Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 13:37:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gse_34233/04_2023/8gse_34233.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gse_34233/04_2023/8gse_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_34233/04_2023/8gse_34233.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gse_34233/04_2023/8gse_34233.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gse_34233/04_2023/8gse_34233.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gse_34233/04_2023/8gse_34233.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-1.21rc1-4938/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: 4.34, per 1000 atoms: 0.58 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: 2.67 Conformation dependent library (CDL) restraints added in 1.1 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: 0.44 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: 1.85 Time building geometry restraints manager: 2.91 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: 0.010 Normalize map: mean=0, sd=1: 2.550 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: 0.010 Extract box with map and model: 12.120 Check model and map are aligned: 0.120 Set scattering table: 0.060 Process input model: 22.010 Find NCS groups from input model: 0.250 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.910 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 0.852 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.2121 time to fit residues: 29.8015 Evaluate side-chains 89 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.862 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2049 ------------------------------------------------------------------------------- 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: 9.9990 chunk 72 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 84 optimal weight: 20.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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: 0.8269 moved from start: 0.0869 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= 0.203 Angle : 0.521 9.365 10471 Z= 0.273 Chirality : 0.043 0.206 1139 Planarity : 0.005 0.047 1351 Dihedral : 4.499 16.486 1034 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer Outliers : 0.61 % 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: -1.69 (0.26), residues: 942 helix: -1.66 (0.70), residues: 50 sheet: 0.10 (0.34), residues: 264 loop : -1.72 (0.23), residues: 628 *********************** 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 101 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 0.838 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 98 average time/residue: 0.2171 time to fit residues: 28.5677 Evaluate side-chains 94 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 91 time to evaluate : 0.850 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0684 time to fit residues: 1.5813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 84 optimal weight: 30.0000 chunk 91 optimal weight: 20.0000 chunk 75 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 67 optimal weight: 9.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- 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: 0.8270 moved from start: 0.1119 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= 0.192 Angle : 0.494 9.017 10471 Z= 0.258 Chirality : 0.042 0.163 1139 Planarity : 0.004 0.044 1351 Dihedral : 4.292 15.677 1034 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer Outliers : 0.73 % 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: -1.57 (0.27), residues: 942 helix: -1.69 (0.68), residues: 50 sheet: 0.27 (0.34), residues: 268 loop : -1.69 (0.23), residues: 624 *********************** 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 104 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 98 time to evaluate : 0.921 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 103 average time/residue: 0.2321 time to fit residues: 31.5797 Evaluate side-chains 95 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 93 time to evaluate : 0.867 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0691 time to fit residues: 1.4856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 43 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 89 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 80 optimal weight: 40.0000 chunk 24 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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: 0.8325 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 7681 Z= 0.330 Angle : 0.573 8.526 10471 Z= 0.302 Chirality : 0.044 0.163 1139 Planarity : 0.005 0.044 1351 Dihedral : 4.638 16.476 1034 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer Outliers : 1.33 % 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: -1.81 (0.68), residues: 49 sheet: 0.31 (0.34), residues: 271 loop : -1.86 (0.22), residues: 622 *********************** 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 107 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 0.896 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 101 average time/residue: 0.2152 time to fit residues: 29.1896 Evaluate side-chains 98 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 91 time to evaluate : 0.756 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0783 time to fit residues: 2.1385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 168 HIS 3 105 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 7681 Z= 0.298 Angle : 0.550 8.358 10471 Z= 0.289 Chirality : 0.044 0.156 1139 Planarity : 0.005 0.046 1351 Dihedral : 4.606 16.336 1034 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer Outliers : 1.21 % 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: -1.77 (0.26), residues: 942 helix: -1.87 (0.66), residues: 49 sheet: 0.37 (0.34), residues: 265 loop : -1.96 (0.22), residues: 628 *********************** 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 105 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 95 time to evaluate : 0.892 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 101 average time/residue: 0.2129 time to fit residues: 28.9873 Evaluate side-chains 97 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 93 time to evaluate : 0.880 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0689 time to fit residues: 1.7261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 2.9990 chunk 80 optimal weight: 50.0000 chunk 17 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 89 optimal weight: 20.0000 chunk 74 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 61 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 7681 Z= 0.315 Angle : 0.560 8.412 10471 Z= 0.295 Chirality : 0.044 0.158 1139 Planarity : 0.005 0.044 1351 Dihedral : 4.663 17.456 1034 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer Outliers : 1.21 % 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: -1.81 (0.26), residues: 942 helix: -1.87 (0.68), residues: 49 sheet: 0.29 (0.35), residues: 265 loop : -1.95 (0.22), residues: 628 *********************** 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 102 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 0.863 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 99 average time/residue: 0.2172 time to fit residues: 28.9015 Evaluate side-chains 97 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 93 time to evaluate : 0.865 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0695 time to fit residues: 1.7300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 89 optimal weight: 20.0000 chunk 56 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 7681 Z= 0.216 Angle : 0.526 8.482 10471 Z= 0.274 Chirality : 0.043 0.147 1139 Planarity : 0.004 0.044 1351 Dihedral : 4.451 16.742 1034 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer Outliers : 0.61 % 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: -1.61 (0.27), residues: 942 helix: -1.82 (0.69), residues: 49 sheet: 0.42 (0.34), residues: 281 loop : -1.85 (0.23), residues: 612 *********************** 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 99 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 94 time to evaluate : 0.844 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 96 average time/residue: 0.2034 time to fit residues: 26.4275 Evaluate side-chains 93 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 0.816 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0685 time to fit residues: 1.5176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 0.0670 chunk 53 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 56 optimal weight: 0.7980 chunk 61 optimal weight: 0.3980 chunk 44 optimal weight: 0.4980 chunk 8 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 81 optimal weight: 20.0000 chunk 85 optimal weight: 10.0000 overall best weight: 1.3520 ------------------------------------------------------------------------------- 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: 0.8270 moved from start: 0.1985 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= 0.151 Angle : 0.488 8.247 10471 Z= 0.251 Chirality : 0.042 0.144 1139 Planarity : 0.004 0.043 1351 Dihedral : 4.097 15.506 1034 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer Outliers : 0.12 % 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: -1.42 (0.27), residues: 942 helix: -1.51 (0.70), residues: 48 sheet: 0.56 (0.34), residues: 277 loop : -1.73 (0.23), residues: 617 *********************** 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 95 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 0.874 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 94 average time/residue: 0.2249 time to fit residues: 28.3635 Evaluate side-chains 91 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.884 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 30.0000 chunk 83 optimal weight: 40.0000 chunk 85 optimal weight: 0.0670 chunk 50 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 65 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 overall best weight: 4.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.060 7681 Z= 0.365 Angle : 0.588 7.834 10471 Z= 0.309 Chirality : 0.045 0.147 1139 Planarity : 0.005 0.048 1351 Dihedral : 4.636 17.983 1034 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer Outliers : 0.48 % 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: -1.74 (0.26), residues: 942 helix: -1.82 (0.70), residues: 49 sheet: 0.40 (0.34), residues: 263 loop : -1.93 (0.23), residues: 630 *********************** 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 95 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 91 time to evaluate : 0.860 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 93 average time/residue: 0.2157 time to fit residues: 27.1387 Evaluate side-chains 87 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 86 time to evaluate : 0.897 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1038 time to fit residues: 1.3794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 92 optimal weight: 0.0770 chunk 85 optimal weight: 0.0970 chunk 73 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 56 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 58 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 34 ASN L 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 7681 Z= 0.121 Angle : 0.491 8.859 10471 Z= 0.251 Chirality : 0.042 0.155 1139 Planarity : 0.004 0.048 1351 Dihedral : 4.048 15.231 1034 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer Outliers : 0.36 % 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: -1.93 (0.64), residues: 54 sheet: 0.52 (0.34), residues: 277 loop : -1.64 (0.24), residues: 611 ********************** 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 101 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 98 time to evaluate : 0.766 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 99 average time/residue: 0.2520 time to fit residues: 34.1199 Evaluate side-chains 93 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.523 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 0.6980 chunk 68 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.3980 chunk 73 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 9 optimal weight: 0.0070 chunk 13 optimal weight: 0.1980 chunk 64 optimal weight: 0.0770 chunk 4 optimal weight: 9.9990 overall best weight: 0.2756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.168447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.133171 restraints weight = 9407.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.129977 restraints weight = 23978.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.124305 restraints weight = 24672.653| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 7681 Z= 0.118 Angle : 0.480 8.098 10471 Z= 0.244 Chirality : 0.041 0.166 1139 Planarity : 0.004 0.049 1351 Dihedral : 3.704 13.652 1034 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer Outliers : 0.24 % 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: -1.18 (0.27), residues: 942 helix: -1.40 (0.69), residues: 49 sheet: 0.65 (0.33), residues: 276 loop : -1.52 (0.24), residues: 617 =============================================================================== Job complete usr+sys time: 1612.65 seconds wall clock time: 29 minutes 58.62 seconds (1798.62 seconds total)