Starting phenix.real_space_refine on Mon Mar 18 09:21:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5x_22683/03_2024/7k5x_22683.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5x_22683/03_2024/7k5x_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_22683/03_2024/7k5x_22683.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5x_22683/03_2024/7k5x_22683.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5x_22683/03_2024/7k5x_22683.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5x_22683/03_2024/7k5x_22683.pdb" } resolution = 2.93 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 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 9.54, per 1000 atoms: 0.52 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: 8.81 Conformation dependent library (CDL) restraints added in 2.1 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: 7.78 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: 7.10 Time building geometry restraints manager: 9.32 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: 8737 34.54 - 69.07: 1865 69.07 - 103.61: 28 103.61 - 138.15: 0 138.15 - 172.69: 2 Dihedral angle restraints: 10632 sinusoidal: 6874 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 10629 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: 1.500 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: 0.020 Extract box with map and model: 4.530 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 54.780 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: 0.000 Load rotamer database and sin/cos tables:10.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.920 ------------------------------------------------------------------------------- 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 : 26.256 172.687 8212 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 % Allowed : 0.09 % Favored : 99.82 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP M 196 HIS 0.005 0.001 HIS F 75 PHE 0.010 0.001 PHE H 65 TYR 0.024 0.002 TYR C 50 ARG 0.011 0.001 ARG E 69 *********************** 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 : 1.500 Fit side-chains REVERT: A 77 ASP cc_start: 0.7299 (m-30) cc_final: 0.6997 (t0) REVERT: A 120 MET cc_start: 0.7852 (mtt) cc_final: 0.7249 (mtt) REVERT: B 84 MET cc_start: 0.8172 (mmm) cc_final: 0.7886 (mmm) REVERT: B 93 GLN cc_start: 0.8346 (mt0) cc_final: 0.8081 (mt0) REVERT: C 19 SER cc_start: 0.8788 (p) cc_final: 0.8398 (p) REVERT: C 61 GLU cc_start: 0.8073 (tp30) cc_final: 0.7611 (tp30) REVERT: C 95 LYS cc_start: 0.8778 (tttm) cc_final: 0.8362 (ttmp) REVERT: E 73 GLU cc_start: 0.7940 (tt0) cc_final: 0.7705 (tt0) REVERT: F 26 ILE cc_start: 0.8793 (tp) cc_final: 0.8551 (tt) REVERT: G 62 ILE cc_start: 0.9050 (mt) cc_final: 0.8795 (mt) REVERT: N 30 MET cc_start: 0.7847 (mpp) cc_final: 0.7398 (mtm) REVERT: N 160 LEU cc_start: 0.7826 (mm) cc_final: 0.7602 (mm) REVERT: N 162 GLU cc_start: 0.7825 (pp20) cc_final: 0.7427 (pp20) REVERT: N 210 ASN cc_start: 0.8533 (t0) cc_final: 0.8137 (t0) REVERT: U 30 MET cc_start: 0.6633 (mtp) cc_final: 0.6317 (mtp) outliers start: 1 outliers final: 0 residues processed: 284 average time/residue: 1.6391 time to fit residues: 506.4396 Evaluate side-chains 211 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 1.340 ------------------------------------------------------------------------------- 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: 2.9990 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 95 ASN ** N 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 36 GLN U 50 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1327 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= 0.278 Angle : 0.600 7.360 27962 Z= 0.353 Chirality : 0.037 0.159 3150 Planarity : 0.005 0.044 2162 Dihedral : 29.750 175.250 5714 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.73 % Allowed : 11.92 % Favored : 85.35 % 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: 1.95 (0.21), residues: 590 sheet: 0.45 (0.32), residues: 252 loop : 0.08 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 196 HIS 0.006 0.001 HIS H 109 PHE 0.010 0.002 PHE N 117 TYR 0.020 0.002 TYR C 50 ARG 0.009 0.001 ARG N 37 *********************** 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 247 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 217 time to evaluate : 1.066 Fit side-chains REVERT: B 93 GLN cc_start: 0.8459 (mt0) cc_final: 0.8228 (mt0) REVERT: C 61 GLU cc_start: 0.8139 (tp30) cc_final: 0.7519 (tp30) REVERT: D 93 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7881 (mp0) REVERT: G 62 ILE cc_start: 0.9157 (mt) cc_final: 0.8941 (mt) REVERT: G 75 LYS cc_start: 0.8672 (mtpt) cc_final: 0.8371 (mtpp) REVERT: M 97 LEU cc_start: 0.8693 (mt) cc_final: 0.8400 (mp) REVERT: M 154 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7598 (tp-100) REVERT: M 230 MET cc_start: 0.8229 (ttp) cc_final: 0.7902 (ttp) REVERT: N 154 GLN cc_start: 0.8557 (mm-40) cc_final: 0.8312 (mm-40) REVERT: U 30 MET cc_start: 0.6707 (mtp) cc_final: 0.6397 (mtp) REVERT: U 67 ILE cc_start: 0.7989 (mt) cc_final: 0.7693 (mt) outliers start: 30 outliers final: 16 residues processed: 227 average time/residue: 1.4707 time to fit residues: 366.0643 Evaluate side-chains 213 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 196 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain N residue 36 GLU Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain U residue 79 VAL 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: 0.9990 chunk 121 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 40 optimal weight: 0.0060 chunk 146 optimal weight: 0.2980 chunk 158 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 overall best weight: 1.0600 ------------------------------------------------------------------------------- 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 G 104 GLN H 82 HIS N 57 GLN N 188 GLN ** N 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 50 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 19444 Z= 0.201 Angle : 0.549 6.698 27962 Z= 0.327 Chirality : 0.035 0.152 3150 Planarity : 0.004 0.043 2162 Dihedral : 29.666 175.888 5714 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.91 % Allowed : 12.83 % Favored : 84.26 % 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 (0.23), residues: 1270 helix: 2.30 (0.21), residues: 590 sheet: 0.80 (0.33), residues: 240 loop : 0.03 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 60 HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE E 67 TYR 0.013 0.001 TYR G 57 ARG 0.010 0.000 ARG N 37 *********************** 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 248 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 216 time to evaluate : 1.466 Fit side-chains REVERT: A 37 LYS cc_start: 0.6983 (ptpp) cc_final: 0.6584 (ptpt) REVERT: A 120 MET cc_start: 0.7958 (mtt) cc_final: 0.7410 (mtt) REVERT: C 61 GLU cc_start: 0.8089 (tp30) cc_final: 0.7633 (tp30) REVERT: C 74 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8093 (mtmm) REVERT: D 47 GLN cc_start: 0.7968 (mt0) cc_final: 0.7749 (mt0) REVERT: D 68 ASP cc_start: 0.8560 (t0) cc_final: 0.8148 (t0) REVERT: D 93 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7862 (mp0) REVERT: F 25 ASN cc_start: 0.8351 (m110) cc_final: 0.8047 (m110) REVERT: G 13 LYS cc_start: 0.8036 (tppp) cc_final: 0.7832 (tppt) REVERT: G 95 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8042 (ttpp) REVERT: M 154 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7653 (tp-100) REVERT: N 101 ASP cc_start: 0.7736 (m-30) cc_final: 0.7500 (m-30) REVERT: U 30 MET cc_start: 0.6706 (mtp) cc_final: 0.6443 (mtp) outliers start: 32 outliers final: 13 residues processed: 227 average time/residue: 1.5553 time to fit residues: 387.2674 Evaluate side-chains 207 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 191 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 195 GLU Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 160 LEU Chi-restraints excluded: chain U residue 79 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 144 optimal weight: 9.9990 chunk 110 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 16 optimal weight: 0.4980 chunk 69 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 129 optimal weight: 10.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 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: 0.7991 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 19444 Z= 0.257 Angle : 0.571 8.382 27962 Z= 0.335 Chirality : 0.036 0.155 3150 Planarity : 0.004 0.041 2162 Dihedral : 29.810 178.626 5714 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.37 % Allowed : 15.20 % Favored : 81.44 % 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: 1.75 (0.23), residues: 1270 helix: 2.19 (0.21), residues: 590 sheet: 0.87 (0.34), residues: 240 loop : -0.03 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP M 60 HIS 0.005 0.001 HIS F 75 PHE 0.009 0.001 PHE N 117 TYR 0.017 0.002 TYR H 40 ARG 0.010 0.001 ARG M 37 *********************** 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 241 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 204 time to evaluate : 1.378 Fit side-chains REVERT: A 37 LYS cc_start: 0.7125 (ptpp) cc_final: 0.6748 (ptpt) REVERT: C 61 GLU cc_start: 0.8113 (tp30) cc_final: 0.7637 (tp30) REVERT: C 74 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8081 (mtmm) REVERT: D 68 ASP cc_start: 0.8533 (t0) cc_final: 0.8116 (t0) REVERT: D 93 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7845 (mp0) REVERT: F 25 ASN cc_start: 0.8420 (m110) cc_final: 0.8151 (m110) REVERT: G 95 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8063 (ttpp) REVERT: M 230 MET cc_start: 0.8274 (ttp) cc_final: 0.7856 (ttm) REVERT: N 101 ASP cc_start: 0.7744 (m-30) cc_final: 0.7469 (m-30) REVERT: N 162 GLU cc_start: 0.7723 (pp20) cc_final: 0.7509 (pp20) REVERT: N 230 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.6601 (tpt) outliers start: 37 outliers final: 17 residues processed: 216 average time/residue: 1.6291 time to fit residues: 384.2710 Evaluate side-chains 210 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 189 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 75 ASP Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 195 GLU Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 230 MET Chi-restraints excluded: chain U residue 79 VAL 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: 0.0070 chunk 64 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 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: 3.9990 overall best weight: 1.5804 ------------------------------------------------------------------------------- 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 M 95 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2204 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= 0.247 Angle : 0.558 7.338 27962 Z= 0.329 Chirality : 0.036 0.154 3150 Planarity : 0.004 0.039 2162 Dihedral : 29.761 179.638 5714 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.55 % Allowed : 16.92 % Favored : 79.53 % 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: 1.76 (0.23), residues: 1270 helix: 2.23 (0.21), residues: 590 sheet: 0.82 (0.33), residues: 240 loop : -0.05 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 60 HIS 0.005 0.001 HIS F 75 PHE 0.009 0.001 PHE M 178 TYR 0.020 0.002 TYR H 40 ARG 0.010 0.000 ARG H 33 *********************** 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 245 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 206 time to evaluate : 1.409 Fit side-chains REVERT: A 37 LYS cc_start: 0.7048 (ptpp) cc_final: 0.6686 (ptpt) REVERT: C 61 GLU cc_start: 0.8197 (tp30) cc_final: 0.7725 (tp30) REVERT: C 73 ASN cc_start: 0.8377 (t0) cc_final: 0.7841 (t0) REVERT: C 74 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8170 (mtmm) REVERT: D 93 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7866 (mp0) REVERT: F 25 ASN cc_start: 0.8445 (m110) cc_final: 0.8162 (m110) REVERT: G 95 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8071 (ttpp) REVERT: M 154 GLN cc_start: 0.8112 (mm-40) cc_final: 0.7881 (tp-100) REVERT: M 230 MET cc_start: 0.8226 (ttp) cc_final: 0.7983 (ttm) REVERT: M 261 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7320 (pt0) REVERT: N 30 MET cc_start: 0.7836 (mtm) cc_final: 0.7594 (mtm) REVERT: N 101 ASP cc_start: 0.7740 (m-30) cc_final: 0.7505 (m-30) REVERT: N 154 GLN cc_start: 0.8527 (mm-40) cc_final: 0.8176 (mm-40) REVERT: N 230 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.6522 (tpt) outliers start: 39 outliers final: 24 residues processed: 221 average time/residue: 1.5761 time to fit residues: 381.9339 Evaluate side-chains 220 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 191 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 23 MET Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 75 ASP Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 195 GLU Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain M residue 261 GLN Chi-restraints excluded: chain N residue 80 ARG Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 230 MET Chi-restraints excluded: chain N residue 257 ASP Chi-restraints excluded: chain U residue 79 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 140 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 91 optimal weight: 30.0000 chunk 38 optimal weight: 0.7980 chunk 155 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 72 optimal weight: 30.0000 chunk 12 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- 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 ** 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: 0.8015 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 19444 Z= 0.310 Angle : 0.594 9.180 27962 Z= 0.346 Chirality : 0.037 0.157 3150 Planarity : 0.004 0.037 2162 Dihedral : 29.969 178.167 5714 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.28 % Allowed : 17.29 % Favored : 78.43 % 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: 1.52 (0.24), residues: 1270 helix: 2.02 (0.21), residues: 590 sheet: 0.55 (0.33), residues: 252 loop : -0.05 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 60 HIS 0.006 0.001 HIS F 75 PHE 0.008 0.002 PHE H 70 TYR 0.025 0.002 TYR H 40 ARG 0.011 0.001 ARG N 37 *********************** 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 244 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 197 time to evaluate : 1.653 Fit side-chains REVERT: A 37 LYS cc_start: 0.6763 (ptpp) cc_final: 0.6465 (ptpt) REVERT: A 73 GLU cc_start: 0.7706 (tt0) cc_final: 0.7481 (tt0) REVERT: B 93 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8016 (mt0) REVERT: C 61 GLU cc_start: 0.8204 (tp30) cc_final: 0.7573 (tp30) REVERT: C 73 ASN cc_start: 0.8483 (t0) cc_final: 0.7976 (t0) REVERT: C 74 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8217 (mtmm) REVERT: D 93 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8087 (mp0) REVERT: F 25 ASN cc_start: 0.8495 (m110) cc_final: 0.8229 (m110) REVERT: G 95 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8099 (ttpp) REVERT: H 33 ARG cc_start: 0.7670 (mtp-110) cc_final: 0.7453 (mtp-110) REVERT: M 154 GLN cc_start: 0.8131 (mm-40) cc_final: 0.7924 (tp-100) REVERT: M 261 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7663 (pt0) REVERT: N 101 ASP cc_start: 0.7776 (m-30) cc_final: 0.7525 (m-30) REVERT: N 154 GLN cc_start: 0.8513 (mm-40) cc_final: 0.8188 (mm-40) REVERT: N 230 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.6587 (tpt) outliers start: 47 outliers final: 27 residues processed: 217 average time/residue: 1.5079 time to fit residues: 359.7703 Evaluate side-chains 226 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 193 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 23 MET Chi-restraints excluded: chain M residue 75 ASP Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 195 GLU Chi-restraints excluded: chain M residue 230 MET Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain M residue 261 GLN Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 80 ARG Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 160 LEU Chi-restraints excluded: chain N residue 230 MET Chi-restraints excluded: chain U residue 79 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 17 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 ** 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: 0.7998 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 19444 Z= 0.266 Angle : 0.572 8.088 27962 Z= 0.335 Chirality : 0.036 0.152 3150 Planarity : 0.004 0.038 2162 Dihedral : 29.858 178.844 5714 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.82 % Allowed : 18.38 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.24), residues: 1270 helix: 2.12 (0.21), residues: 590 sheet: 0.62 (0.33), residues: 252 loop : -0.09 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP M 60 HIS 0.005 0.001 HIS F 75 PHE 0.009 0.001 PHE E 67 TYR 0.025 0.002 TYR H 40 ARG 0.012 0.001 ARG N 37 *********************** 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 242 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 200 time to evaluate : 1.533 Fit side-chains REVERT: A 37 LYS cc_start: 0.6738 (ptpp) cc_final: 0.6444 (ptpt) REVERT: B 84 MET cc_start: 0.8480 (mmm) cc_final: 0.7800 (mmm) REVERT: C 61 GLU cc_start: 0.8195 (tp30) cc_final: 0.7514 (tp30) REVERT: C 73 ASN cc_start: 0.8426 (t0) cc_final: 0.7885 (t0) REVERT: C 74 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8129 (mtmm) REVERT: D 93 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7923 (mp0) REVERT: F 22 LEU cc_start: 0.7125 (mt) cc_final: 0.6792 (mp) REVERT: G 90 ASP cc_start: 0.8743 (t70) cc_final: 0.8301 (t0) REVERT: G 95 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8097 (ttpp) REVERT: M 230 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7991 (ttm) REVERT: N 101 ASP cc_start: 0.7774 (m-30) cc_final: 0.7531 (m-30) REVERT: N 154 GLN cc_start: 0.8508 (mm-40) cc_final: 0.8176 (mm-40) REVERT: N 230 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.6527 (tpt) outliers start: 42 outliers final: 29 residues processed: 216 average time/residue: 1.5677 time to fit residues: 374.6630 Evaluate side-chains 226 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 192 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 37 LYS Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 23 MET Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 75 ASP Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 195 GLU Chi-restraints excluded: chain M residue 230 MET Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 80 ARG Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 160 LEU Chi-restraints excluded: chain N residue 230 MET Chi-restraints excluded: chain N residue 257 ASP Chi-restraints excluded: chain U residue 79 VAL 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: 1.9990 chunk 30 optimal weight: 0.7980 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: 7.9990 chunk 141 optimal weight: 0.9980 chunk 148 optimal weight: 4.9990 chunk 135 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 95 ASN M 261 GLN ** 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: 0.8001 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 19444 Z= 0.269 Angle : 0.583 10.287 27962 Z= 0.339 Chirality : 0.036 0.153 3150 Planarity : 0.004 0.037 2162 Dihedral : 29.890 177.693 5714 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.55 % Allowed : 18.93 % Favored : 77.53 % 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: 1.58 (0.24), residues: 1270 helix: 2.08 (0.21), residues: 590 sheet: 0.74 (0.34), residues: 240 loop : -0.14 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 60 HIS 0.005 0.001 HIS F 75 PHE 0.008 0.001 PHE E 67 TYR 0.027 0.002 TYR H 40 ARG 0.013 0.001 ARG N 37 *********************** 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 232 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 193 time to evaluate : 1.563 Fit side-chains REVERT: A 37 LYS cc_start: 0.6734 (ptpp) cc_final: 0.6446 (ptpt) REVERT: B 93 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7995 (mt0) REVERT: C 61 GLU cc_start: 0.8203 (tp30) cc_final: 0.7846 (tp30) REVERT: C 73 ASN cc_start: 0.8435 (t0) cc_final: 0.7891 (t0) REVERT: C 74 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8179 (mtmm) REVERT: D 93 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7971 (mp0) REVERT: D 121 TYR cc_start: 0.8026 (t80) cc_final: 0.7755 (t80) REVERT: F 22 LEU cc_start: 0.7344 (mt) cc_final: 0.6998 (mp) REVERT: G 95 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8096 (ttpp) REVERT: M 154 GLN cc_start: 0.8223 (mm-40) cc_final: 0.7933 (tp-100) REVERT: N 101 ASP cc_start: 0.7776 (m-30) cc_final: 0.7533 (m-30) REVERT: N 154 GLN cc_start: 0.8518 (mm-40) cc_final: 0.8185 (mm-40) REVERT: N 230 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.6514 (tpt) outliers start: 39 outliers final: 29 residues processed: 209 average time/residue: 1.5596 time to fit residues: 357.7582 Evaluate side-chains 223 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 189 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 37 LYS Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 23 MET Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 195 GLU Chi-restraints excluded: chain M residue 230 MET Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 80 ARG Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 160 LEU Chi-restraints excluded: chain N residue 230 MET Chi-restraints excluded: chain N residue 257 ASP Chi-restraints excluded: chain U residue 79 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 144 optimal weight: 0.5980 chunk 148 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 62 optimal weight: 0.0770 chunk 113 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 136 optimal weight: 0.9980 chunk 94 optimal weight: 7.9990 chunk 152 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 overall best weight: 1.1340 ------------------------------------------------------------------------------- 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 ** 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: 0.7980 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19444 Z= 0.208 Angle : 0.564 8.748 27962 Z= 0.329 Chirality : 0.035 0.151 3150 Planarity : 0.004 0.050 2162 Dihedral : 29.806 177.744 5714 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.28 % Allowed : 19.84 % Favored : 76.89 % 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: 1.77 (0.24), residues: 1270 helix: 2.27 (0.21), residues: 590 sheet: 0.85 (0.34), residues: 240 loop : -0.11 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP M 60 HIS 0.004 0.001 HIS F 75 PHE 0.010 0.001 PHE E 67 TYR 0.022 0.001 TYR H 40 ARG 0.014 0.000 ARG H 33 *********************** 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 232 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 196 time to evaluate : 1.352 Fit side-chains REVERT: A 37 LYS cc_start: 0.6975 (ptpp) cc_final: 0.6644 (ptpt) REVERT: B 84 MET cc_start: 0.8473 (mmm) cc_final: 0.7830 (mmm) REVERT: B 93 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.7986 (mt0) REVERT: C 61 GLU cc_start: 0.8181 (tp30) cc_final: 0.7687 (tp30) REVERT: C 73 ASN cc_start: 0.8394 (t0) cc_final: 0.7878 (t0) REVERT: C 74 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8108 (mtmm) REVERT: D 93 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7834 (mp0) REVERT: D 121 TYR cc_start: 0.8067 (t80) cc_final: 0.7806 (t80) REVERT: F 22 LEU cc_start: 0.7210 (mt) cc_final: 0.6938 (mp) REVERT: F 25 ASN cc_start: 0.8530 (m110) cc_final: 0.8262 (m110) REVERT: G 95 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8081 (ttpp) REVERT: M 154 GLN cc_start: 0.8144 (mm-40) cc_final: 0.7909 (tp-100) REVERT: M 230 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7983 (ttm) REVERT: N 101 ASP cc_start: 0.7766 (m-30) cc_final: 0.7526 (m-30) REVERT: N 154 GLN cc_start: 0.8503 (mm-40) cc_final: 0.8169 (mm-40) REVERT: N 230 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.6441 (tpt) outliers start: 36 outliers final: 23 residues processed: 212 average time/residue: 1.4763 time to fit residues: 344.2205 Evaluate side-chains 223 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 194 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 37 LYS Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain M residue 23 MET Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 230 MET Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain N residue 80 ARG Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 160 LEU Chi-restraints excluded: chain N residue 230 MET Chi-restraints excluded: chain N residue 257 ASP Chi-restraints excluded: chain U residue 79 VAL 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: 9.9990 chunk 147 optimal weight: 0.7980 chunk 127 optimal weight: 0.0970 chunk 13 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN E 68 GLN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 82 HIS M 95 ASN ** 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: 0.7948 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19444 Z= 0.183 Angle : 0.554 11.362 27962 Z= 0.322 Chirality : 0.034 0.149 3150 Planarity : 0.004 0.055 2162 Dihedral : 29.587 177.652 5714 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.64 % Allowed : 20.66 % Favored : 76.71 % 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: 1.97 (0.24), residues: 1270 helix: 2.46 (0.21), residues: 590 sheet: 1.00 (0.35), residues: 240 loop : -0.09 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP M 60 HIS 0.004 0.001 HIS F 75 PHE 0.010 0.001 PHE E 67 TYR 0.022 0.001 TYR H 40 ARG 0.016 0.001 ARG N 37 ********************** 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 241 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 212 time to evaluate : 1.580 Fit side-chains REVERT: A 37 LYS cc_start: 0.6938 (ptpp) cc_final: 0.6620 (ptpt) REVERT: B 84 MET cc_start: 0.8464 (mmm) cc_final: 0.7865 (mmm) REVERT: B 93 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7986 (mt0) REVERT: C 61 GLU cc_start: 0.8148 (tp30) cc_final: 0.7689 (tp30) REVERT: C 73 ASN cc_start: 0.8399 (t0) cc_final: 0.8013 (t0) REVERT: C 74 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8122 (mtmm) REVERT: D 93 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7718 (mp0) REVERT: F 22 LEU cc_start: 0.7243 (mt) cc_final: 0.6986 (mp) REVERT: F 25 ASN cc_start: 0.8532 (m110) cc_final: 0.8269 (m110) REVERT: G 95 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8399 (ttpt) REVERT: M 154 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7819 (tp-100) REVERT: M 230 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7949 (ttm) REVERT: N 31 HIS cc_start: 0.7369 (m-70) cc_final: 0.6963 (m-70) REVERT: N 101 ASP cc_start: 0.7766 (m-30) cc_final: 0.7531 (m-30) REVERT: N 154 GLN cc_start: 0.8498 (mm-40) cc_final: 0.8164 (mm-40) REVERT: N 230 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.6144 (tpt) outliers start: 29 outliers final: 21 residues processed: 222 average time/residue: 1.5115 time to fit residues: 368.9067 Evaluate side-chains 223 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 196 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain M residue 23 MET Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 222 ASP Chi-restraints excluded: chain M residue 230 MET Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain N residue 80 ARG Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 160 LEU Chi-restraints excluded: chain N residue 230 MET Chi-restraints excluded: chain N residue 257 ASP Chi-restraints excluded: chain U residue 79 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 117 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 131 optimal weight: 4.9990 chunk 16 optimal weight: 0.0370 chunk 23 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 92 optimal weight: 20.0000 overall best weight: 1.3862 ------------------------------------------------------------------------------- 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 ** N 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.156261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.102988 restraints weight = 27140.323| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.50 r_work: 0.3212 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 19444 Z= 0.233 Angle : 0.576 9.462 27962 Z= 0.333 Chirality : 0.035 0.153 3150 Planarity : 0.004 0.053 2162 Dihedral : 29.672 176.783 5714 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.82 % Allowed : 21.11 % Favored : 76.07 % 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: 1.76 (0.24), residues: 1270 helix: 2.20 (0.21), residues: 602 sheet: 1.05 (0.35), residues: 232 loop : -0.21 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP M 60 HIS 0.005 0.001 HIS F 75 PHE 0.009 0.001 PHE E 67 TYR 0.030 0.002 TYR U 52 ARG 0.016 0.001 ARG N 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6588.58 seconds wall clock time: 118 minutes 34.54 seconds (7114.54 seconds total)