Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 16:56:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5x_22683/04_2023/7k5x_22683.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5x_22683/04_2023/7k5x_22683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5x_22683/04_2023/7k5x_22683.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5x_22683/04_2023/7k5x_22683.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5x_22683/04_2023/7k5x_22683.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5x_22683/04_2023/7k5x_22683.pdb" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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 33 5.16 5 C 10258 2.51 5 N 3350 2.21 5 O 4256 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 81": "OD1" <-> "OD2" Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 106": "OD1" <-> "OD2" Residue "A ASP 123": "OD1" <-> "OD2" Residue "B ASP 24": "OD1" <-> "OD2" Residue "B TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 51": "OD1" <-> "OD2" Residue "D ASP 68": "OD1" <-> "OD2" Residue "D PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 73": "OE1" <-> "OE2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "E ASP 106": "OD1" <-> "OD2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F ASP 68": "OD1" <-> "OD2" Residue "F ASP 85": "OD1" <-> "OD2" Residue "F TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 56": "OE1" <-> "OE2" Residue "G GLU 64": "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 93": "OE1" <-> "OE2" Residue "H GLU 113": "OE1" <-> "OE2" Residue "M ASP 20": "OD1" <-> "OD2" Residue "M ARG 37": "NH1" <-> "NH2" Residue "M TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 75": "OD1" <-> "OD2" Residue "M ARG 80": "NH1" <-> "NH2" Residue "M PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 89": "OD1" <-> "OD2" Residue "M ASP 101": "OD1" <-> "OD2" Residue "M TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 211": "OE1" <-> "OE2" Residue "M TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 37": "NH1" <-> "NH2" Residue "N ASP 47": "OD1" <-> "OD2" 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 ASP 89": "OD1" <-> "OD2" Residue "N PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 124": "OE1" <-> "OE2" Residue "N TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 238": "OE1" <-> "OE2" Residue "N TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 29": "OD1" <-> "OD2" Residue "U GLU 61": "OE1" <-> "OE2" Residue "U PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 18291 Number of models: 1 Model: "" Number of chains: 13 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 Chain: "U" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 568 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Time building chain proxies: 9.12, per 1000 atoms: 0.50 Number of scatterers: 18291 At special positions: 0 Unit cell: (133.875, 123.375, 200.812, 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 33 16.00 P 394 15.00 O 4256 8.00 N 3350 7.00 C 10258 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: 8.49 Conformation dependent library (CDL) restraints added in 1.8 seconds 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2408 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 23 sheets defined 48.6% alpha, 20.9% beta 197 base pairs and 340 stacking pairs defined. Time for finding SS restraints: 6.98 Creating SS restraints... Processing helix chain 'A' and resid 45 through 57 removed outlier: 3.694A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.849A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.633A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.526A 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: 3.626A 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: 4.312A 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 124 removed outlier: 3.719A 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 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.660A 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 73 removed outlier: 4.249A 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 104 through 124 removed outlier: 3.718A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 102 removed outlier: 3.702A 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: 3.721A 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: 3.512A 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 helix chain 'U' and resid 26 through 38 removed outlier: 3.605A pdb=" N MET U 30 " --> pdb=" O LYS U 26 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU U 38 " --> pdb=" O ALA U 34 " (cutoff:3.500A) Processing helix chain 'U' and resid 46 through 57 removed outlier: 3.633A pdb=" N LYS U 54 " --> pdb=" O GLN U 50 " (cutoff:3.500A) Processing helix chain 'U' and resid 62 through 77 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.684A 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 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.327A 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: 6.624A 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: 6.672A 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: 7.241A 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: 3.634A 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: 3.566A pdb=" N GLU M 124 " --> pdb=" O MET M 30 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU M 52 " --> pdb=" O TYR M 68 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N TYR M 68 " --> pdb=" O LEU M 52 " (cutoff:3.500A) removed outlier: 6.459A 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: 3.566A pdb=" N GLU M 124 " --> pdb=" O MET M 30 " (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: 6.479A pdb=" N ILE M 183 " --> pdb=" O TYR M 199 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TYR M 199 " --> pdb=" O ILE M 183 " (cutoff:3.500A) removed outlier: 6.874A 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: 4.045A 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: 3.559A 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: 6.785A pdb=" N LEU N 52 " --> pdb=" O TYR N 68 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TYR N 68 " --> pdb=" O LEU N 52 " (cutoff:3.500A) removed outlier: 6.476A 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 removed outlier: 3.528A pdb=" N THR N 116 " --> pdb=" O GLN N 109 " (cutoff:3.500A) 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: 8.076A pdb=" N TYR N 181 " --> pdb=" O TYR N 201 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N TYR N 201 " --> pdb=" O TYR N 181 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE N 183 " --> pdb=" O TYR N 199 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N TYR N 199 " --> pdb=" O ILE N 183 " (cutoff:3.500A) removed outlier: 6.866A 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: 3.942A pdb=" N TYR N 258 " --> pdb=" O ARG N 247 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'U' and resid 44 through 45 removed outlier: 6.653A pdb=" N SER U 91 " --> pdb=" O THR U 83 " (cutoff:3.500A) 615 hydrogen bonds defined for protein. 1692 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 510 hydrogen bonds 1020 hydrogen bond angles 0 basepair planarities 197 basepair parallelities 340 stacking parallelities Total time for adding SS restraints: 7.29 Time building geometry restraints manager: 8.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4002 1.33 - 1.45: 5933 1.45 - 1.57: 8669 1.57 - 1.69: 786 1.69 - 1.81: 54 Bond restraints: 19444 Sorted by residual: bond pdb=" CA ASP F 24 " pdb=" CB ASP F 24 " ideal model delta sigma weight residual 1.527 1.539 -0.012 7.60e-03 1.73e+04 2.40e+00 bond pdb=" C3' DT J 153 " pdb=" O3' DT J 153 " ideal model delta sigma weight residual 1.422 1.463 -0.041 3.00e-02 1.11e+03 1.86e+00 bond pdb=" N ASP A 81 " pdb=" CA ASP A 81 " ideal model delta sigma weight residual 1.457 1.474 -0.016 1.29e-02 6.01e+03 1.59e+00 bond pdb=" CG1 ILE C 87 " pdb=" CD1 ILE C 87 " ideal model delta sigma weight residual 1.513 1.470 0.043 3.90e-02 6.57e+02 1.23e+00 bond pdb=" C3' DG J 119 " pdb=" O3' DG J 119 " ideal model delta sigma weight residual 1.422 1.454 -0.032 3.00e-02 1.11e+03 1.15e+00 ... (remaining 19439 not shown) Histogram of bond angle deviations from ideal: 98.05 - 105.24: 1712 105.24 - 112.43: 10822 112.43 - 119.61: 6065 119.61 - 126.80: 8212 126.80 - 133.99: 1151 Bond angle restraints: 27962 Sorted by residual: angle pdb=" N ARG B 23 " pdb=" CA ARG B 23 " pdb=" C ARG B 23 " ideal model delta sigma weight residual 110.80 115.93 -5.13 2.13e+00 2.20e-01 5.80e+00 angle pdb=" C3' DC I 72 " pdb=" C2' DC I 72 " pdb=" C1' DC I 72 " ideal model delta sigma weight residual 101.60 98.05 3.55 1.50e+00 4.44e-01 5.61e+00 angle pdb=" CA GLN N 192 " pdb=" CB GLN N 192 " pdb=" CG GLN N 192 " ideal model delta sigma weight residual 114.10 118.75 -4.65 2.00e+00 2.50e-01 5.40e+00 angle pdb=" C TYR M 69 " pdb=" N ALA M 70 " pdb=" CA ALA M 70 " ideal model delta sigma weight residual 121.54 125.94 -4.40 1.91e+00 2.74e-01 5.31e+00 angle pdb=" CA ARG B 23 " pdb=" C ARG B 23 " pdb=" N ASP B 24 " ideal model delta sigma weight residual 116.84 120.66 -3.82 1.71e+00 3.42e-01 5.00e+00 ... (remaining 27957 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.54: 8433 34.54 - 69.07: 1845 69.07 - 103.61: 28 103.61 - 138.15: 0 138.15 - 172.69: 2 Dihedral angle restraints: 10308 sinusoidal: 6550 harmonic: 3758 Sorted by residual: dihedral pdb=" CA PRO D 103 " pdb=" C PRO D 103 " pdb=" N GLY D 104 " pdb=" CA GLY D 104 " ideal model delta harmonic sigma weight residual 180.00 160.05 19.95 0 5.00e+00 4.00e-02 1.59e+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 47.31 172.69 1 3.50e+01 8.16e-04 1.56e+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 67.79 152.21 1 3.50e+01 8.16e-04 1.48e+01 ... (remaining 10305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2104 0.032 - 0.064: 792 0.064 - 0.095: 177 0.095 - 0.127: 67 0.127 - 0.159: 10 Chirality restraints: 3150 Sorted by residual: 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 6.32e-01 chirality pdb=" CA ASP A 81 " pdb=" N ASP A 81 " pdb=" C ASP A 81 " pdb=" CB ASP A 81 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.62e-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 2.37 0.14 2.00e-01 2.50e+01 4.77e-01 ... (remaining 3147 not shown) Planarity restraints: 2162 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY M 157 " -0.040 5.00e-02 4.00e+02 6.03e-02 5.81e+00 pdb=" N PRO M 158 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO M 158 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO M 158 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 125 " -0.026 2.00e-02 2.50e+03 1.09e-02 3.56e+00 pdb=" N9 DG I 125 " 0.025 2.00e-02 2.50e+03 pdb=" C8 DG I 125 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DG I 125 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DG I 125 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DG I 125 " -0.002 2.00e-02 2.50e+03 pdb=" O6 DG I 125 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 125 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DG I 125 " -0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 125 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DG I 125 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 125 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 31 " -0.030 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO B 32 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " -0.025 5.00e-02 4.00e+02 ... (remaining 2159 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1905 2.75 - 3.29: 16528 3.29 - 3.82: 35552 3.82 - 4.36: 42582 4.36 - 4.90: 62107 Nonbonded interactions: 158674 Sorted by model distance: nonbonded pdb=" OE2 GLU D 113 " pdb=" NH1 ARG M 253 " model vdw 2.211 2.520 nonbonded pdb=" OE2 GLU C 41 " pdb=" OG SER D 87 " model vdw 2.226 2.440 nonbonded pdb=" OE1 GLU C 92 " pdb=" NH1 ARG M 251 " model vdw 2.238 2.520 nonbonded pdb=" OG1 THR F 82 " pdb=" OD2 ASP F 85 " model vdw 2.253 2.440 nonbonded pdb=" OD2 ASP D 68 " pdb=" OH TYR F 98 " model vdw 2.276 2.440 ... (remaining 158669 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 5.310 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 51.490 Find NCS groups from input model: 0.640 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: 0.000 Load rotamer database and sin/cos tables:13.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 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 0.050 19444 Z= 0.207 Angle : 0.605 5.782 27962 Z= 0.373 Chirality : 0.037 0.159 3150 Planarity : 0.004 0.060 2162 Dihedral : 26.423 172.687 7888 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer Outliers : 0.09 % 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: 1.31 (0.23), residues: 1270 helix: 1.84 (0.21), residues: 585 sheet: 0.07 (0.31), residues: 262 loop : 0.17 (0.31), residues: 423 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 283 time to evaluate : 1.458 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 284 average time/residue: 1.6870 time to fit residues: 522.6619 Evaluate side-chains 198 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 1.555 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 135 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 146 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN D 95 GLN E 76 GLN G 104 GLN H 63 ASN M 95 ASN M 261 GLN N 57 GLN N 95 ASN N 188 GLN ** N 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 36 GLN U 50 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.066 19444 Z= 0.279 Angle : 0.606 8.292 27962 Z= 0.356 Chirality : 0.037 0.156 3150 Planarity : 0.005 0.048 2162 Dihedral : 30.302 176.136 5390 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer Outliers : 3.18 % 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: 1.46 (0.23), residues: 1270 helix: 1.93 (0.21), residues: 590 sheet: 0.50 (0.33), residues: 240 loop : 0.02 (0.29), residues: 440 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 229 time to evaluate : 1.520 Fit side-chains outliers start: 35 outliers final: 17 residues processed: 239 average time/residue: 1.6140 time to fit residues: 422.6125 Evaluate side-chains 209 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 192 time to evaluate : 1.385 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 8 residues processed: 9 average time/residue: 0.6653 time to fit residues: 8.9599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 121 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 146 optimal weight: 0.1980 chunk 158 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 145 optimal weight: 0.0870 chunk 49 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN D 47 GLN E 108 ASN F 27 GLN G 104 GLN H 82 HIS ** N 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 19444 Z= 0.167 Angle : 0.540 6.529 27962 Z= 0.321 Chirality : 0.034 0.149 3150 Planarity : 0.004 0.044 2162 Dihedral : 30.102 175.901 5390 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer Outliers : 2.27 % 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: 1.99 (0.24), residues: 1270 helix: 2.47 (0.21), residues: 590 sheet: 0.78 (0.33), residues: 240 loop : 0.08 (0.29), residues: 440 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 226 time to evaluate : 1.503 Fit side-chains outliers start: 25 outliers final: 10 residues processed: 235 average time/residue: 1.6102 time to fit residues: 415.0898 Evaluate side-chains 210 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 200 time to evaluate : 1.465 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 5 residues processed: 5 average time/residue: 0.8167 time to fit residues: 6.6095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 144 optimal weight: 5.9990 chunk 110 optimal weight: 0.0470 chunk 76 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 139 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 129 optimal weight: 5.9990 overall best weight: 1.5484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 GLN G 104 GLN H 63 ASN H 82 HIS ** N 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 19444 Z= 0.248 Angle : 0.568 8.543 27962 Z= 0.334 Chirality : 0.036 0.161 3150 Planarity : 0.004 0.041 2162 Dihedral : 30.290 178.955 5390 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer Outliers : 2.55 % 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: 1270 helix: 2.18 (0.21), residues: 602 sheet: 0.93 (0.34), residues: 232 loop : -0.14 (0.29), residues: 436 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 210 time to evaluate : 1.667 Fit side-chains outliers start: 28 outliers final: 16 residues processed: 221 average time/residue: 1.6489 time to fit residues: 398.5934 Evaluate side-chains 203 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 187 time to evaluate : 1.416 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 9 residues processed: 8 average time/residue: 0.9846 time to fit residues: 10.7643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 88 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 132 optimal weight: 0.0050 chunk 107 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 139 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 GLN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 19444 Z= 0.230 Angle : 0.559 7.222 27962 Z= 0.328 Chirality : 0.035 0.153 3150 Planarity : 0.004 0.039 2162 Dihedral : 30.237 179.569 5390 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer Outliers : 2.64 % 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: 1.73 (0.24), residues: 1270 helix: 2.20 (0.21), residues: 602 sheet: 0.96 (0.34), residues: 232 loop : -0.21 (0.29), residues: 436 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 210 time to evaluate : 1.498 Fit side-chains outliers start: 29 outliers final: 20 residues processed: 224 average time/residue: 1.5509 time to fit residues: 382.6899 Evaluate side-chains 215 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 195 time to evaluate : 1.592 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 12 residues processed: 9 average time/residue: 0.5719 time to fit residues: 8.3083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 140 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 91 optimal weight: 30.0000 chunk 38 optimal weight: 0.0870 chunk 155 optimal weight: 4.9990 chunk 129 optimal weight: 8.9990 chunk 72 optimal weight: 30.0000 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 overall best weight: 1.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 GLN F 25 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 82 HIS ** N 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 19444 Z= 0.289 Angle : 0.587 9.355 27962 Z= 0.341 Chirality : 0.037 0.155 3150 Planarity : 0.004 0.037 2162 Dihedral : 30.411 178.364 5390 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 3.00 % 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: 1.49 (0.23), residues: 1270 helix: 1.98 (0.21), residues: 602 sheet: 0.81 (0.34), residues: 232 loop : -0.28 (0.29), residues: 436 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 196 time to evaluate : 1.613 Fit side-chains outliers start: 33 outliers final: 24 residues processed: 214 average time/residue: 1.5432 time to fit residues: 363.5615 Evaluate side-chains 215 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 191 time to evaluate : 1.618 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 14 residues processed: 10 average time/residue: 1.1618 time to fit residues: 15.0451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 17 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 113 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 24 GLN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 82 HIS M 31 HIS ** N 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 19444 Z= 0.283 Angle : 0.581 8.222 27962 Z= 0.338 Chirality : 0.036 0.154 3150 Planarity : 0.004 0.037 2162 Dihedral : 30.421 178.601 5390 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 2.91 % 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: 1.41 (0.23), residues: 1270 helix: 1.95 (0.21), residues: 602 sheet: 0.74 (0.34), residues: 232 loop : -0.33 (0.29), residues: 436 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 201 time to evaluate : 1.531 Fit side-chains outliers start: 32 outliers final: 20 residues processed: 218 average time/residue: 1.6504 time to fit residues: 394.1704 Evaluate side-chains 207 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 187 time to evaluate : 1.472 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 14 residues processed: 6 average time/residue: 0.4332 time to fit residues: 5.2582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 92 optimal weight: 20.0000 chunk 46 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 141 optimal weight: 0.9980 chunk 148 optimal weight: 0.9980 chunk 135 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 82 HIS M 31 HIS ** N 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 19444 Z= 0.184 Angle : 0.570 10.275 27962 Z= 0.331 Chirality : 0.035 0.156 3150 Planarity : 0.004 0.060 2162 Dihedral : 30.392 178.191 5390 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 2.27 % 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: 1.66 (0.24), residues: 1270 helix: 2.20 (0.21), residues: 602 sheet: 0.82 (0.34), residues: 232 loop : -0.27 (0.29), residues: 436 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 192 time to evaluate : 1.444 Fit side-chains outliers start: 25 outliers final: 20 residues processed: 209 average time/residue: 1.5343 time to fit residues: 353.8566 Evaluate side-chains 208 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 188 time to evaluate : 1.513 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 13 residues processed: 7 average time/residue: 1.0404 time to fit residues: 10.1690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 144 optimal weight: 9.9990 chunk 148 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 136 optimal weight: 0.4980 chunk 94 optimal weight: 7.9990 chunk 152 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 82 HIS M 31 HIS ** N 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 19444 Z= 0.199 Angle : 0.561 8.237 27962 Z= 0.327 Chirality : 0.034 0.150 3150 Planarity : 0.004 0.052 2162 Dihedral : 30.232 178.350 5390 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 1.91 % 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: 1.69 (0.24), residues: 1270 helix: 2.23 (0.21), residues: 602 sheet: 0.87 (0.35), residues: 232 loop : -0.29 (0.29), residues: 436 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 204 time to evaluate : 1.568 Fit side-chains outliers start: 21 outliers final: 17 residues processed: 220 average time/residue: 1.5570 time to fit residues: 376.8519 Evaluate side-chains 211 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 194 time to evaluate : 1.554 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 14 residues processed: 3 average time/residue: 0.7818 time to fit residues: 4.6923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 72 optimal weight: 30.0000 chunk 106 optimal weight: 5.9990 chunk 160 optimal weight: 10.0000 chunk 147 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 63 ASN H 82 HIS M 31 HIS ** N 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 19444 Z= 0.248 Angle : 0.582 10.311 27962 Z= 0.336 Chirality : 0.035 0.153 3150 Planarity : 0.004 0.051 2162 Dihedral : 30.307 177.000 5390 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 1.64 % 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: 1.53 (0.24), residues: 1270 helix: 2.06 (0.21), residues: 602 sheet: 0.84 (0.34), residues: 232 loop : -0.33 (0.29), residues: 436 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 187 time to evaluate : 1.657 Fit side-chains outliers start: 18 outliers final: 16 residues processed: 204 average time/residue: 1.6617 time to fit residues: 372.4851 Evaluate side-chains 204 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 188 time to evaluate : 1.595 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 15 residues processed: 1 average time/residue: 0.1603 time to fit residues: 2.1649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 117 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 chunk 53 optimal weight: 0.1980 chunk 131 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 7 optimal weight: 0.3980 chunk 92 optimal weight: 20.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 82 HIS M 31 HIS ** N 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.156608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.103263 restraints weight = 27174.859| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.50 r_work: 0.3219 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 19444 Z= 0.196 Angle : 0.566 8.693 27962 Z= 0.329 Chirality : 0.034 0.151 3150 Planarity : 0.004 0.058 2162 Dihedral : 30.265 177.028 5390 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 2.09 % 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: 1.64 (0.24), residues: 1270 helix: 2.17 (0.21), residues: 602 sheet: 0.87 (0.35), residues: 232 loop : -0.31 (0.29), residues: 436 =============================================================================== Job complete usr+sys time: 6656.21 seconds wall clock time: 118 minutes 42.56 seconds (7122.56 seconds total)