (t0) REVERT: I 138 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8220 (pt) REVERT: J 108 ASN cc_start: 0.8297 (OUTLIER) cc_final: 0.8034 (t0) REVERT: J 112 MET cc_start: 0.8000 (mtm) cc_final: 0.7770 (mtm) outliers start: 18 outliers final: 10 residues processed: 84 average time/residue: 0.1041 time to fit residues: 11.0178 Evaluate side-chains 86 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain J residue 108 ASN Chi-restraints excluded: chain J residue 138 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 19 optimal weight: 0.0970 chunk 34 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 2820 Z= 0.466 Angle : 0.889 5.990 3760 Z= 0.450 Chirality : 0.048 0.132 390 Planarity : 0.003 0.010 480 Dihedral : 5.155 19.062 420 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 6.80 % Allowed : 20.80 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.19 (0.32), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.25), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS I 140 PHE 0.011 0.004 PHE G 141 TYR 0.007 0.001 TYR J 145 ARG 0.001 0.000 ARG F 136 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 77 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: B 110 LYS cc_start: 0.8442 (mttp) cc_final: 0.8226 (mttp) REVERT: I 138 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8233 (pt) REVERT: J 108 ASN cc_start: 0.8344 (OUTLIER) cc_final: 0.8065 (m110) REVERT: J 112 MET cc_start: 0.8156 (mtm) cc_final: 0.7923 (mtm) outliers start: 17 outliers final: 10 residues processed: 87 average time/residue: 0.1209 time to fit residues: 12.8744 Evaluate side-chains 90 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 78 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain J residue 108 ASN Chi-restraints excluded: chain J residue 138 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 2820 Z= 0.385 Angle : 0.842 7.169 3760 Z= 0.425 Chirality : 0.048 0.132 390 Planarity : 0.002 0.012 480 Dihedral : 5.089 19.571 420 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 7.20 % Allowed : 18.00 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.21 (0.32), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.25), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS D 111 PHE 0.008 0.003 PHE G 141 TYR 0.005 0.001 TYR H 145 ARG 0.002 0.000 ARG G 136 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 75 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: I 138 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8203 (pt) REVERT: J 108 ASN cc_start: 0.8247 (OUTLIER) cc_final: 0.8024 (m110) REVERT: J 112 MET cc_start: 0.8106 (mtm) cc_final: 0.7866 (mtm) outliers start: 18 outliers final: 12 residues processed: 87 average time/residue: 0.1168 time to fit residues: 12.4998 Evaluate side-chains 87 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 73 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain J residue 108 ASN Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain J residue 138 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 0.0020 overall best weight: 2.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 2820 Z= 0.359 Angle : 0.818 8.828 3760 Z= 0.417 Chirality : 0.047 0.132 390 Planarity : 0.002 0.017 480 Dihedral : 5.059 20.226 420 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 6.00 % Allowed : 20.40 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.26 (0.32), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.24), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS D 111 PHE 0.007 0.003 PHE G 141 TYR 0.004 0.001 TYR H 145 ARG 0.001 0.000 ARG G 136 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 78 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 138 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8212 (pt) outliers start: 15 outliers final: 12 residues processed: 90 average time/residue: 0.1186 time to fit residues: 13.3179 Evaluate side-chains 90 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 77 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain J residue 138 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 26 optimal weight: 0.0970 chunk 19 optimal weight: 3.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2820 Z= 0.271 Angle : 0.749 6.922 3760 Z= 0.382 Chirality : 0.047 0.129 390 Planarity : 0.002 0.014 480 Dihedral : 4.875 21.153 420 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 5.60 % Allowed : 21.60 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.37 (0.31), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.24), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS D 111 PHE 0.005 0.002 PHE I 141 TYR 0.004 0.001 TYR H 128 ARG 0.001 0.000 ARG D 136 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 78 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: A 112 MET cc_start: 0.8008 (mtm) cc_final: 0.7728 (mtt) REVERT: D 108 ASN cc_start: 0.7976 (t0) cc_final: 0.7726 (t0) REVERT: D 110 LYS cc_start: 0.8289 (mptt) cc_final: 0.8016 (mptt) REVERT: I 138 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8158 (pt) outliers start: 14 outliers final: 12 residues processed: 88 average time/residue: 0.1100 time to fit residues: 12.0376 Evaluate side-chains 89 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 76 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain J residue 138 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2820 Z= 0.237 Angle : 0.714 6.457 3760 Z= 0.364 Chirality : 0.047 0.129 390 Planarity : 0.002 0.014 480 Dihedral : 4.690 19.233 420 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 6.80 % Allowed : 20.40 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.44 (0.31), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.38 (0.24), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS D 111 PHE 0.003 0.001 PHE G 141 TYR 0.004 0.001 TYR F 128 ARG 0.001 0.000 ARG D 136 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 81 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: D 110 LYS cc_start: 0.8269 (mptt) cc_final: 0.7944 (mptt) REVERT: F 108 ASN cc_start: 0.7565 (t0) cc_final: 0.7343 (t0) REVERT: I 109 MET cc_start: 0.7243 (ttt) cc_final: 0.6888 (ttt) REVERT: I 138 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8151 (pt) REVERT: J 112 MET cc_start: 0.7594 (mtm) cc_final: 0.7347 (mtm) outliers start: 17 outliers final: 14 residues processed: 93 average time/residue: 0.1298 time to fit residues: 14.5957 Evaluate side-chains 91 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 76 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain J residue 138 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 39 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 2820 Z= 0.308 Angle : 0.789 7.417 3760 Z= 0.402 Chirality : 0.047 0.131 390 Planarity : 0.002 0.014 480 Dihedral : 4.811 19.299 420 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 6.80 % Allowed : 22.00 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.50 (0.31), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.42 (0.23), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 111 PHE 0.006 0.002 PHE G 141 TYR 0.004 0.001 TYR A 128 ARG 0.002 0.000 ARG G 136 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 75 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: I 138 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8215 (pt) REVERT: J 112 MET cc_start: 0.7577 (mtm) cc_final: 0.7334 (mtm) outliers start: 17 outliers final: 14 residues processed: 90 average time/residue: 0.1177 time to fit residues: 12.9876 Evaluate side-chains 87 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain J residue 138 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2820 Z= 0.232 Angle : 0.744 6.973 3760 Z= 0.379 Chirality : 0.047 0.129 390 Planarity : 0.002 0.014 480 Dihedral : 4.635 19.682 420 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 7.20 % Allowed : 20.40 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.55 (0.31), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.46 (0.23), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS C 111 PHE 0.003 0.001 PHE G 141 TYR 0.003 0.001 TYR D 128 ARG 0.002 0.000 ARG D 136 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 75 time to evaluate : 0.332 Fit side-chains REVERT: I 108 ASN cc_start: 0.8020 (t0) cc_final: 0.7810 (t0) REVERT: I 138 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8165 (pt) outliers start: 18 outliers final: 15 residues processed: 88 average time/residue: 0.1102 time to fit residues: 12.1719 Evaluate side-chains 89 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 73 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain J residue 138 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 10.0000 chunk 36 optimal weight: 0.0370 chunk 21 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 overall best weight: 3.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 140 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 = 0.4492 r_free = 0.4492 target = 0.151234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.125727 restraints weight = 3627.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.128341 restraints weight = 2003.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.129605 restraints weight = 1467.677| |-----------------------------------------------------------------------------| r_work (final): 0.4222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 2820 Z= 0.461 Angle : 0.919 7.852 3760 Z= 0.468 Chirality : 0.049 0.131 390 Planarity : 0.003 0.014 480 Dihedral : 5.126 21.432 420 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.11 % Favored : 87.89 % Rotamer: Outliers : 6.80 % Allowed : 19.60 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.62 (0.31), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.51 (0.23), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS G 140 PHE 0.011 0.004 PHE H 141 TYR 0.006 0.001 TYR C 145 ARG 0.002 0.000 ARG G 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1222.86 seconds wall clock time: 22 minutes 46.42 seconds (1366.42 seconds total)