Starting phenix.real_space_refine on Thu Jan 18 02:31:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gse_34233/01_2024/8gse_34233.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gse_34233/01_2024/8gse_34233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gse_34233/01_2024/8gse_34233.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gse_34233/01_2024/8gse_34233.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gse_34233/01_2024/8gse_34233.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gse_34233/01_2024/8gse_34233.pdb" } resolution = 3.7 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= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 4751 2.51 5 N 1252 2.21 5 O 1424 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 205": "OE1" <-> "OE2" Residue "2 TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 119": "OE1" <-> "OE2" Residue "2 GLU 143": "OE1" <-> "OE2" Residue "2 TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 207": "OE1" <-> "OE2" Residue "2 GLU 209": "OE1" <-> "OE2" Residue "2 GLU 218": "OE1" <-> "OE2" Residue "2 ASP 280": "OD1" <-> "OD2" Residue "2 PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 302": "OE1" <-> "OE2" Residue "3 GLU 60": "OE1" <-> "OE2" Residue "3 TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 219": "OD1" <-> "OD2" Residue "L TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 7474 Number of models: 1 Model: "" Number of chains: 5 Chain: "1" Number of atoms: 1900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1900 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 17, 'TRANS': 219} Chain: "2" Number of atoms: 1964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1964 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 238} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "3" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1816 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 18, 'TRANS': 215} Chain: "H" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 907 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 111} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 887 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 108} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 4.20, per 1000 atoms: 0.56 Number of scatterers: 7474 At special positions: 0 Unit cell: (110.7, 86.4, 132.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 47 16.00 O 1424 8.00 N 1252 7.00 C 4751 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " 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: 2.94 Conformation dependent library (CDL) restraints added in 1.8 seconds 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1776 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 15 sheets defined 10.9% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain '1' and resid 59 through 62 Processing helix chain '1' and resid 63 through 69 Processing helix chain '1' and resid 100 through 109 Processing helix chain '1' and resid 159 through 164 Processing helix chain '2' and resid 152 through 156 Processing helix chain '2' and resid 158 through 168 removed outlier: 3.767A pdb=" N GLY 2 162 " --> pdb=" O MET 2 158 " (cutoff:3.500A) Processing helix chain '2' and resid 211 through 216 removed outlier: 3.937A pdb=" N LEU 2 215 " --> pdb=" O VAL 2 211 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N SER 2 216 " --> pdb=" O ALA 2 212 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 211 through 216' Processing helix chain '2' and resid 238 through 242 Processing helix chain '2' and resid 247 through 254 removed outlier: 3.816A pdb=" N LEU 2 251 " --> pdb=" O VAL 2 248 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N THR 2 252 " --> pdb=" O GLY 2 249 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE 2 253 " --> pdb=" O ASN 2 250 " (cutoff:3.500A) Processing helix chain '3' and resid 7 through 11 removed outlier: 3.572A pdb=" N ASN 3 11 " --> pdb=" O PRO 3 8 " (cutoff:3.500A) Processing helix chain '3' and resid 43 through 48 removed outlier: 3.574A pdb=" N ALA 3 47 " --> pdb=" O LEU 3 43 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU 3 48 " --> pdb=" O MET 3 44 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 43 through 48' Processing helix chain '3' and resid 64 through 69 removed outlier: 3.646A pdb=" N ALA 3 67 " --> pdb=" O SER 3 64 " (cutoff:3.500A) Processing helix chain '3' and resid 98 through 105 Processing helix chain '3' and resid 144 through 150 Processing helix chain 'H' and resid 61 through 65 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.829A pdb=" N ASP H 90 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain '1' and resid 72 through 79 removed outlier: 6.690A pdb=" N VAL 1 238 " --> pdb=" O VAL 1 74 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE 1 76 " --> pdb=" O LEU 1 236 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU 1 236 " --> pdb=" O ILE 1 76 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N THR 1 78 " --> pdb=" O SER 1 234 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N SER 1 234 " --> pdb=" O THR 1 78 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS 1 243 " --> pdb=" O ASP 1 116 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL 1 245 " --> pdb=" O ARG 1 114 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG 1 114 " --> pdb=" O VAL 1 245 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ALA 1 247 " --> pdb=" O TYR 1 112 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TYR 1 112 " --> pdb=" O ALA 1 247 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N VAL 1 249 " --> pdb=" O PHE 1 110 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N PHE 1 110 " --> pdb=" O VAL 1 249 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA 1 179 " --> pdb=" O PHE 1 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '1' and resid 72 through 79 removed outlier: 6.690A pdb=" N VAL 1 238 " --> pdb=" O VAL 1 74 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE 1 76 " --> pdb=" O LEU 1 236 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU 1 236 " --> pdb=" O ILE 1 76 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N THR 1 78 " --> pdb=" O SER 1 234 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N SER 1 234 " --> pdb=" O THR 1 78 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS 1 243 " --> pdb=" O ASP 1 116 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL 1 245 " --> pdb=" O ARG 1 114 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG 1 114 " --> pdb=" O VAL 1 245 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ALA 1 247 " --> pdb=" O TYR 1 112 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TYR 1 112 " --> pdb=" O ALA 1 247 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N VAL 1 249 " --> pdb=" O PHE 1 110 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N PHE 1 110 " --> pdb=" O VAL 1 249 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '1' and resid 90 through 94 Processing sheet with id=AA4, first strand: chain '2' and resid 83 through 84 Processing sheet with id=AA5, first strand: chain '2' and resid 133 through 140 removed outlier: 5.298A pdb=" N THR 2 134 " --> pdb=" O VAL 2 314 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL 2 314 " --> pdb=" O THR 2 134 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ASP 2 136 " --> pdb=" O VAL 2 312 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL 2 312 " --> pdb=" O ASP 2 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '2' and resid 133 through 140 removed outlier: 5.298A pdb=" N THR 2 134 " --> pdb=" O VAL 2 314 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL 2 314 " --> pdb=" O THR 2 134 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ASP 2 136 " --> pdb=" O VAL 2 312 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL 2 312 " --> pdb=" O ASP 2 136 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ARG 2 172 " --> pdb=" O ALA 2 319 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA 2 319 " --> pdb=" O ARG 2 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '2' and resid 222 through 223 removed outlier: 3.685A pdb=" N LYS 2 222 " --> pdb=" O TRP 2 148 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N CYS 2 190 " --> pdb=" O PHE 2 295 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N LYS 2 297 " --> pdb=" O GLN 2 188 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLN 2 188 " --> pdb=" O LYS 2 297 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '3' and resid 51 through 52 removed outlier: 3.600A pdb=" N SER 3 51 " --> pdb=" O ALA 3 214 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL 3 72 " --> pdb=" O CYS 3 208 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '3' and resid 51 through 52 removed outlier: 3.600A pdb=" N SER 3 51 " --> pdb=" O ALA 3 214 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '3' and resid 81 through 86 removed outlier: 7.149A pdb=" N GLN 3 81 " --> pdb=" O TYR 3 194 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N TYR 3 194 " --> pdb=" O GLN 3 81 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE 3 83 " --> pdb=" O CYS 3 192 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR 3 189 " --> pdb=" O SER 3 135 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR 3 152 " --> pdb=" O TYR 3 134 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '3' and resid 177 through 178 removed outlier: 3.507A pdb=" N ARG 3 177 " --> pdb=" O TRP 3 110 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N TYR 3 107 " --> pdb=" O LEU 3 225 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU 3 225 " --> pdb=" O TYR 3 107 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 57 through 58 removed outlier: 3.845A pdb=" N ASP H 57 " --> pdb=" O TYR H 52 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR H 52 " --> pdb=" O ASP H 57 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N TRP H 47 " --> pdb=" O LYS H 38 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LYS H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP H 36 " --> pdb=" O GLY H 49 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 68 through 71 removed outlier: 3.542A pdb=" N THR H 69 " --> pdb=" O GLN H 82 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AB6, first strand: chain 'L' and resid 59 through 60 removed outlier: 6.683A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N TYR L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N LEU L 39 " --> pdb=" O TYR L 55 " (cutoff:3.500A) 196 hydrogen bonds defined for protein. 486 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.74 Time building geometry restraints manager: 3.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2395 1.34 - 1.46: 1887 1.46 - 1.58: 3326 1.58 - 1.70: 0 1.70 - 1.81: 73 Bond restraints: 7681 Sorted by residual: bond pdb=" CB PHE 3 220 " pdb=" CG PHE 3 220 " ideal model delta sigma weight residual 1.502 1.473 0.029 2.30e-02 1.89e+03 1.61e+00 bond pdb=" CA ILE 3 168 " pdb=" CB ILE 3 168 " ideal model delta sigma weight residual 1.533 1.521 0.013 1.05e-02 9.07e+03 1.45e+00 bond pdb=" C PHE 2 254 " pdb=" N PRO 2 255 " ideal model delta sigma weight residual 1.332 1.345 -0.013 1.12e-02 7.97e+03 1.37e+00 bond pdb=" N ILE 2 293 " pdb=" CA ILE 2 293 " ideal model delta sigma weight residual 1.454 1.463 -0.009 7.70e-03 1.69e+04 1.34e+00 bond pdb=" C THR 3 196 " pdb=" N GLY 3 197 " ideal model delta sigma weight residual 1.334 1.322 0.012 1.12e-02 7.97e+03 1.24e+00 ... (remaining 7676 not shown) Histogram of bond angle deviations from ideal: 99.81 - 106.66: 284 106.66 - 113.51: 4093 113.51 - 120.36: 2722 120.36 - 127.21: 3266 127.21 - 134.06: 106 Bond angle restraints: 10471 Sorted by residual: angle pdb=" N VAL 2 102 " pdb=" CA VAL 2 102 " pdb=" C VAL 2 102 " ideal model delta sigma weight residual 111.91 108.18 3.73 8.90e-01 1.26e+00 1.75e+01 angle pdb=" C TYR H 32 " pdb=" N GLY H 33 " pdb=" CA GLY H 33 " ideal model delta sigma weight residual 121.61 118.58 3.03 7.70e-01 1.69e+00 1.55e+01 angle pdb=" N VAL 2 248 " pdb=" CA VAL 2 248 " pdb=" C VAL 2 248 " ideal model delta sigma weight residual 113.00 108.89 4.11 1.30e+00 5.92e-01 9.99e+00 angle pdb=" N ASP 1 136 " pdb=" CA ASP 1 136 " pdb=" C ASP 1 136 " ideal model delta sigma weight residual 110.06 114.41 -4.35 1.43e+00 4.89e-01 9.25e+00 angle pdb=" N PHE 3 220 " pdb=" CA PHE 3 220 " pdb=" C PHE 3 220 " ideal model delta sigma weight residual 110.35 114.20 -3.85 1.36e+00 5.41e-01 8.01e+00 ... (remaining 10466 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 4083 17.51 - 35.01: 351 35.01 - 52.52: 62 52.52 - 70.03: 10 70.03 - 87.53: 10 Dihedral angle restraints: 4516 sinusoidal: 1742 harmonic: 2774 Sorted by residual: dihedral pdb=" CA PHE 3 220 " pdb=" C PHE 3 220 " pdb=" N SER 3 221 " pdb=" CA SER 3 221 " ideal model delta harmonic sigma weight residual 180.00 154.86 25.14 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 94 " pdb=" CB CYS L 94 " ideal model delta sinusoidal sigma weight residual 93.00 57.81 35.19 1 1.00e+01 1.00e-02 1.75e+01 dihedral pdb=" CA GLU 3 102 " pdb=" C GLU 3 102 " pdb=" N ILE 3 103 " pdb=" CA ILE 3 103 " ideal model delta harmonic sigma weight residual 180.00 163.36 16.64 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 4513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 939 0.058 - 0.117: 181 0.117 - 0.175: 17 0.175 - 0.233: 0 0.233 - 0.292: 2 Chirality restraints: 1139 Sorted by residual: chirality pdb=" CB ILE 3 231 " pdb=" CA ILE 3 231 " pdb=" CG1 ILE 3 231 " pdb=" CG2 ILE 3 231 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CB ILE 1 186 " pdb=" CA ILE 1 186 " pdb=" CG1 ILE 1 186 " pdb=" CG2 ILE 1 186 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA ASN 1 211 " pdb=" N ASN 1 211 " pdb=" C ASN 1 211 " pdb=" CB ASN 1 211 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.15e-01 ... (remaining 1136 not shown) Planarity restraints: 1351 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE 3 220 " 0.029 2.00e-02 2.50e+03 2.34e-02 9.60e+00 pdb=" CG PHE 3 220 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE 3 220 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE 3 220 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE 3 220 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE 3 220 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE 3 220 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR 3 228 " 0.034 5.00e-02 4.00e+02 5.18e-02 4.29e+00 pdb=" N PRO 3 229 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO 3 229 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO 3 229 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 36 " -0.012 2.00e-02 2.50e+03 1.18e-02 3.47e+00 pdb=" CG TRP H 36 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP H 36 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP H 36 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP H 36 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP H 36 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 36 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 36 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 36 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP H 36 " 0.001 2.00e-02 2.50e+03 ... (remaining 1348 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1546 2.78 - 3.31: 6334 3.31 - 3.84: 11250 3.84 - 4.37: 12980 4.37 - 4.90: 23811 Nonbonded interactions: 55921 Sorted by model distance: nonbonded pdb=" OD1 ASP 2 280 " pdb=" N ASN 2 281 " model vdw 2.246 2.520 nonbonded pdb=" OG1 THR 2 252 " pdb=" O ASP 3 50 " model vdw 2.261 2.440 nonbonded pdb=" OE2 GLU 3 66 " pdb=" NH1 ARG 3 69 " model vdw 2.274 2.520 nonbonded pdb=" OD2 ASP 3 182 " pdb=" OH TYR 3 184 " model vdw 2.276 2.440 nonbonded pdb=" NH2 ARG 2 262 " pdb=" O VAL 3 158 " model vdw 2.300 2.520 ... (remaining 55916 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 11.760 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 23.110 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 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 : 0.005 0.040 7681 Z= 0.311 Angle : 0.676 10.354 10471 Z= 0.396 Chirality : 0.046 0.292 1139 Planarity : 0.005 0.052 1351 Dihedral : 13.931 87.533 2734 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.94 (0.26), residues: 942 helix: -1.62 (0.70), residues: 48 sheet: -0.04 (0.34), residues: 257 loop : -1.92 (0.22), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP H 36 HIS 0.007 0.001 HIS 1 223 PHE 0.053 0.002 PHE 3 220 TYR 0.025 0.002 TYR 3 107 ARG 0.007 0.001 ARG 2 208 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.890 Fit side-chains REVERT: 2 148 TRP cc_start: 0.7953 (p-90) cc_final: 0.7414 (p-90) REVERT: 2 303 GLN cc_start: 0.5311 (tt0) cc_final: 0.4833 (pp30) REVERT: 3 34 MET cc_start: 0.8738 (ptm) cc_final: 0.8301 (ptm) REVERT: 3 35 LYS cc_start: 0.8894 (mmtm) cc_final: 0.8553 (tttp) REVERT: H 91 SER cc_start: 0.4209 (m) cc_final: 0.3478 (t) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.2117 time to fit residues: 29.6238 Evaluate side-chains 89 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 8.9990 chunk 70 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 20.0000 chunk 37 optimal weight: 3.9990 chunk 72 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 84 optimal weight: 20.0000 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 109 HIS 3 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.0834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7681 Z= 0.174 Angle : 0.501 9.315 10471 Z= 0.262 Chirality : 0.042 0.206 1139 Planarity : 0.004 0.046 1351 Dihedral : 4.406 16.206 1034 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.61 % Allowed : 5.70 % Favored : 93.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.62 (0.26), residues: 942 helix: -1.62 (0.70), residues: 50 sheet: 0.11 (0.33), residues: 266 loop : -1.67 (0.23), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 36 HIS 0.004 0.001 HIS 1 223 PHE 0.026 0.001 PHE 3 220 TYR 0.013 0.001 TYR 3 107 ARG 0.004 0.000 ARG 1 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 99 time to evaluate : 0.797 Fit side-chains REVERT: 2 148 TRP cc_start: 0.8044 (p-90) cc_final: 0.7650 (p-90) REVERT: 2 303 GLN cc_start: 0.5648 (tt0) cc_final: 0.5041 (pp30) REVERT: 3 35 LYS cc_start: 0.8938 (mmtm) cc_final: 0.8590 (tttp) REVERT: 3 220 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.6790 (m-80) outliers start: 5 outliers final: 3 residues processed: 101 average time/residue: 0.2126 time to fit residues: 28.5647 Evaluate side-chains 95 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 91 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 278 ILE Chi-restraints excluded: chain 3 residue 103 ILE Chi-restraints excluded: chain 3 residue 220 PHE Chi-restraints excluded: chain L residue 82 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 70 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 84 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 180 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7681 Z= 0.134 Angle : 0.458 8.569 10471 Z= 0.236 Chirality : 0.041 0.165 1139 Planarity : 0.004 0.040 1351 Dihedral : 4.012 13.683 1034 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.97 % Allowed : 9.58 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.40 (0.27), residues: 942 helix: -1.44 (0.70), residues: 49 sheet: 0.25 (0.34), residues: 270 loop : -1.51 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 36 HIS 0.004 0.001 HIS 1 223 PHE 0.021 0.001 PHE 3 220 TYR 0.010 0.001 TYR 2 240 ARG 0.004 0.000 ARG 1 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 99 time to evaluate : 0.702 Fit side-chains REVERT: 2 148 TRP cc_start: 0.7927 (p-90) cc_final: 0.7691 (p-90) REVERT: 2 201 MET cc_start: 0.8867 (mmt) cc_final: 0.8471 (mmt) REVERT: 2 303 GLN cc_start: 0.5663 (tt0) cc_final: 0.5091 (pp30) REVERT: 3 220 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.6470 (m-80) REVERT: H 35 GLN cc_start: 0.2341 (OUTLIER) cc_final: -0.0765 (tm-30) outliers start: 8 outliers final: 3 residues processed: 105 average time/residue: 0.2130 time to fit residues: 29.6394 Evaluate side-chains 100 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 95 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 278 ILE Chi-restraints excluded: chain 2 residue 97 CYS Chi-restraints excluded: chain 2 residue 301 THR Chi-restraints excluded: chain 3 residue 220 PHE Chi-restraints excluded: chain H residue 35 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 43 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 chunk 84 optimal weight: 0.5980 chunk 89 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7681 Z= 0.131 Angle : 0.455 7.258 10471 Z= 0.237 Chirality : 0.041 0.161 1139 Planarity : 0.004 0.040 1351 Dihedral : 3.853 14.203 1034 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.45 % Allowed : 11.15 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.28 (0.27), residues: 942 helix: -1.38 (0.69), residues: 49 sheet: 0.29 (0.33), residues: 280 loop : -1.44 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 2 148 HIS 0.004 0.001 HIS 1 223 PHE 0.022 0.001 PHE 3 220 TYR 0.011 0.001 TYR 2 240 ARG 0.005 0.000 ARG 1 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 100 time to evaluate : 0.907 Fit side-chains REVERT: 2 133 TYR cc_start: 0.9115 (m-80) cc_final: 0.8869 (m-80) REVERT: 2 303 GLN cc_start: 0.5566 (tt0) cc_final: 0.5042 (pp30) REVERT: 3 58 THR cc_start: 0.8464 (m) cc_final: 0.8165 (t) REVERT: 3 220 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.6572 (m-80) REVERT: H 35 GLN cc_start: 0.1884 (OUTLIER) cc_final: -0.0908 (tm-30) outliers start: 12 outliers final: 5 residues processed: 106 average time/residue: 0.1868 time to fit residues: 26.6620 Evaluate side-chains 100 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 93 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 263 ASN Chi-restraints excluded: chain 1 residue 278 ILE Chi-restraints excluded: chain 2 residue 301 THR Chi-restraints excluded: chain 3 residue 103 ILE Chi-restraints excluded: chain 3 residue 220 PHE Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain L residue 82 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 30.0000 chunk 51 optimal weight: 10.0000 chunk 1 optimal weight: 0.2980 chunk 66 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 76 optimal weight: 0.4980 chunk 62 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7681 Z= 0.242 Angle : 0.510 6.834 10471 Z= 0.268 Chirality : 0.043 0.161 1139 Planarity : 0.004 0.041 1351 Dihedral : 4.130 15.845 1034 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.58 % Allowed : 12.24 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.27), residues: 942 helix: -1.61 (0.69), residues: 50 sheet: 0.44 (0.35), residues: 260 loop : -1.62 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP 2 148 HIS 0.004 0.001 HIS 1 223 PHE 0.029 0.001 PHE 3 220 TYR 0.013 0.001 TYR 2 240 ARG 0.005 0.000 ARG 1 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 0.833 Fit side-chains REVERT: 2 148 TRP cc_start: 0.7985 (p-90) cc_final: 0.7538 (p-90) REVERT: 2 201 MET cc_start: 0.8872 (mmt) cc_final: 0.8439 (mmt) REVERT: 2 303 GLN cc_start: 0.5572 (tt0) cc_final: 0.5034 (pp30) REVERT: 3 58 THR cc_start: 0.8581 (m) cc_final: 0.8168 (t) REVERT: 3 220 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.7292 (m-80) REVERT: H 35 GLN cc_start: 0.2452 (OUTLIER) cc_final: -0.1077 (tp40) outliers start: 13 outliers final: 7 residues processed: 103 average time/residue: 0.1876 time to fit residues: 25.6613 Evaluate side-chains 103 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 94 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 278 ILE Chi-restraints excluded: chain 2 residue 97 CYS Chi-restraints excluded: chain 2 residue 301 THR Chi-restraints excluded: chain 3 residue 175 HIS Chi-restraints excluded: chain 3 residue 220 PHE Chi-restraints excluded: chain 3 residue 222 VAL Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 82 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 4.9990 chunk 80 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 chunk 41 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 29 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 201 HIS 2 168 HIS ** 3 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 7681 Z= 0.435 Angle : 0.627 8.080 10471 Z= 0.334 Chirality : 0.046 0.151 1139 Planarity : 0.005 0.058 1351 Dihedral : 4.891 17.527 1034 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 1.94 % Allowed : 13.45 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 (0.26), residues: 942 helix: -2.01 (0.66), residues: 49 sheet: 0.15 (0.35), residues: 253 loop : -1.93 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP 2 148 HIS 0.006 0.001 HIS 3 41 PHE 0.035 0.002 PHE 3 220 TYR 0.017 0.002 TYR 2 240 ARG 0.004 0.001 ARG 1 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 0.869 Fit side-chains REVERT: 1 108 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7824 (mt-10) REVERT: 1 181 MET cc_start: 0.8529 (ptp) cc_final: 0.8292 (ptp) REVERT: 2 148 TRP cc_start: 0.8128 (p-90) cc_final: 0.7556 (p-90) REVERT: 2 201 MET cc_start: 0.8851 (mmt) cc_final: 0.8396 (mmt) REVERT: 2 303 GLN cc_start: 0.5502 (tt0) cc_final: 0.4948 (pp30) REVERT: 3 220 PHE cc_start: 0.9069 (OUTLIER) cc_final: 0.7845 (m-80) REVERT: H 35 GLN cc_start: 0.2550 (OUTLIER) cc_final: -0.1374 (tt0) REVERT: L 29 LEU cc_start: 0.6530 (mp) cc_final: 0.6228 (mp) outliers start: 16 outliers final: 11 residues processed: 104 average time/residue: 0.2074 time to fit residues: 28.8413 Evaluate side-chains 101 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 88 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 278 ILE Chi-restraints excluded: chain 2 residue 97 CYS Chi-restraints excluded: chain 2 residue 244 MET Chi-restraints excluded: chain 2 residue 301 THR Chi-restraints excluded: chain 2 residue 302 GLU Chi-restraints excluded: chain 3 residue 103 ILE Chi-restraints excluded: chain 3 residue 175 HIS Chi-restraints excluded: chain 3 residue 220 PHE Chi-restraints excluded: chain 3 residue 221 SER Chi-restraints excluded: chain 3 residue 222 VAL Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 82 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 214 ASN 1 225 ASN 3 61 ASN 3 105 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 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 : 0.003 0.033 7681 Z= 0.170 Angle : 0.499 8.730 10471 Z= 0.261 Chirality : 0.042 0.151 1139 Planarity : 0.004 0.042 1351 Dihedral : 4.293 16.850 1034 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.33 % Allowed : 14.55 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.26), residues: 942 helix: -2.24 (0.63), residues: 55 sheet: 0.30 (0.35), residues: 256 loop : -1.76 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP 2 148 HIS 0.003 0.001 HIS 1 223 PHE 0.029 0.001 PHE 3 220 TYR 0.012 0.001 TYR 2 240 ARG 0.005 0.000 ARG 1 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 0.685 Fit side-chains REVERT: 2 148 TRP cc_start: 0.8153 (p-90) cc_final: 0.7654 (p-90) REVERT: 2 201 MET cc_start: 0.8827 (mmt) cc_final: 0.8424 (mmt) REVERT: 2 303 GLN cc_start: 0.5646 (tt0) cc_final: 0.4764 (pp30) REVERT: 3 220 PHE cc_start: 0.8958 (OUTLIER) cc_final: 0.7542 (m-80) REVERT: H 35 GLN cc_start: 0.2441 (OUTLIER) cc_final: -0.1158 (tt0) REVERT: L 29 LEU cc_start: 0.6525 (mp) cc_final: 0.6230 (mp) outliers start: 11 outliers final: 6 residues processed: 102 average time/residue: 0.1671 time to fit residues: 22.9383 Evaluate side-chains 103 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 263 ASN Chi-restraints excluded: chain 1 residue 278 ILE Chi-restraints excluded: chain 2 residue 97 CYS Chi-restraints excluded: chain 2 residue 301 THR Chi-restraints excluded: chain 3 residue 103 ILE Chi-restraints excluded: chain 3 residue 220 PHE Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain L residue 82 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 27 optimal weight: 0.1980 chunk 17 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 44 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 chunk 85 optimal weight: 10.0000 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 7681 Z= 0.317 Angle : 0.559 8.460 10471 Z= 0.296 Chirality : 0.044 0.157 1139 Planarity : 0.005 0.048 1351 Dihedral : 4.535 17.722 1034 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 1.82 % Allowed : 14.67 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 (0.26), residues: 942 helix: -1.94 (0.69), residues: 49 sheet: 0.31 (0.34), residues: 262 loop : -1.89 (0.22), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP 2 148 HIS 0.004 0.001 HIS 1 223 PHE 0.032 0.002 PHE 3 220 TYR 0.014 0.001 TYR 2 240 ARG 0.006 0.001 ARG 2 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 95 time to evaluate : 0.812 Fit side-chains REVERT: 2 148 TRP cc_start: 0.8079 (p-90) cc_final: 0.7586 (p-90) REVERT: 2 201 MET cc_start: 0.8881 (mmt) cc_final: 0.8419 (mmt) REVERT: 2 303 GLN cc_start: 0.5615 (tt0) cc_final: 0.5049 (pp30) REVERT: 3 58 THR cc_start: 0.8622 (m) cc_final: 0.8271 (t) REVERT: 3 220 PHE cc_start: 0.9004 (OUTLIER) cc_final: 0.7814 (m-80) REVERT: H 35 GLN cc_start: 0.2468 (OUTLIER) cc_final: -0.1326 (tt0) REVERT: L 112 ILE cc_start: 0.1746 (OUTLIER) cc_final: 0.1475 (tt) outliers start: 15 outliers final: 9 residues processed: 105 average time/residue: 0.2111 time to fit residues: 29.9306 Evaluate side-chains 107 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 263 ASN Chi-restraints excluded: chain 1 residue 278 ILE Chi-restraints excluded: chain 2 residue 97 CYS Chi-restraints excluded: chain 2 residue 244 MET Chi-restraints excluded: chain 2 residue 301 THR Chi-restraints excluded: chain 2 residue 302 GLU Chi-restraints excluded: chain 3 residue 220 PHE Chi-restraints excluded: chain 3 residue 228 THR Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 82 SER Chi-restraints excluded: chain L residue 112 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.0010 chunk 83 optimal weight: 40.0000 chunk 85 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 36 optimal weight: 0.3980 chunk 65 optimal weight: 9.9990 chunk 25 optimal weight: 0.8980 chunk 75 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 overall best weight: 1.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7681 Z= 0.137 Angle : 0.478 8.667 10471 Z= 0.248 Chirality : 0.042 0.152 1139 Planarity : 0.004 0.047 1351 Dihedral : 4.037 15.810 1034 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.09 % Allowed : 15.15 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.27), residues: 942 helix: -2.12 (0.63), residues: 54 sheet: 0.44 (0.35), residues: 256 loop : -1.66 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP 2 148 HIS 0.002 0.000 HIS 1 223 PHE 0.026 0.001 PHE 3 220 TYR 0.011 0.001 TYR 2 240 ARG 0.007 0.000 ARG 2 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 101 time to evaluate : 0.913 Fit side-chains REVERT: 2 148 TRP cc_start: 0.7811 (p-90) cc_final: 0.7379 (p-90) REVERT: 2 201 MET cc_start: 0.8859 (mmt) cc_final: 0.8400 (mmt) REVERT: 2 303 GLN cc_start: 0.5701 (tt0) cc_final: 0.4826 (pp30) REVERT: 3 58 THR cc_start: 0.8525 (m) cc_final: 0.8229 (t) REVERT: 3 220 PHE cc_start: 0.8878 (OUTLIER) cc_final: 0.7390 (m-80) REVERT: H 35 GLN cc_start: 0.2321 (OUTLIER) cc_final: -0.0802 (tm-30) REVERT: L 112 ILE cc_start: 0.1888 (OUTLIER) cc_final: 0.1645 (tt) outliers start: 9 outliers final: 5 residues processed: 108 average time/residue: 0.1952 time to fit residues: 28.4241 Evaluate side-chains 107 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 99 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 263 ASN Chi-restraints excluded: chain 1 residue 278 ILE Chi-restraints excluded: chain 2 residue 97 CYS Chi-restraints excluded: chain 2 residue 301 THR Chi-restraints excluded: chain 3 residue 220 PHE Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain L residue 82 SER Chi-restraints excluded: chain L residue 112 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 92 optimal weight: 30.0000 chunk 85 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 58 optimal weight: 8.9990 chunk 78 optimal weight: 8.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7681 Z= 0.196 Angle : 0.506 7.861 10471 Z= 0.261 Chirality : 0.042 0.167 1139 Planarity : 0.004 0.050 1351 Dihedral : 4.066 16.120 1034 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.45 % Allowed : 15.39 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.50 (0.27), residues: 942 helix: -1.70 (0.69), residues: 48 sheet: 0.42 (0.34), residues: 265 loop : -1.68 (0.23), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP 2 148 HIS 0.003 0.001 HIS 1 223 PHE 0.028 0.001 PHE 3 220 TYR 0.012 0.001 TYR 2 240 ARG 0.007 0.000 ARG 2 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 100 time to evaluate : 0.824 Fit side-chains REVERT: 2 148 TRP cc_start: 0.7928 (p-90) cc_final: 0.7449 (p-90) REVERT: 2 201 MET cc_start: 0.8872 (mmt) cc_final: 0.8475 (mmt) REVERT: 2 303 GLN cc_start: 0.5566 (tt0) cc_final: 0.4718 (pp30) REVERT: 3 58 THR cc_start: 0.8594 (m) cc_final: 0.8267 (t) REVERT: 3 220 PHE cc_start: 0.8883 (OUTLIER) cc_final: 0.7415 (m-80) REVERT: H 35 GLN cc_start: 0.2439 (OUTLIER) cc_final: -0.0804 (tm-30) REVERT: L 9 SER cc_start: 0.5778 (p) cc_final: 0.5259 (m) REVERT: L 112 ILE cc_start: 0.1574 (OUTLIER) cc_final: 0.1321 (tt) outliers start: 12 outliers final: 8 residues processed: 108 average time/residue: 0.2081 time to fit residues: 30.3323 Evaluate side-chains 108 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 263 ASN Chi-restraints excluded: chain 1 residue 278 ILE Chi-restraints excluded: chain 2 residue 97 CYS Chi-restraints excluded: chain 2 residue 301 THR Chi-restraints excluded: chain 2 residue 302 GLU Chi-restraints excluded: chain 3 residue 184 TYR Chi-restraints excluded: chain 3 residue 220 PHE Chi-restraints excluded: chain 3 residue 228 THR Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain L residue 82 SER Chi-restraints excluded: chain L residue 112 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 20 optimal weight: 0.0570 chunk 73 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 75 optimal weight: 20.0000 chunk 9 optimal weight: 0.4980 chunk 13 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.5104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.166519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.132069 restraints weight = 9428.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.129853 restraints weight = 22924.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.128058 restraints weight = 21824.807| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7681 Z= 0.160 Angle : 0.492 7.870 10471 Z= 0.252 Chirality : 0.042 0.166 1139 Planarity : 0.004 0.051 1351 Dihedral : 3.955 15.848 1034 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.33 % Allowed : 15.76 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.47 (0.27), residues: 942 helix: -1.63 (0.69), residues: 48 sheet: 0.42 (0.34), residues: 262 loop : -1.65 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP 2 148 HIS 0.003 0.001 HIS 1 223 PHE 0.027 0.001 PHE 3 220 TYR 0.011 0.001 TYR 2 240 ARG 0.007 0.000 ARG 2 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1596.60 seconds wall clock time: 36 minutes 2.60 seconds (2162.60 seconds total)