Starting phenix.real_space_refine on Mon Mar 18 04:34:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k61_22686/03_2024/7k61_22686.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k61_22686/03_2024/7k61_22686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k61_22686/03_2024/7k61_22686.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k61_22686/03_2024/7k61_22686.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k61_22686/03_2024/7k61_22686.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k61_22686/03_2024/7k61_22686.pdb" } resolution = 2.85 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 Anisotropic ADP refinement not supported. Converting 2242 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 394 5.49 5 S 32 5.16 5 C 9904 2.51 5 N 3243 2.21 5 O 4150 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A ASP 77": "OD1" <-> "OD2" Residue "A ASP 106": "OD1" <-> "OD2" Residue "A ASP 123": "OD1" <-> "OD2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "B ASP 68": "OD1" <-> "OD2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "B TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 68": "OD1" <-> "OD2" Residue "D PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 73": "OE1" <-> "OE2" Residue "E ASP 77": "OD1" <-> "OD2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E ASP 106": "OD1" <-> "OD2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "F ASP 68": "OD1" <-> "OD2" Residue "F PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 35": "OE1" <-> "OE2" Residue "H TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 76": "OE1" <-> "OE2" Residue "H GLU 113": "OE1" <-> "OE2" Residue "M ARG 37": "NH1" <-> "NH2" Residue "M TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 80": "NH1" <-> "NH2" Residue "M PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 98": "OE1" <-> "OE2" Residue "M ASP 101": "OD1" <-> "OD2" Residue "M TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 195": "OE1" <-> "OE2" Residue "M TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 37": "NH1" <-> "NH2" Residue "N TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 75": "OD1" <-> "OD2" Residue "N ARG 80": "NH1" <-> "NH2" Residue "N PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 98": "OE1" <-> "OE2" Residue "N GLU 150": "OE1" <-> "OE2" Residue "N GLU 195": "OE1" <-> "OE2" Residue "N TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 238": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17723 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 4015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 4015 Classifications: {'DNA': 197} Link IDs: {'rna3p': 196} Chain: "J" Number of atoms: 4062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 4062 Classifications: {'DNA': 197} Link IDs: {'rna3p': 196} Chain: "M" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1777 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain breaks: 1 Chain: "N" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1777 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain breaks: 1 Time building chain proxies: 9.29, per 1000 atoms: 0.52 Number of scatterers: 17723 At special positions: 0 Unit cell: (131.886, 122.314, 195.702, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 394 15.00 O 4150 8.00 N 3243 7.00 C 9904 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS M 42 " - pdb=" SG CYS M 107 " distance=2.03 Simple disulfide: pdb=" SG CYS M 171 " - pdb=" SG CYS M 245 " distance=2.03 Simple disulfide: pdb=" SG CYS N 42 " - pdb=" SG CYS N 107 " distance=2.04 Simple disulfide: pdb=" SG CYS N 171 " - pdb=" SG CYS N 245 " distance=2.03 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: 9.21 Conformation dependent library (CDL) restraints added in 2.1 seconds 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2272 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 22 sheets defined 48.4% alpha, 21.7% beta 197 base pairs and 347 stacking pairs defined. Time for finding SS restraints: 8.43 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.891A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.593A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.533A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.221A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.709A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.599A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.559A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 74 removed outlier: 4.251A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 removed outlier: 3.634A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 102 removed outlier: 3.607A pdb=" N THR M 102 " --> pdb=" O SER M 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 177 through 179 No H-bonds generated for 'chain 'M' and resid 177 through 179' Processing helix chain 'M' and resid 211 through 214 removed outlier: 3.649A pdb=" N LYS M 214 " --> pdb=" O GLU M 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 211 through 214' Processing helix chain 'M' and resid 236 through 240 Processing helix chain 'N' and resid 98 through 102 Processing helix chain 'N' and resid 177 through 179 No H-bonds generated for 'chain 'N' and resid 177 through 179' Processing helix chain 'N' and resid 211 through 214 removed outlier: 3.580A pdb=" N LYS N 214 " --> pdb=" O GLU N 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 211 through 214' Processing helix chain 'N' and resid 236 through 240 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.593A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.415A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.051A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.502A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.739A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.021A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'M' and resid 23 through 25 removed outlier: 3.702A pdb=" N ASP M 89 " --> pdb=" O SER M 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 29 through 32 removed outlier: 6.365A pdb=" N MET M 30 " --> pdb=" O GLU M 124 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU M 52 " --> pdb=" O TYR M 68 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TYR M 68 " --> pdb=" O LEU M 52 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TRP M 54 " --> pdb=" O LEU M 66 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 29 through 32 removed outlier: 6.365A pdb=" N MET M 30 " --> pdb=" O GLU M 124 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 152 through 155 Processing sheet with id=AB6, first strand: chain 'M' and resid 159 through 161 removed outlier: 6.089A pdb=" N GLU M 159 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE M 183 " --> pdb=" O TYR M 199 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TYR M 199 " --> pdb=" O ILE M 183 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N TRP M 185 " --> pdb=" O ILE M 197 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 159 through 161 removed outlier: 6.089A pdb=" N GLU M 159 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TYR M 258 " --> pdb=" O ARG M 247 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 23 through 24 removed outlier: 3.555A pdb=" N ASP N 89 " --> pdb=" O SER N 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 29 through 32 removed outlier: 6.628A pdb=" N LEU N 52 " --> pdb=" O TYR N 68 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TYR N 68 " --> pdb=" O LEU N 52 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TRP N 54 " --> pdb=" O LEU N 66 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 29 through 32 Processing sheet with id=AC2, first strand: chain 'N' and resid 152 through 155 Processing sheet with id=AC3, first strand: chain 'N' and resid 159 through 161 removed outlier: 6.483A pdb=" N ILE N 183 " --> pdb=" O TYR N 199 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TYR N 199 " --> pdb=" O ILE N 183 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TRP N 185 " --> pdb=" O ILE N 197 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 159 through 161 removed outlier: 3.800A pdb=" N TYR N 258 " --> pdb=" O ARG N 247 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N SER N 249 " --> pdb=" O LEU N 256 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU N 256 " --> pdb=" O SER N 249 " (cutoff:3.500A) 576 hydrogen bonds defined for protein. 1584 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 510 hydrogen bonds 1020 hydrogen bond angles 0 basepair planarities 197 basepair parallelities 347 stacking parallelities Total time for adding SS restraints: 7.39 Time building geometry restraints manager: 9.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3737 1.33 - 1.45: 6089 1.45 - 1.57: 8206 1.57 - 1.69: 786 1.69 - 1.82: 52 Bond restraints: 18870 Sorted by residual: bond pdb=" CA ASN G 89 " pdb=" C ASN G 89 " ideal model delta sigma weight residual 1.523 1.492 0.031 1.80e-02 3.09e+03 3.03e+00 bond pdb=" CB THR H 52 " pdb=" CG2 THR H 52 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.56e+00 bond pdb=" CG1 ILE C 62 " pdb=" CD1 ILE C 62 " ideal model delta sigma weight residual 1.513 1.453 0.060 3.90e-02 6.57e+02 2.36e+00 bond pdb=" CG1 ILE D 61 " pdb=" CD1 ILE D 61 " ideal model delta sigma weight residual 1.513 1.456 0.057 3.90e-02 6.57e+02 2.14e+00 bond pdb=" CB PRO E 66 " pdb=" CG PRO E 66 " ideal model delta sigma weight residual 1.492 1.424 0.068 5.00e-02 4.00e+02 1.86e+00 ... (remaining 18865 not shown) Histogram of bond angle deviations from ideal: 97.33 - 104.66: 1567 104.66 - 112.00: 10497 112.00 - 119.33: 5567 119.33 - 126.66: 8380 126.66 - 134.00: 1186 Bond angle restraints: 27197 Sorted by residual: angle pdb=" CA ASN G 73 " pdb=" CB ASN G 73 " pdb=" CG ASN G 73 " ideal model delta sigma weight residual 112.60 115.50 -2.90 1.00e+00 1.00e+00 8.42e+00 angle pdb=" N GLN N 88 " pdb=" CA GLN N 88 " pdb=" C GLN N 88 " ideal model delta sigma weight residual 114.31 110.82 3.49 1.29e+00 6.01e-01 7.34e+00 angle pdb=" C TYR N 69 " pdb=" N ALA N 70 " pdb=" CA ALA N 70 " ideal model delta sigma weight residual 121.54 126.44 -4.90 1.91e+00 2.74e-01 6.59e+00 angle pdb=" C LEU F 22 " pdb=" N ARG F 23 " pdb=" CA ARG F 23 " ideal model delta sigma weight residual 122.15 114.90 7.25 2.83e+00 1.25e-01 6.56e+00 angle pdb=" N ASN G 73 " pdb=" CA ASN G 73 " pdb=" C ASN G 73 " ideal model delta sigma weight residual 113.28 110.18 3.10 1.22e+00 6.72e-01 6.48e+00 ... (remaining 27192 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.34: 8344 35.34 - 70.68: 1908 70.68 - 106.02: 20 106.02 - 141.35: 0 141.35 - 176.69: 2 Dihedral angle restraints: 10274 sinusoidal: 6728 harmonic: 3546 Sorted by residual: dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual 180.00 159.26 20.74 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" C4' DT J 153 " pdb=" C3' DT J 153 " pdb=" O3' DT J 153 " pdb=" P DC J 154 " ideal model delta sinusoidal sigma weight residual 220.00 43.31 176.69 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J 119 " pdb=" C3' DG J 119 " pdb=" O3' DG J 119 " pdb=" P DG J 120 " ideal model delta sinusoidal sigma weight residual 220.00 69.48 150.52 1 3.50e+01 8.16e-04 1.47e+01 ... (remaining 10271 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1923 0.035 - 0.069: 879 0.069 - 0.104: 198 0.104 - 0.138: 58 0.138 - 0.173: 6 Chirality restraints: 3064 Sorted by residual: chirality pdb=" CB THR M 177 " pdb=" CA THR M 177 " pdb=" OG1 THR M 177 " pdb=" CG2 THR M 177 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.47e-01 chirality pdb=" CA SER M 113 " pdb=" N SER M 113 " pdb=" C SER M 113 " pdb=" CB SER M 113 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.41e-01 chirality pdb=" CB THR M 102 " pdb=" CA THR M 102 " pdb=" OG1 THR M 102 " pdb=" CG2 THR M 102 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.26e-01 ... (remaining 3061 not shown) Planarity restraints: 2066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR N 201 " -0.021 2.00e-02 2.50e+03 2.01e-02 8.06e+00 pdb=" CG TYR N 201 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR N 201 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR N 201 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR N 201 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR N 201 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR N 201 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR N 201 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN G 73 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.30e+00 pdb=" C ASN G 73 " -0.036 2.00e-02 2.50e+03 pdb=" O ASN G 73 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS G 74 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " -0.033 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO D 103 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " -0.027 5.00e-02 4.00e+02 ... (remaining 2063 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 630 2.68 - 3.24: 15654 3.24 - 3.79: 34537 3.79 - 4.35: 44656 4.35 - 4.90: 63674 Nonbonded interactions: 159151 Sorted by model distance: nonbonded pdb=" OD2 ASP D 68 " pdb=" OH TYR F 98 " model vdw 2.130 2.440 nonbonded pdb=" NH1 ARG H 31 " pdb=" OP1 DG J 150 " model vdw 2.207 2.520 nonbonded pdb=" O THR G 76 " pdb=" OG1 THR H 52 " model vdw 2.217 2.440 nonbonded pdb=" NH2 ARG G 32 " pdb=" OE1 GLU H 35 " model vdw 2.271 2.520 nonbonded pdb=" O THR C 76 " pdb=" OG1 THR D 52 " model vdw 2.280 2.440 ... (remaining 159146 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 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 7.840 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 56.700 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 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 : 0.007 0.068 18870 Z= 0.433 Angle : 0.669 7.247 27197 Z= 0.401 Chirality : 0.041 0.173 3064 Planarity : 0.004 0.049 2066 Dihedral : 27.102 176.693 7990 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.24), residues: 1198 helix: 1.55 (0.21), residues: 550 sheet: 0.29 (0.34), residues: 242 loop : 0.13 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP M 196 HIS 0.005 0.002 HIS H 49 PHE 0.018 0.002 PHE M 117 TYR 0.049 0.002 TYR N 201 ARG 0.008 0.001 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 1.532 Fit side-chains REVERT: A 56 LYS cc_start: 0.8783 (tttp) cc_final: 0.8570 (ttmt) REVERT: A 105 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7334 (mt-10) REVERT: C 56 GLU cc_start: 0.8491 (tt0) cc_final: 0.8246 (tt0) REVERT: C 61 GLU cc_start: 0.8342 (tp30) cc_final: 0.7984 (mm-30) REVERT: D 116 LYS cc_start: 0.8884 (ttpt) cc_final: 0.8616 (ttpp) REVERT: G 110 ASN cc_start: 0.8905 (t0) cc_final: 0.8673 (t0) REVERT: H 86 ARG cc_start: 0.8295 (mmt-90) cc_final: 0.7972 (mmt90) REVERT: M 98 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7668 (mp0) outliers start: 0 outliers final: 2 residues processed: 240 average time/residue: 1.8717 time to fit residues: 485.1346 Evaluate side-chains 193 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 191 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 51 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 64 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 120 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 73 optimal weight: 30.0000 chunk 89 optimal weight: 8.9990 chunk 139 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 125 GLN B 93 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 192 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18870 Z= 0.237 Angle : 0.565 6.519 27197 Z= 0.335 Chirality : 0.035 0.142 3064 Planarity : 0.004 0.051 2066 Dihedral : 30.211 176.177 5638 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.83 % Allowed : 10.40 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.24), residues: 1198 helix: 2.14 (0.21), residues: 552 sheet: 0.44 (0.33), residues: 240 loop : 0.29 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 185 HIS 0.003 0.001 HIS H 49 PHE 0.009 0.001 PHE A 67 TYR 0.029 0.002 TYR N 201 ARG 0.004 0.000 ARG N 80 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 214 time to evaluate : 1.452 Fit side-chains REVERT: C 95 LYS cc_start: 0.9056 (ttmm) cc_final: 0.8847 (ttmt) REVERT: G 73 ASN cc_start: 0.8617 (t0) cc_final: 0.8324 (t0) REVERT: G 110 ASN cc_start: 0.8921 (t0) cc_final: 0.8715 (t0) REVERT: H 42 TYR cc_start: 0.7783 (t80) cc_final: 0.7569 (t80) REVERT: H 86 ARG cc_start: 0.8213 (mmt-90) cc_final: 0.7890 (mmt90) REVERT: M 98 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7581 (mp0) REVERT: M 239 ASP cc_start: 0.8360 (m-30) cc_final: 0.8074 (m-30) REVERT: N 23 MET cc_start: 0.9226 (mmp) cc_final: 0.8879 (mmm) outliers start: 19 outliers final: 8 residues processed: 218 average time/residue: 1.6965 time to fit residues: 401.4194 Evaluate side-chains 205 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 197 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain M residue 23 MET Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 228 VAL Chi-restraints excluded: chain N residue 265 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 0.0470 chunk 116 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 138 optimal weight: 7.9990 chunk 47 optimal weight: 0.3980 chunk 112 optimal weight: 5.9990 overall best weight: 2.6884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN B 75 HIS D 47 GLN D 84 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN M 110 HIS N 152 GLN N 154 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 18870 Z= 0.476 Angle : 0.628 6.944 27197 Z= 0.364 Chirality : 0.041 0.157 3064 Planarity : 0.004 0.050 2066 Dihedral : 30.559 178.198 5636 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.28 % Allowed : 11.66 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.24), residues: 1198 helix: 1.85 (0.21), residues: 552 sheet: 0.40 (0.33), residues: 240 loop : 0.19 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP N 185 HIS 0.005 0.002 HIS F 75 PHE 0.014 0.002 PHE M 117 TYR 0.031 0.002 TYR N 201 ARG 0.006 0.001 ARG E 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 211 time to evaluate : 1.493 Fit side-chains REVERT: A 105 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7383 (mt-10) REVERT: B 95 ARG cc_start: 0.8030 (mmt180) cc_final: 0.7695 (mtp-110) REVERT: C 95 LYS cc_start: 0.9088 (ttmm) cc_final: 0.8859 (ttmp) REVERT: D 113 GLU cc_start: 0.8261 (mm-30) cc_final: 0.8054 (tp30) REVERT: D 116 LYS cc_start: 0.8883 (ttpt) cc_final: 0.8667 (ttpp) REVERT: E 56 LYS cc_start: 0.8726 (ttpp) cc_final: 0.8480 (ttpp) REVERT: F 77 LYS cc_start: 0.9133 (OUTLIER) cc_final: 0.8626 (mtpt) REVERT: G 73 ASN cc_start: 0.8685 (t0) cc_final: 0.8292 (t0) REVERT: G 74 LYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8688 (mtmm) REVERT: H 86 ARG cc_start: 0.8323 (mmt-90) cc_final: 0.7939 (mmt90) REVERT: M 95 ASN cc_start: 0.8860 (m-40) cc_final: 0.8419 (m-40) REVERT: M 98 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7709 (mp0) REVERT: M 239 ASP cc_start: 0.8339 (m-30) cc_final: 0.8006 (m-30) outliers start: 34 outliers final: 14 residues processed: 217 average time/residue: 1.8152 time to fit residues: 426.6831 Evaluate side-chains 221 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 205 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain M residue 19 MET Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 228 VAL Chi-restraints excluded: chain N residue 265 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 72 optimal weight: 20.0000 chunk 15 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 94 optimal weight: 4.9990 chunk 140 optimal weight: 0.7980 chunk 148 optimal weight: 0.7980 chunk 73 optimal weight: 20.0000 chunk 133 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 18870 Z= 0.210 Angle : 0.575 7.718 27197 Z= 0.340 Chirality : 0.036 0.178 3064 Planarity : 0.004 0.037 2066 Dihedral : 30.590 178.267 5636 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.18 % Allowed : 13.20 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.24), residues: 1198 helix: 2.08 (0.21), residues: 552 sheet: 0.48 (0.33), residues: 240 loop : 0.32 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 185 HIS 0.004 0.001 HIS M 31 PHE 0.007 0.001 PHE A 67 TYR 0.015 0.001 TYR N 201 ARG 0.003 0.000 ARG M 49 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 214 time to evaluate : 1.398 Fit side-chains REVERT: A 105 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7347 (mt-10) REVERT: B 95 ARG cc_start: 0.7869 (mmt180) cc_final: 0.7586 (mtp-110) REVERT: C 95 LYS cc_start: 0.9084 (ttmm) cc_final: 0.8839 (ttmp) REVERT: D 113 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7930 (tp30) REVERT: E 56 LYS cc_start: 0.8717 (ttpp) cc_final: 0.8462 (ttpp) REVERT: F 77 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8633 (mtpt) REVERT: G 73 ASN cc_start: 0.8701 (t0) cc_final: 0.8337 (t0) REVERT: G 74 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8675 (mtmm) REVERT: H 86 ARG cc_start: 0.8234 (mmt-90) cc_final: 0.7859 (mmt90) REVERT: M 98 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7700 (mp0) REVERT: M 239 ASP cc_start: 0.8306 (m-30) cc_final: 0.7976 (m-30) outliers start: 33 outliers final: 12 residues processed: 224 average time/residue: 1.7364 time to fit residues: 422.0191 Evaluate side-chains 215 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 201 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 228 VAL Chi-restraints excluded: chain N residue 257 ASP Chi-restraints excluded: chain N residue 265 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 133 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 18870 Z= 0.433 Angle : 0.611 7.179 27197 Z= 0.354 Chirality : 0.040 0.150 3064 Planarity : 0.004 0.042 2066 Dihedral : 30.568 178.482 5634 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.37 % Allowed : 14.07 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.24), residues: 1198 helix: 2.00 (0.21), residues: 550 sheet: 0.59 (0.34), residues: 230 loop : 0.05 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP N 185 HIS 0.004 0.001 HIS M 110 PHE 0.011 0.002 PHE C 25 TYR 0.018 0.002 TYR N 201 ARG 0.006 0.001 ARG M 37 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 210 time to evaluate : 1.355 Fit side-chains REVERT: A 105 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7346 (mt-10) REVERT: B 95 ARG cc_start: 0.7996 (mmt180) cc_final: 0.7777 (mtp-110) REVERT: C 95 LYS cc_start: 0.9090 (ttmm) cc_final: 0.8862 (ttmt) REVERT: D 113 GLU cc_start: 0.8237 (mm-30) cc_final: 0.8035 (mm-30) REVERT: D 116 LYS cc_start: 0.8867 (ttpt) cc_final: 0.8553 (ttpp) REVERT: E 56 LYS cc_start: 0.8723 (ttpp) cc_final: 0.8475 (ttpp) REVERT: E 94 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7630 (mp0) REVERT: F 77 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8624 (mtpt) REVERT: G 73 ASN cc_start: 0.8719 (t0) cc_final: 0.8321 (t0) REVERT: G 74 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8599 (mtmm) REVERT: G 90 ASP cc_start: 0.8738 (OUTLIER) cc_final: 0.8331 (t0) REVERT: G 91 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7767 (tt0) REVERT: H 43 LYS cc_start: 0.9098 (mttt) cc_final: 0.8782 (mtpp) REVERT: H 86 ARG cc_start: 0.8327 (mmt-90) cc_final: 0.7924 (mmt90) REVERT: M 21 ILE cc_start: 0.9466 (OUTLIER) cc_final: 0.9187 (mp) REVERT: M 37 ARG cc_start: 0.8644 (ttm-80) cc_final: 0.7931 (ttm-80) REVERT: M 239 ASP cc_start: 0.8345 (m-30) cc_final: 0.8021 (m-30) REVERT: N 37 ARG cc_start: 0.8470 (mmm-85) cc_final: 0.8148 (ttm-80) outliers start: 35 outliers final: 16 residues processed: 221 average time/residue: 1.7569 time to fit residues: 420.4547 Evaluate side-chains 231 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 209 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 228 VAL Chi-restraints excluded: chain M residue 267 VAL Chi-restraints excluded: chain N residue 122 LYS Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 265 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 0.8980 chunk 134 optimal weight: 7.9990 chunk 29 optimal weight: 0.0670 chunk 87 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 149 optimal weight: 0.2980 chunk 123 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18870 Z= 0.190 Angle : 0.564 8.118 27197 Z= 0.334 Chirality : 0.035 0.147 3064 Planarity : 0.004 0.034 2066 Dihedral : 30.568 178.493 5634 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.89 % Allowed : 14.45 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.24), residues: 1198 helix: 2.15 (0.21), residues: 552 sheet: 0.65 (0.34), residues: 230 loop : 0.19 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 60 HIS 0.003 0.001 HIS B 75 PHE 0.008 0.001 PHE E 67 TYR 0.017 0.001 TYR H 42 ARG 0.008 0.000 ARG M 37 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 213 time to evaluate : 1.419 Fit side-chains REVERT: A 105 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7343 (mt-10) REVERT: B 95 ARG cc_start: 0.7853 (mmt180) cc_final: 0.7647 (mtp-110) REVERT: C 95 LYS cc_start: 0.9099 (ttmm) cc_final: 0.8876 (ttmt) REVERT: D 113 GLU cc_start: 0.8205 (mm-30) cc_final: 0.8003 (mm-30) REVERT: D 116 LYS cc_start: 0.8876 (ttpt) cc_final: 0.8590 (ttpp) REVERT: E 56 LYS cc_start: 0.8729 (ttpp) cc_final: 0.8484 (ttpp) REVERT: F 77 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8623 (mtpt) REVERT: G 73 ASN cc_start: 0.8722 (t0) cc_final: 0.8324 (t0) REVERT: G 74 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8604 (mtmm) REVERT: G 90 ASP cc_start: 0.8677 (OUTLIER) cc_final: 0.8286 (t0) REVERT: H 43 LYS cc_start: 0.9078 (mttt) cc_final: 0.8795 (mtpp) REVERT: H 86 ARG cc_start: 0.8243 (mmt-90) cc_final: 0.7843 (mmt90) REVERT: M 30 MET cc_start: 0.8390 (ptp) cc_final: 0.8171 (ptm) REVERT: M 239 ASP cc_start: 0.8317 (m-30) cc_final: 0.7967 (m-30) REVERT: N 23 MET cc_start: 0.9305 (mmp) cc_final: 0.8920 (mmm) REVERT: N 37 ARG cc_start: 0.8378 (mmm-85) cc_final: 0.8145 (ttm-80) outliers start: 30 outliers final: 11 residues processed: 223 average time/residue: 1.7969 time to fit residues: 437.0561 Evaluate side-chains 216 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 202 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain N residue 122 LYS Chi-restraints excluded: chain N residue 257 ASP Chi-restraints excluded: chain N residue 265 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 125 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 148 optimal weight: 0.0870 chunk 92 optimal weight: 30.0000 chunk 90 optimal weight: 20.0000 chunk 68 optimal weight: 0.5980 chunk 91 optimal weight: 30.0000 overall best weight: 1.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 18870 Z= 0.276 Angle : 0.559 6.628 27197 Z= 0.329 Chirality : 0.036 0.133 3064 Planarity : 0.004 0.049 2066 Dihedral : 30.264 179.182 5634 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.99 % Allowed : 14.74 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.24), residues: 1198 helix: 2.29 (0.22), residues: 550 sheet: 0.64 (0.34), residues: 230 loop : 0.16 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 60 HIS 0.003 0.001 HIS B 75 PHE 0.008 0.001 PHE C 25 TYR 0.014 0.001 TYR D 40 ARG 0.010 0.000 ARG M 37 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 205 time to evaluate : 1.257 Fit side-chains REVERT: A 105 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7259 (mt-10) REVERT: C 95 LYS cc_start: 0.9103 (ttmm) cc_final: 0.8873 (ttmt) REVERT: D 116 LYS cc_start: 0.8877 (ttpt) cc_final: 0.8594 (ttpp) REVERT: E 56 LYS cc_start: 0.8743 (ttpp) cc_final: 0.8496 (ttpp) REVERT: E 94 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7643 (mp0) REVERT: E 97 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7368 (mp0) REVERT: F 77 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8605 (mtpt) REVERT: G 73 ASN cc_start: 0.8721 (t0) cc_final: 0.8331 (t0) REVERT: G 74 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8609 (mtmm) REVERT: G 90 ASP cc_start: 0.8719 (OUTLIER) cc_final: 0.8321 (t0) REVERT: H 43 LYS cc_start: 0.9107 (mttt) cc_final: 0.8873 (mtpp) REVERT: H 86 ARG cc_start: 0.8264 (mmt-90) cc_final: 0.7861 (mmt90) REVERT: M 239 ASP cc_start: 0.8151 (m-30) cc_final: 0.7863 (m-30) REVERT: N 23 MET cc_start: 0.9223 (mmp) cc_final: 0.8760 (mmm) REVERT: N 37 ARG cc_start: 0.8396 (mmm-85) cc_final: 0.8174 (ttm-80) outliers start: 31 outliers final: 14 residues processed: 213 average time/residue: 1.7750 time to fit residues: 409.3806 Evaluate side-chains 217 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 198 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain N residue 122 LYS Chi-restraints excluded: chain N residue 257 ASP Chi-restraints excluded: chain N residue 265 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 29 optimal weight: 0.0770 chunk 28 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 73 optimal weight: 30.0000 chunk 13 optimal weight: 0.6980 chunk 116 optimal weight: 8.9990 chunk 135 optimal weight: 2.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18870 Z= 0.204 Angle : 0.558 12.523 27197 Z= 0.328 Chirality : 0.034 0.134 3064 Planarity : 0.004 0.045 2066 Dihedral : 30.261 179.186 5634 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.50 % Allowed : 15.90 % Favored : 81.60 % 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: 1.90 (0.24), residues: 1198 helix: 2.37 (0.22), residues: 550 sheet: 0.73 (0.35), residues: 218 loop : 0.15 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 60 HIS 0.004 0.001 HIS M 31 PHE 0.008 0.001 PHE A 67 TYR 0.018 0.001 TYR H 42 ARG 0.014 0.000 ARG M 37 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 198 time to evaluate : 1.673 Fit side-chains REVERT: C 95 LYS cc_start: 0.9103 (ttmm) cc_final: 0.8877 (ttmt) REVERT: E 56 LYS cc_start: 0.8739 (ttpp) cc_final: 0.8490 (ttpp) REVERT: E 94 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7635 (mp0) REVERT: E 97 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: F 77 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8603 (mtpt) REVERT: G 73 ASN cc_start: 0.8728 (t0) cc_final: 0.8334 (t0) REVERT: G 74 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8606 (mtmm) REVERT: G 90 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.8308 (t0) REVERT: H 43 LYS cc_start: 0.9103 (mttt) cc_final: 0.8828 (mtpp) REVERT: H 76 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7229 (tm-30) REVERT: H 86 ARG cc_start: 0.8240 (mmt-90) cc_final: 0.7852 (mmt90) REVERT: M 23 MET cc_start: 0.9085 (tpp) cc_final: 0.8668 (tpt) REVERT: M 239 ASP cc_start: 0.8093 (m-30) cc_final: 0.7784 (m-30) REVERT: N 23 MET cc_start: 0.9224 (mmp) cc_final: 0.8757 (mmm) outliers start: 26 outliers final: 14 residues processed: 206 average time/residue: 1.7482 time to fit residues: 390.8075 Evaluate side-chains 218 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 198 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain N residue 122 LYS Chi-restraints excluded: chain N residue 257 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 8.9990 chunk 129 optimal weight: 10.0000 chunk 138 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 108 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 18870 Z= 0.306 Angle : 0.568 6.774 27197 Z= 0.333 Chirality : 0.036 0.137 3064 Planarity : 0.004 0.061 2066 Dihedral : 30.269 179.725 5634 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.41 % Allowed : 16.28 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.24), residues: 1198 helix: 2.30 (0.22), residues: 550 sheet: 0.71 (0.34), residues: 218 loop : 0.08 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 60 HIS 0.003 0.001 HIS M 110 PHE 0.008 0.001 PHE C 25 TYR 0.015 0.002 TYR D 40 ARG 0.014 0.001 ARG M 37 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 197 time to evaluate : 1.360 Fit side-chains REVERT: A 105 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7335 (mt-10) REVERT: E 56 LYS cc_start: 0.8741 (ttpp) cc_final: 0.8491 (ttpp) REVERT: E 94 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7652 (mp0) REVERT: E 97 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7310 (mp0) REVERT: F 77 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8657 (mtpt) REVERT: G 73 ASN cc_start: 0.8729 (t0) cc_final: 0.8323 (t0) REVERT: G 90 ASP cc_start: 0.8747 (OUTLIER) cc_final: 0.8345 (t0) REVERT: H 43 LYS cc_start: 0.9097 (mttt) cc_final: 0.8831 (mtpp) REVERT: H 86 ARG cc_start: 0.8265 (mmt-90) cc_final: 0.7857 (mmt90) REVERT: M 23 MET cc_start: 0.9095 (tpp) cc_final: 0.8705 (tpt) REVERT: M 239 ASP cc_start: 0.8177 (m-30) cc_final: 0.7877 (m-30) outliers start: 25 outliers final: 14 residues processed: 205 average time/residue: 1.7081 time to fit residues: 380.1644 Evaluate side-chains 213 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 195 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain N residue 122 LYS Chi-restraints excluded: chain N residue 257 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 0.0010 chunk 89 optimal weight: 8.9990 chunk 69 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 12 optimal weight: 0.5980 chunk 94 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18870 Z= 0.252 Angle : 0.573 14.829 27197 Z= 0.332 Chirality : 0.035 0.138 3064 Planarity : 0.004 0.042 2066 Dihedral : 30.275 179.829 5634 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.50 % Allowed : 16.38 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.24), residues: 1198 helix: 2.32 (0.22), residues: 550 sheet: 0.70 (0.34), residues: 218 loop : 0.11 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 60 HIS 0.003 0.001 HIS B 75 PHE 0.008 0.001 PHE C 25 TYR 0.021 0.002 TYR H 42 ARG 0.014 0.000 ARG M 37 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 195 time to evaluate : 1.373 Fit side-chains REVERT: E 56 LYS cc_start: 0.8739 (ttpp) cc_final: 0.8489 (ttpp) REVERT: E 94 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7648 (mp0) REVERT: E 97 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7320 (mp0) REVERT: F 77 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8600 (mtpt) REVERT: G 73 ASN cc_start: 0.8701 (t0) cc_final: 0.8294 (t0) REVERT: G 90 ASP cc_start: 0.8733 (OUTLIER) cc_final: 0.8328 (t0) REVERT: H 43 LYS cc_start: 0.9067 (mttt) cc_final: 0.8799 (mtpp) REVERT: H 86 ARG cc_start: 0.8247 (mmt-90) cc_final: 0.7842 (mmt90) REVERT: M 23 MET cc_start: 0.9090 (tpp) cc_final: 0.8701 (tpt) REVERT: M 230 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.8070 (ttp) REVERT: M 239 ASP cc_start: 0.8078 (m-30) cc_final: 0.7775 (m-30) REVERT: N 23 MET cc_start: 0.9218 (mmp) cc_final: 0.8735 (mmm) outliers start: 26 outliers final: 16 residues processed: 205 average time/residue: 1.7119 time to fit residues: 380.7799 Evaluate side-chains 218 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 197 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 230 MET Chi-restraints excluded: chain N residue 122 LYS Chi-restraints excluded: chain N residue 257 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 112 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 122 optimal weight: 7.9990 chunk 51 optimal weight: 0.8980 chunk 125 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.126398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.078469 restraints weight = 30823.856| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.43 r_work: 0.2877 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18870 Z= 0.214 Angle : 0.559 8.566 27197 Z= 0.328 Chirality : 0.035 0.135 3064 Planarity : 0.004 0.051 2066 Dihedral : 30.259 179.764 5634 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.41 % Allowed : 16.38 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.24), residues: 1198 helix: 2.36 (0.21), residues: 550 sheet: 0.68 (0.34), residues: 218 loop : 0.13 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 60 HIS 0.003 0.001 HIS B 75 PHE 0.008 0.001 PHE E 67 TYR 0.018 0.001 TYR M 203 ARG 0.014 0.000 ARG M 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6822.37 seconds wall clock time: 120 minutes 48.01 seconds (7248.01 seconds total)