Starting phenix.real_space_refine on Mon Mar 18 09:03:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5y_22684/03_2024/7k5y_22684.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5y_22684/03_2024/7k5y_22684.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5y_22684/03_2024/7k5y_22684.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5y_22684/03_2024/7k5y_22684.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5y_22684/03_2024/7k5y_22684.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5y_22684/03_2024/7k5y_22684.pdb" } resolution = 2.76 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= -0.002 sd= 0.105 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2242 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 394 5.49 5 S 32 5.16 5 C 10240 2.51 5 N 3340 2.21 5 O 4252 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 73": "OE1" <-> "OE2" Residue "A ASP 77": "OD1" <-> "OD2" Residue "A ASP 106": "OD1" <-> "OD2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "B ASP 85": "OD1" <-> "OD2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 72": "OD1" <-> "OD2" Residue "D PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 93": "OE1" <-> "OE2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "E ASP 77": "OD1" <-> "OD2" Residue "E ASP 81": "OD1" <-> "OD2" Residue "E ASP 123": "OD1" <-> "OD2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "F ASP 85": "OD1" <-> "OD2" Residue "G ASP 72": "OD1" <-> "OD2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "H GLU 93": "OE1" <-> "OE2" Residue "M ARG 37": "NH1" <-> "NH2" Residue "M ASP 75": "OD1" <-> "OD2" Residue "M ARG 80": "NH1" <-> "NH2" Residue "M PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 98": "OE1" <-> "OE2" Residue "M TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 239": "OD1" <-> "OD2" Residue "N ARG 37": "NH1" <-> "NH2" Residue "N TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 75": "OD1" <-> "OD2" Residue "N ARG 80": "NH1" <-> "NH2" Residue "N PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 89": "OD1" <-> "OD2" Residue "N ASP 100": "OD1" <-> "OD2" Residue "N ASP 101": "OD1" <-> "OD2" Residue "N TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 150": "OE1" <-> "OE2" Residue "N TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 231": "OE1" <-> "OE2" Residue "N GLU 238": "OE1" <-> "OE2" Residue "U ARG 53": "NH1" <-> "NH2" Residue "U TYR 70": "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: 18258 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: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 535 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Time building chain proxies: 9.89, per 1000 atoms: 0.54 Number of scatterers: 18258 At special positions: 0 Unit cell: (133.056, 121.968, 197.568, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 394 15.00 O 4252 8.00 N 3340 7.00 C 10240 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.61 Conformation dependent library (CDL) restraints added in 2.0 seconds 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2406 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 23 sheets defined 49.0% alpha, 20.8% beta 194 base pairs and 357 stacking pairs defined. Time for finding SS restraints: 8.99 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.801A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.826A 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: 3.764A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (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: 4.353A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 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: 3.604A 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: 4.321A 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 Processing helix chain 'M' and resid 98 through 102 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: 3.516A 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: 3.600A 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 38 through 51 removed outlier: 3.737A pdb=" N LEU U 42 " --> pdb=" O PRO U 38 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER U 50 " --> pdb=" O ALA U 46 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS U 51 " --> pdb=" O VAL U 47 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 69 Processing helix chain 'U' and resid 71 through 74 removed outlier: 3.639A pdb=" N LYS U 74 " --> pdb=" O ASP U 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 71 through 74' Processing helix chain 'U' and resid 75 through 89 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.726A 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: 7.112A 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 101 through 102 removed outlier: 6.587A 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: 6.601A 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: 6.999A 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: 3.753A pdb=" N ASP M 89 " --> pdb=" O SER M 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 29 through 32 removed outlier: 6.213A pdb=" N MET M 30 " --> pdb=" O GLU M 124 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU M 52 " --> pdb=" O TYR M 68 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N TYR M 68 " --> pdb=" O LEU M 52 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TRP M 54 " --> pdb=" O LEU M 66 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 29 through 32 removed outlier: 6.213A pdb=" N MET M 30 " --> pdb=" O GLU M 124 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 152 through 155 Processing sheet with id=AB6, first strand: chain 'M' and resid 159 through 161 removed outlier: 6.208A pdb=" N GLU M 159 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N TYR M 181 " --> pdb=" O TYR M 201 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N TYR M 201 " --> pdb=" O TYR M 181 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE M 183 " --> pdb=" O TYR M 199 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TYR M 199 " --> pdb=" O ILE M 183 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TRP M 185 " --> pdb=" O ILE M 197 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 159 through 161 removed outlier: 6.208A pdb=" N GLU M 159 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 4.003A 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 25 removed outlier: 3.778A 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: 6.808A pdb=" N LEU N 52 " --> pdb=" O TYR N 68 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N TYR N 68 " --> pdb=" O LEU N 52 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP N 54 " --> pdb=" O LEU N 66 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 29 through 32 Processing sheet with id=AC2, first strand: chain 'N' and resid 152 through 155 Processing sheet with id=AC3, first strand: chain 'N' and resid 159 through 161 removed outlier: 6.602A pdb=" N ILE N 183 " --> pdb=" O TYR N 199 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYR N 199 " --> pdb=" O ILE N 183 " (cutoff:3.500A) removed outlier: 6.806A 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: 3.859A pdb=" N TYR N 258 " --> pdb=" O ARG N 247 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N SER N 249 " --> pdb=" O LEU N 256 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LEU N 256 " --> pdb=" O SER N 249 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'U' and resid 56 through 57 612 hydrogen bonds defined for protein. 1683 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 504 hydrogen bonds 1008 hydrogen bond angles 0 basepair planarities 194 basepair parallelities 357 stacking parallelities Total time for adding SS restraints: 8.03 Time building geometry restraints manager: 9.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3473 1.33 - 1.45: 6143 1.45 - 1.57: 8954 1.57 - 1.69: 786 1.69 - 1.81: 52 Bond restraints: 19408 Sorted by residual: bond pdb=" N SER M 26 " pdb=" CA SER M 26 " ideal model delta sigma weight residual 1.463 1.490 -0.027 6.90e-03 2.10e+04 1.50e+01 bond pdb=" C SER M 26 " pdb=" O SER M 26 " ideal model delta sigma weight residual 1.244 1.260 -0.016 9.10e-03 1.21e+04 3.15e+00 bond pdb=" C3' DG J 119 " pdb=" O3' DG J 119 " ideal model delta sigma weight residual 1.422 1.471 -0.049 3.00e-02 1.11e+03 2.68e+00 bond pdb=" CA SER M 26 " pdb=" C SER M 26 " ideal model delta sigma weight residual 1.521 1.505 0.016 1.08e-02 8.57e+03 2.14e+00 bond pdb=" C3' DG I 153 " pdb=" O3' DG I 153 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.59e+00 ... (remaining 19403 not shown) Histogram of bond angle deviations from ideal: 97.81 - 105.05: 1737 105.05 - 112.29: 10727 112.29 - 119.53: 5900 119.53 - 126.78: 8402 126.78 - 134.02: 1149 Bond angle restraints: 27915 Sorted by residual: angle pdb=" CA SER M 26 " pdb=" C SER M 26 " pdb=" N PRO M 27 " ideal model delta sigma weight residual 120.58 122.54 -1.96 7.40e-01 1.83e+00 6.99e+00 angle pdb=" N GLY D 104 " pdb=" CA GLY D 104 " pdb=" C GLY D 104 " ideal model delta sigma weight residual 113.18 119.19 -6.01 2.37e+00 1.78e-01 6.42e+00 angle pdb=" C3' DG J 128 " pdb=" C2' DG J 128 " pdb=" C1' DG J 128 " ideal model delta sigma weight residual 101.60 97.81 3.79 1.50e+00 4.44e-01 6.39e+00 angle pdb=" C3' DT J 153 " pdb=" O3' DT J 153 " pdb=" P DC J 154 " ideal model delta sigma weight residual 120.20 123.94 -3.74 1.50e+00 4.44e-01 6.20e+00 angle pdb=" N SER N 50 " pdb=" CA SER N 50 " pdb=" CB SER N 50 " ideal model delta sigma weight residual 113.65 110.00 3.65 1.47e+00 4.63e-01 6.16e+00 ... (remaining 27910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.24: 8535 34.24 - 68.47: 2039 68.47 - 102.71: 22 102.71 - 136.95: 3 136.95 - 171.18: 2 Dihedral angle restraints: 10601 sinusoidal: 6846 harmonic: 3755 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 180.00 159.44 20.56 0 5.00e+00 4.00e-02 1.69e+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 48.82 171.18 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 51.89 168.11 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 10598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2308 0.038 - 0.076: 668 0.076 - 0.113: 147 0.113 - 0.151: 27 0.151 - 0.189: 2 Chirality restraints: 3152 Sorted by residual: chirality pdb=" CG LEU M 252 " pdb=" CB LEU M 252 " pdb=" CD1 LEU M 252 " pdb=" CD2 LEU M 252 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.91e-01 chirality pdb=" CB THR M 177 " pdb=" CA THR M 177 " pdb=" OG1 THR M 177 " pdb=" CG2 THR M 177 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.54e-01 chirality pdb=" CG LEU N 252 " pdb=" CB LEU N 252 " pdb=" CD1 LEU N 252 " pdb=" CD2 LEU N 252 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 3149 not shown) Planarity restraints: 2154 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY M 157 " -0.038 5.00e-02 4.00e+02 5.76e-02 5.31e+00 pdb=" N PRO M 158 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO M 158 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO M 158 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " 0.030 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO D 103 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 45 " 0.021 2.00e-02 2.50e+03 1.02e-02 2.86e+00 pdb=" N9 DA I 45 " -0.026 2.00e-02 2.50e+03 pdb=" C8 DA I 45 " -0.000 2.00e-02 2.50e+03 pdb=" N7 DA I 45 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 45 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DA I 45 " 0.001 2.00e-02 2.50e+03 pdb=" N6 DA I 45 " 0.005 2.00e-02 2.50e+03 pdb=" N1 DA I 45 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 45 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA I 45 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DA I 45 " -0.002 2.00e-02 2.50e+03 ... (remaining 2151 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 491 2.67 - 3.22: 15344 3.22 - 3.78: 33372 3.78 - 4.34: 45180 4.34 - 4.90: 64961 Nonbonded interactions: 159348 Sorted by model distance: nonbonded pdb=" OD2 ASP G 90 " pdb=" NH2 ARG N 251 " model vdw 2.108 2.520 nonbonded pdb=" O SER N 156 " pdb=" OG1 THR N 263 " model vdw 2.171 2.440 nonbonded pdb=" OD2 ASP U 71 " pdb=" NZ LYS U 74 " model vdw 2.224 2.520 nonbonded pdb=" OG SER H 56 " pdb=" OP2 DA I 45 " model vdw 2.258 2.440 nonbonded pdb=" O GLN N 155 " pdb=" NE2 GLN N 261 " model vdw 2.275 2.520 ... (remaining 159343 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 7.930 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 57.770 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.090 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:13.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 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 0.049 19408 Z= 0.242 Angle : 0.647 6.616 27915 Z= 0.397 Chirality : 0.038 0.189 3152 Planarity : 0.004 0.058 2154 Dihedral : 27.043 171.183 8195 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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: 1.74 (0.23), residues: 1271 helix: 2.37 (0.21), residues: 584 sheet: 0.64 (0.33), residues: 252 loop : -0.19 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP M 185 HIS 0.005 0.001 HIS D 49 PHE 0.015 0.002 PHE D 65 TYR 0.026 0.002 TYR N 201 ARG 0.014 0.001 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 1.432 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7645 (mt-10) REVERT: E 123 ASP cc_start: 0.8714 (m-30) cc_final: 0.8467 (m-30) REVERT: G 94 ASN cc_start: 0.9158 (t0) cc_final: 0.8954 (t0) REVERT: H 42 TYR cc_start: 0.8151 (t80) cc_final: 0.7855 (t80) REVERT: M 96 ASN cc_start: 0.8143 (m-40) cc_final: 0.7910 (m-40) REVERT: M 160 LEU cc_start: 0.8575 (mm) cc_final: 0.8307 (mm) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 1.8041 time to fit residues: 526.9449 Evaluate side-chains 204 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.365 ------------------------------------------------------------------------------- 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: 2.9990 chunk 122 optimal weight: 0.0970 chunk 67 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 146 optimal weight: 2.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN F 93 GLN M 25 GLN U 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 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 0.046 19408 Z= 0.258 Angle : 0.593 6.556 27915 Z= 0.352 Chirality : 0.036 0.156 3152 Planarity : 0.004 0.048 2154 Dihedral : 30.552 170.330 5711 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.10 % Allowed : 11.51 % Favored : 86.39 % 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: 2.09 (0.24), residues: 1271 helix: 2.70 (0.21), residues: 586 sheet: 0.86 (0.33), residues: 262 loop : -0.15 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 185 HIS 0.005 0.001 HIS D 49 PHE 0.008 0.001 PHE H 70 TYR 0.028 0.002 TYR N 201 ARG 0.006 0.001 ARG H 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 211 time to evaluate : 1.311 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7618 (mtp85) REVERT: A 76 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7968 (tt0) REVERT: B 95 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7899 (mtt-85) REVERT: C 90 ASP cc_start: 0.8717 (OUTLIER) cc_final: 0.8464 (t0) REVERT: F 95 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.7729 (mtp-110) REVERT: G 94 ASN cc_start: 0.9163 (t0) cc_final: 0.8922 (t0) REVERT: M 96 ASN cc_start: 0.8224 (m-40) cc_final: 0.7917 (m-40) REVERT: M 160 LEU cc_start: 0.8554 (mm) cc_final: 0.8236 (mm) REVERT: N 230 MET cc_start: 0.8431 (ttt) cc_final: 0.8038 (ttt) outliers start: 23 outliers final: 12 residues processed: 223 average time/residue: 1.6865 time to fit residues: 409.8499 Evaluate side-chains 207 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 190 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain M residue 228 VAL Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 211 GLU Chi-restraints excluded: chain N residue 242 VAL Chi-restraints excluded: chain N residue 257 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 158 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN F 93 GLN G 24 GLN H 63 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19408 Z= 0.300 Angle : 0.590 6.982 27915 Z= 0.348 Chirality : 0.037 0.146 3152 Planarity : 0.004 0.044 2154 Dihedral : 30.296 171.958 5711 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.11 % Allowed : 13.88 % Favored : 83.01 % 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: 1271 helix: 2.60 (0.21), residues: 586 sheet: 0.87 (0.33), residues: 262 loop : -0.23 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 185 HIS 0.005 0.001 HIS D 49 PHE 0.007 0.001 PHE G 25 TYR 0.022 0.002 TYR N 201 ARG 0.006 0.001 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 194 time to evaluate : 1.342 Fit side-chains REVERT: B 92 ARG cc_start: 0.8773 (ptm-80) cc_final: 0.8524 (ptm160) REVERT: C 99 ARG cc_start: 0.8204 (mmm160) cc_final: 0.8004 (mmm160) REVERT: F 95 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.7676 (mtp-110) REVERT: G 94 ASN cc_start: 0.9181 (t0) cc_final: 0.8930 (t0) REVERT: H 86 ARG cc_start: 0.8304 (mmt-90) cc_final: 0.8048 (mmt-90) REVERT: M 96 ASN cc_start: 0.8272 (m-40) cc_final: 0.7952 (m-40) REVERT: M 160 LEU cc_start: 0.8583 (mm) cc_final: 0.8242 (mm) REVERT: N 230 MET cc_start: 0.8418 (ttt) cc_final: 0.8107 (ttt) REVERT: U 96 LYS cc_start: 0.5900 (OUTLIER) cc_final: 0.5487 (ttpp) outliers start: 34 outliers final: 15 residues processed: 213 average time/residue: 1.7034 time to fit residues: 394.0883 Evaluate side-chains 203 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 186 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain H residue 34 LYS Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain M residue 228 VAL Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain N residue 211 GLU Chi-restraints excluded: chain N residue 257 ASP Chi-restraints excluded: chain U residue 96 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 144 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 146 optimal weight: 0.3980 chunk 155 optimal weight: 8.9990 chunk 139 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 19408 Z= 0.325 Angle : 0.581 6.943 27915 Z= 0.343 Chirality : 0.037 0.138 3152 Planarity : 0.004 0.052 2154 Dihedral : 30.115 173.917 5711 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.02 % Allowed : 13.88 % Favored : 82.10 % 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: 1.91 (0.24), residues: 1271 helix: 2.54 (0.21), residues: 586 sheet: 0.88 (0.33), residues: 262 loop : -0.29 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP M 185 HIS 0.004 0.001 HIS N 110 PHE 0.008 0.001 PHE C 25 TYR 0.017 0.002 TYR N 201 ARG 0.007 0.001 ARG H 33 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 198 time to evaluate : 1.112 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8143 (tt0) REVERT: B 92 ARG cc_start: 0.8774 (ptm-80) cc_final: 0.8512 (ptm160) REVERT: B 95 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7881 (mtt-85) REVERT: D 35 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7326 (mt-10) REVERT: D 85 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8504 (mppt) REVERT: F 95 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.7715 (mtp-110) REVERT: G 64 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8093 (tt0) REVERT: G 73 ASN cc_start: 0.8086 (m110) cc_final: 0.7883 (t160) REVERT: G 94 ASN cc_start: 0.9195 (t0) cc_final: 0.8934 (t0) REVERT: M 96 ASN cc_start: 0.8356 (m-40) cc_final: 0.8049 (m-40) REVERT: M 160 LEU cc_start: 0.8568 (mm) cc_final: 0.8214 (mm) REVERT: N 230 MET cc_start: 0.8449 (ttt) cc_final: 0.8113 (ttt) REVERT: U 96 LYS cc_start: 0.6070 (OUTLIER) cc_final: 0.5599 (ttpp) outliers start: 44 outliers final: 20 residues processed: 214 average time/residue: 1.7848 time to fit residues: 414.2662 Evaluate side-chains 214 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 187 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain M residue 228 VAL Chi-restraints excluded: chain M residue 239 ASP Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 257 ASP Chi-restraints excluded: chain U residue 96 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 88 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 115 optimal weight: 0.0570 chunk 64 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 139 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN H 47 GLN H 63 ASN M 154 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 19408 Z= 0.296 Angle : 0.566 6.803 27915 Z= 0.335 Chirality : 0.036 0.150 3152 Planarity : 0.004 0.045 2154 Dihedral : 29.931 174.957 5711 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.01 % Allowed : 15.53 % Favored : 81.46 % 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: 1.92 (0.24), residues: 1271 helix: 2.54 (0.21), residues: 592 sheet: 0.82 (0.33), residues: 262 loop : -0.27 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 185 HIS 0.004 0.001 HIS M 110 PHE 0.007 0.001 PHE C 25 TYR 0.015 0.002 TYR D 40 ARG 0.008 0.000 ARG H 33 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 188 time to evaluate : 1.556 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8118 (tt0) REVERT: B 92 ARG cc_start: 0.8810 (ptm-80) cc_final: 0.8538 (ptm160) REVERT: B 95 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7879 (mtt-85) REVERT: D 35 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7346 (mt-10) REVERT: D 85 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8508 (mppt) REVERT: F 95 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8104 (mtt-85) REVERT: G 64 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8109 (tt0) REVERT: G 94 ASN cc_start: 0.9187 (t0) cc_final: 0.8933 (t0) REVERT: H 86 ARG cc_start: 0.8332 (mmt-90) cc_final: 0.8098 (mmt90) REVERT: M 96 ASN cc_start: 0.8317 (m-40) cc_final: 0.8066 (m-40) REVERT: M 160 LEU cc_start: 0.8528 (mm) cc_final: 0.8184 (mm) REVERT: N 230 MET cc_start: 0.8436 (ttt) cc_final: 0.8105 (ttt) REVERT: U 96 LYS cc_start: 0.5858 (OUTLIER) cc_final: 0.5428 (ttpp) outliers start: 33 outliers final: 18 residues processed: 204 average time/residue: 1.7483 time to fit residues: 387.3379 Evaluate side-chains 212 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 187 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 34 LYS Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain M residue 239 ASP Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 257 ASP Chi-restraints excluded: chain U residue 96 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 140 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 91 optimal weight: 30.0000 chunk 38 optimal weight: 2.9990 chunk 155 optimal weight: 8.9990 chunk 129 optimal weight: 10.0000 chunk 72 optimal weight: 30.0000 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 19408 Z= 0.291 Angle : 0.561 6.855 27915 Z= 0.333 Chirality : 0.036 0.157 3152 Planarity : 0.004 0.044 2154 Dihedral : 29.828 174.670 5711 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.38 % Allowed : 15.89 % Favored : 80.73 % 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: 1.95 (0.24), residues: 1271 helix: 2.59 (0.21), residues: 586 sheet: 0.82 (0.33), residues: 262 loop : -0.26 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 185 HIS 0.008 0.001 HIS D 49 PHE 0.007 0.001 PHE C 25 TYR 0.014 0.002 TYR D 40 ARG 0.009 0.000 ARG H 33 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 192 time to evaluate : 1.412 Fit side-chains REVERT: A 76 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8116 (tt0) REVERT: B 92 ARG cc_start: 0.8808 (ptm-80) cc_final: 0.8544 (ptm160) REVERT: B 95 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7725 (mtt-85) REVERT: D 35 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7335 (mt-10) REVERT: D 85 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8511 (mppt) REVERT: F 95 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.7665 (mtp-110) REVERT: G 64 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8110 (tt0) REVERT: G 94 ASN cc_start: 0.9188 (t0) cc_final: 0.8934 (t0) REVERT: H 86 ARG cc_start: 0.8335 (mmt-90) cc_final: 0.8103 (mmt90) REVERT: M 96 ASN cc_start: 0.8349 (m-40) cc_final: 0.8021 (m-40) REVERT: M 160 LEU cc_start: 0.8522 (mm) cc_final: 0.8136 (mm) REVERT: N 230 MET cc_start: 0.8432 (ttt) cc_final: 0.8117 (ttt) REVERT: U 96 LYS cc_start: 0.6045 (OUTLIER) cc_final: 0.5576 (ttpp) outliers start: 37 outliers final: 23 residues processed: 211 average time/residue: 1.7739 time to fit residues: 406.0819 Evaluate side-chains 218 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 188 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 34 LYS Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain M residue 228 VAL Chi-restraints excluded: chain M residue 239 ASP Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 211 GLU Chi-restraints excluded: chain N residue 257 ASP Chi-restraints excluded: chain U residue 96 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 17 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 155 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN ** M 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 19408 Z= 0.317 Angle : 0.575 6.980 27915 Z= 0.340 Chirality : 0.037 0.161 3152 Planarity : 0.004 0.045 2154 Dihedral : 29.843 175.435 5711 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.65 % Allowed : 15.98 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.24), residues: 1271 helix: 2.48 (0.21), residues: 586 sheet: 0.78 (0.33), residues: 262 loop : -0.33 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 185 HIS 0.005 0.001 HIS D 49 PHE 0.008 0.001 PHE C 25 TYR 0.014 0.002 TYR D 40 ARG 0.010 0.000 ARG H 33 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 191 time to evaluate : 1.333 Fit side-chains REVERT: A 76 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8108 (tt0) REVERT: A 133 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6891 (mt-10) REVERT: B 92 ARG cc_start: 0.8775 (ptm-80) cc_final: 0.8531 (ptm160) REVERT: C 36 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8007 (mppt) REVERT: D 35 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7362 (mt-10) REVERT: D 85 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8510 (mppt) REVERT: F 95 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8106 (mtt-85) REVERT: G 64 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8148 (tt0) REVERT: G 94 ASN cc_start: 0.9190 (t0) cc_final: 0.8928 (t0) REVERT: H 86 ARG cc_start: 0.8354 (mmt-90) cc_final: 0.8119 (mmt90) REVERT: M 160 LEU cc_start: 0.8495 (mm) cc_final: 0.8120 (mm) REVERT: N 230 MET cc_start: 0.8479 (ttt) cc_final: 0.8169 (ttt) REVERT: U 96 LYS cc_start: 0.5845 (OUTLIER) cc_final: 0.5414 (ttpp) outliers start: 40 outliers final: 22 residues processed: 211 average time/residue: 1.7471 time to fit residues: 401.2755 Evaluate side-chains 215 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 186 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 34 LYS Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain M residue 228 VAL Chi-restraints excluded: chain M residue 239 ASP Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 161 VAL Chi-restraints excluded: chain N residue 211 GLU Chi-restraints excluded: chain N residue 257 ASP Chi-restraints excluded: chain U residue 96 LYS 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: 0.6980 chunk 30 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 121 optimal weight: 5.9990 chunk 141 optimal weight: 0.9980 chunk 148 optimal weight: 0.5980 chunk 135 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN H 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19408 Z= 0.195 Angle : 0.556 6.901 27915 Z= 0.331 Chirality : 0.035 0.159 3152 Planarity : 0.004 0.059 2154 Dihedral : 29.839 175.566 5711 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.83 % Allowed : 17.17 % Favored : 80.00 % 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: 2.00 (0.24), residues: 1271 helix: 2.64 (0.21), residues: 586 sheet: 0.81 (0.33), residues: 262 loop : -0.21 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 185 HIS 0.004 0.001 HIS D 49 PHE 0.007 0.001 PHE A 67 TYR 0.014 0.001 TYR D 40 ARG 0.013 0.000 ARG H 33 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 190 time to evaluate : 1.480 Fit side-chains REVERT: A 76 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8078 (tt0) REVERT: A 133 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6885 (mt-10) REVERT: B 92 ARG cc_start: 0.8751 (ptm-80) cc_final: 0.8519 (ptm160) REVERT: C 36 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.7968 (mppt) REVERT: D 35 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7339 (mt-10) REVERT: F 95 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8100 (mtt-85) REVERT: G 13 LYS cc_start: 0.8382 (mmmm) cc_final: 0.8033 (tmtt) REVERT: G 64 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8048 (tt0) REVERT: G 94 ASN cc_start: 0.9163 (t0) cc_final: 0.8911 (t0) REVERT: H 86 ARG cc_start: 0.8312 (mmt-90) cc_final: 0.8084 (mmt90) REVERT: M 160 LEU cc_start: 0.8502 (mm) cc_final: 0.8137 (mm) REVERT: N 230 MET cc_start: 0.8429 (ttt) cc_final: 0.8127 (ttt) REVERT: U 96 LYS cc_start: 0.5851 (OUTLIER) cc_final: 0.5401 (ttpp) outliers start: 31 outliers final: 22 residues processed: 206 average time/residue: 1.6933 time to fit residues: 380.3599 Evaluate side-chains 214 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 186 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain M residue 239 ASP Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 161 VAL Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 211 GLU Chi-restraints excluded: chain N residue 257 ASP Chi-restraints excluded: chain U residue 96 LYS 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: 1.9990 chunk 87 optimal weight: 4.9990 chunk 62 optimal weight: 0.1980 chunk 113 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19408 Z= 0.208 Angle : 0.554 11.481 27915 Z= 0.328 Chirality : 0.034 0.152 3152 Planarity : 0.004 0.063 2154 Dihedral : 29.790 175.387 5711 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.47 % Allowed : 17.72 % Favored : 79.82 % 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: 2.01 (0.24), residues: 1271 helix: 2.63 (0.21), residues: 592 sheet: 0.76 (0.33), residues: 262 loop : -0.16 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 185 HIS 0.003 0.001 HIS M 110 PHE 0.007 0.001 PHE A 67 TYR 0.013 0.001 TYR D 40 ARG 0.013 0.000 ARG H 33 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 187 time to evaluate : 1.567 Fit side-chains REVERT: A 76 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8078 (tt0) REVERT: A 129 ARG cc_start: 0.8282 (tpt90) cc_final: 0.8027 (tpt90) REVERT: A 133 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6896 (mt-10) REVERT: B 92 ARG cc_start: 0.8747 (ptm-80) cc_final: 0.8517 (ptm160) REVERT: D 35 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7343 (mt-10) REVERT: F 95 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7624 (mtp-110) REVERT: G 64 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8067 (tt0) REVERT: G 94 ASN cc_start: 0.9169 (t0) cc_final: 0.8917 (t0) REVERT: H 86 ARG cc_start: 0.8309 (mmt-90) cc_final: 0.8088 (mmt90) REVERT: M 160 LEU cc_start: 0.8526 (mm) cc_final: 0.8154 (mm) REVERT: N 230 MET cc_start: 0.8430 (ttt) cc_final: 0.8129 (ttt) REVERT: U 96 LYS cc_start: 0.5891 (OUTLIER) cc_final: 0.5411 (ttpp) outliers start: 27 outliers final: 21 residues processed: 203 average time/residue: 1.7244 time to fit residues: 380.6895 Evaluate side-chains 211 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 185 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain M residue 239 ASP Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 161 VAL Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 211 GLU Chi-restraints excluded: chain N residue 257 ASP Chi-restraints excluded: chain U residue 96 LYS 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: 4.9990 chunk 160 optimal weight: 20.0000 chunk 147 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 19408 Z= 0.293 Angle : 0.566 6.946 27915 Z= 0.335 Chirality : 0.036 0.155 3152 Planarity : 0.004 0.058 2154 Dihedral : 29.747 175.215 5711 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.56 % Allowed : 17.63 % Favored : 79.82 % 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: 1.92 (0.24), residues: 1271 helix: 2.53 (0.21), residues: 592 sheet: 0.77 (0.33), residues: 262 loop : -0.21 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 185 HIS 0.004 0.001 HIS D 49 PHE 0.008 0.001 PHE C 25 TYR 0.013 0.002 TYR D 40 ARG 0.014 0.000 ARG H 33 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 189 time to evaluate : 1.388 Fit side-chains REVERT: A 76 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8114 (tt0) REVERT: A 133 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6896 (mt-10) REVERT: B 92 ARG cc_start: 0.8783 (ptm-80) cc_final: 0.8533 (ptm160) REVERT: D 35 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7354 (mt-10) REVERT: F 95 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8133 (mtt-85) REVERT: G 13 LYS cc_start: 0.8364 (mmmm) cc_final: 0.8014 (tmtt) REVERT: G 64 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8117 (tt0) REVERT: G 94 ASN cc_start: 0.9188 (t0) cc_final: 0.8937 (t0) REVERT: H 86 ARG cc_start: 0.8347 (mmt-90) cc_final: 0.8109 (mmt90) REVERT: M 160 LEU cc_start: 0.8502 (mm) cc_final: 0.8096 (mm) REVERT: N 230 MET cc_start: 0.8453 (ttt) cc_final: 0.8159 (ttt) REVERT: U 96 LYS cc_start: 0.6049 (OUTLIER) cc_final: 0.5566 (ttpp) outliers start: 28 outliers final: 20 residues processed: 206 average time/residue: 1.7532 time to fit residues: 392.7999 Evaluate side-chains 213 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 188 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain M residue 239 ASP Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 161 VAL Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 211 GLU Chi-restraints excluded: chain N residue 257 ASP Chi-restraints excluded: chain U residue 96 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 117 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 131 optimal weight: 0.5980 chunk 16 optimal weight: 0.0870 chunk 23 optimal weight: 0.1980 chunk 112 optimal weight: 6.9990 chunk 7 optimal weight: 0.6980 chunk 92 optimal weight: 20.0000 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.172188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.129114 restraints weight = 22887.662| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 1.20 r_work: 0.3621 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19408 Z= 0.175 Angle : 0.556 9.656 27915 Z= 0.329 Chirality : 0.034 0.154 3152 Planarity : 0.004 0.064 2154 Dihedral : 29.758 175.645 5711 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.47 % Allowed : 17.99 % Favored : 79.54 % 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: 2.08 (0.24), residues: 1271 helix: 2.68 (0.21), residues: 592 sheet: 0.77 (0.33), residues: 262 loop : -0.10 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 185 HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE A 67 TYR 0.014 0.001 TYR D 40 ARG 0.014 0.000 ARG H 33 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6783.21 seconds wall clock time: 124 minutes 0.57 seconds (7440.57 seconds total)