Starting phenix.real_space_refine on Fri Dec 8 02:25:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmr_33302/12_2023/7xmr_33302.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmr_33302/12_2023/7xmr_33302.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmr_33302/12_2023/7xmr_33302.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmr_33302/12_2023/7xmr_33302.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmr_33302/12_2023/7xmr_33302.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmr_33302/12_2023/7xmr_33302.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 52 5.16 5 C 4250 2.51 5 N 1091 2.21 5 O 1218 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 90": "OE1" <-> "OE2" Residue "R ARG 116": "NH1" <-> "NH2" Residue "R ASP 122": "OD1" <-> "OD2" Residue "R ARG 140": "NH1" <-> "NH2" Residue "R ARG 190": "NH1" <-> "NH2" Residue "R ARG 247": "NH1" <-> "NH2" Residue "R ARG 256": "NH1" <-> "NH2" Residue "A GLU 14": "OE1" <-> "OE2" Residue "A GLU 25": "OE1" <-> "OE2" Residue "A ASP 193": "OD1" <-> "OD2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 315": "OD1" <-> "OD2" Residue "A ASP 328": "OD1" <-> "OD2" Residue "A ASP 341": "OD1" <-> "OD2" Residue "A ASP 350": "OD1" <-> "OD2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "B ASP 322": "OD1" <-> "OD2" Residue "C ASP 48": "OD1" <-> "OD2" Residue "C GLU 58": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 6611 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2165 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 11, 'TRANS': 273} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "A" Number of atoms: 1728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1728 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2351 Classifications: {'peptide': 314} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 308} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 43 Chain: "C" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 253 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 4, 'TRANS': 29} Chain: "L" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 114 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" N LEU A 234 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU A 234 " occ=0.00 residue: pdb=" N ALA A 235 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA A 235 " occ=0.00 residue: pdb=" N GLU A 236 " occ=0.00 ... (3 atoms not shown) pdb=" CB GLU A 236 " occ=0.00 residue: pdb=" N ASP A 237 " occ=0.00 ... (3 atoms not shown) pdb=" CB ASP A 237 " occ=0.00 residue: pdb=" N GLU A 238 " occ=0.00 ... (3 atoms not shown) pdb=" CB GLU A 238 " occ=0.00 residue: pdb=" N GLU A 239 " occ=0.00 ... (3 atoms not shown) pdb=" CB GLU A 239 " occ=0.00 residue: pdb=" N MET A 240 " occ=0.00 ... (3 atoms not shown) pdb=" CB MET A 240 " occ=0.00 Time building chain proxies: 4.36, per 1000 atoms: 0.66 Number of scatterers: 6611 At special positions: 0 Unit cell: (111.815, 114.95, 80.465, 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 52 16.00 O 1218 8.00 N 1091 7.00 C 4250 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 115 " - pdb=" SG CYS R 193 " distance=2.03 Simple disulfide: pdb=" SG CYS L 3 " - pdb=" SG CYS L 14 " 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: 2.35 Conformation dependent library (CDL) restraints added in 1.5 seconds 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1640 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 9 sheets defined 43.2% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'R' and resid 39 through 70 removed outlier: 3.507A pdb=" N ASN R 43 " --> pdb=" O ASP R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 95 Processing helix chain 'R' and resid 95 through 105 removed outlier: 3.539A pdb=" N LEU R 105 " --> pdb=" O MET R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 112 through 146 Processing helix chain 'R' and resid 149 through 154 Processing helix chain 'R' and resid 155 through 173 Processing helix chain 'R' and resid 174 through 180 Processing helix chain 'R' and resid 203 through 217 removed outlier: 3.625A pdb=" N LEU R 215 " --> pdb=" O TYR R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 243 Processing helix chain 'R' and resid 246 through 282 removed outlier: 3.796A pdb=" N SER R 250 " --> pdb=" O LYS R 246 " (cutoff:3.500A) Proline residue: R 271 - end of helix removed outlier: 3.560A pdb=" N MET R 282 " --> pdb=" O SER R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 287 through 315 Proline residue: R 309 - end of helix removed outlier: 3.590A pdb=" N LEU R 315 " --> pdb=" O LEU R 311 " (cutoff:3.500A) Processing helix chain 'R' and resid 316 through 323 removed outlier: 3.531A pdb=" N LYS R 320 " --> pdb=" O SER R 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 33 Processing helix chain 'A' and resid 47 through 53 removed outlier: 3.856A pdb=" N LYS A 51 " --> pdb=" O CYS A 47 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.593A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 279 Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.650A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 352 removed outlier: 3.765A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 47 through 52 removed outlier: 3.980A pdb=" N LEU C 51 " --> pdb=" O GLU C 47 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 181 through 185 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.507A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 4.182A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B 338 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.306A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.118A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.891A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 190 Processing sheet with id=AA8, first strand: chain 'B' and resid 231 through 234 removed outlier: 3.723A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 277 removed outlier: 3.934A pdb=" N TYR B 289 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) 361 hydrogen bonds defined for protein. 1044 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: 1.91 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2095 1.34 - 1.46: 1549 1.46 - 1.58: 3039 1.58 - 1.69: 0 1.69 - 1.81: 71 Bond restraints: 6754 Sorted by residual: bond pdb=" C ILE B 270 " pdb=" O ILE B 270 " ideal model delta sigma weight residual 1.236 1.245 -0.009 1.19e-02 7.06e+03 5.74e-01 bond pdb=" C LEU R 270 " pdb=" N PRO R 271 " ideal model delta sigma weight residual 1.335 1.342 -0.008 1.28e-02 6.10e+03 3.65e-01 bond pdb=" C GLY B 144 " pdb=" O GLY B 144 " ideal model delta sigma weight residual 1.230 1.237 -0.007 1.37e-02 5.33e+03 2.99e-01 bond pdb=" C ASP C 48 " pdb=" N PRO C 49 " ideal model delta sigma weight residual 1.335 1.341 -0.006 1.19e-02 7.06e+03 2.95e-01 bond pdb=" C LEU R 96 " pdb=" O LEU R 96 " ideal model delta sigma weight residual 1.238 1.244 -0.007 1.28e-02 6.10e+03 2.67e-01 ... (remaining 6749 not shown) Histogram of bond angle deviations from ideal: 100.73 - 107.38: 175 107.38 - 114.03: 3925 114.03 - 120.68: 2734 120.68 - 127.33: 2289 127.33 - 133.98: 70 Bond angle restraints: 9193 Sorted by residual: angle pdb=" CA LEU R 96 " pdb=" C LEU R 96 " pdb=" N PRO R 97 " ideal model delta sigma weight residual 118.44 121.60 -3.16 1.59e+00 3.96e-01 3.95e+00 angle pdb=" CA ILE B 270 " pdb=" C ILE B 270 " pdb=" N CYS B 271 " ideal model delta sigma weight residual 116.60 119.46 -2.86 1.45e+00 4.76e-01 3.90e+00 angle pdb=" N ILE R 210 " pdb=" CA ILE R 210 " pdb=" C ILE R 210 " ideal model delta sigma weight residual 113.16 110.44 2.72 1.49e+00 4.50e-01 3.33e+00 angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 109.34 113.08 -3.74 2.08e+00 2.31e-01 3.23e+00 angle pdb=" N LEU R 96 " pdb=" CA LEU R 96 " pdb=" C LEU R 96 " ideal model delta sigma weight residual 109.81 113.55 -3.74 2.21e+00 2.05e-01 2.87e+00 ... (remaining 9188 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 3697 17.17 - 34.35: 212 34.35 - 51.52: 35 51.52 - 68.69: 3 68.69 - 85.87: 3 Dihedral angle restraints: 3950 sinusoidal: 1418 harmonic: 2532 Sorted by residual: dihedral pdb=" CB CYS L 3 " pdb=" SG CYS L 3 " pdb=" SG CYS L 14 " pdb=" CB CYS L 14 " ideal model delta sinusoidal sigma weight residual -86.00 -130.68 44.68 1 1.00e+01 1.00e-02 2.77e+01 dihedral pdb=" CB GLU B 215 " pdb=" CG GLU B 215 " pdb=" CD GLU B 215 " pdb=" OE1 GLU B 215 " ideal model delta sinusoidal sigma weight residual 0.00 85.87 -85.87 1 3.00e+01 1.11e-03 9.90e+00 dihedral pdb=" CB GLU C 42 " pdb=" CG GLU C 42 " pdb=" CD GLU C 42 " pdb=" OE1 GLU C 42 " ideal model delta sinusoidal sigma weight residual 0.00 -85.81 85.81 1 3.00e+01 1.11e-03 9.89e+00 ... (remaining 3947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 685 0.026 - 0.051: 257 0.051 - 0.077: 81 0.077 - 0.102: 38 0.102 - 0.128: 24 Chirality restraints: 1085 Sorted by residual: chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.91e-01 chirality pdb=" CA ILE A 265 " pdb=" N ILE A 265 " pdb=" C ILE A 265 " pdb=" CB ILE A 265 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 ... (remaining 1082 not shown) Planarity restraints: 1148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " 0.019 5.00e-02 4.00e+02 2.82e-02 1.27e+00 pdb=" N PRO B 194 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 96 " 0.016 5.00e-02 4.00e+02 2.39e-02 9.15e-01 pdb=" N PRO R 97 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO R 97 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO R 97 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG R 155 " 0.015 5.00e-02 4.00e+02 2.24e-02 8.00e-01 pdb=" N PRO R 156 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO R 156 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO R 156 " 0.013 5.00e-02 4.00e+02 ... (remaining 1145 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1492 2.78 - 3.31: 6170 3.31 - 3.84: 10874 3.84 - 4.37: 12706 4.37 - 4.90: 22023 Nonbonded interactions: 53265 Sorted by model distance: nonbonded pdb=" OG SER B 277 " pdb=" O LEU B 318 " model vdw 2.250 2.440 nonbonded pdb=" OG1 THR B 65 " pdb=" O PRO B 107 " model vdw 2.287 2.440 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.298 2.440 nonbonded pdb=" OH TYR R 205 " pdb=" O ALA L 1 " model vdw 2.317 2.440 nonbonded pdb=" O ARG B 52 " pdb=" NZ LYS B 89 " model vdw 2.318 2.520 ... (remaining 53260 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 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: 3.950 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 22.390 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6108 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 : 0.001 0.017 6754 Z= 0.084 Angle : 0.400 5.729 9193 Z= 0.231 Chirality : 0.036 0.128 1085 Planarity : 0.002 0.028 1148 Dihedral : 10.864 85.867 2304 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.23), residues: 859 helix: -2.56 (0.19), residues: 349 sheet: -1.24 (0.38), residues: 155 loop : -2.21 (0.29), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 63 HIS 0.006 0.001 HIS A 188 PHE 0.006 0.000 PHE R 51 TYR 0.004 0.000 TYR B 289 ARG 0.001 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2312 time to fit residues: 48.0519 Evaluate side-chains 119 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.808 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 0.0010 chunk 49 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 43 ASN R 146 HIS R 186 ASN R 276 ASN R 304 ASN A 22 ASN A 188 HIS A 331 ASN A 333 GLN B 62 HIS B 110 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6754 Z= 0.318 Angle : 0.658 7.216 9193 Z= 0.343 Chirality : 0.044 0.156 1085 Planarity : 0.005 0.058 1148 Dihedral : 3.858 24.993 921 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.58 % Allowed : 13.92 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.27), residues: 859 helix: -0.04 (0.26), residues: 349 sheet: -1.12 (0.36), residues: 168 loop : -1.48 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 99 HIS 0.010 0.002 HIS B 311 PHE 0.017 0.002 PHE R 272 TYR 0.016 0.002 TYR R 228 ARG 0.007 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 127 time to evaluate : 0.701 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 133 average time/residue: 0.1910 time to fit residues: 33.3592 Evaluate side-chains 112 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 104 time to evaluate : 0.691 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0626 time to fit residues: 1.8710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 42 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 64 optimal weight: 0.0050 chunk 52 optimal weight: 0.0670 chunk 21 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 26 optimal weight: 0.2980 chunk 62 optimal weight: 0.6980 overall best weight: 0.3732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6754 Z= 0.155 Angle : 0.531 7.409 9193 Z= 0.273 Chirality : 0.040 0.138 1085 Planarity : 0.003 0.034 1148 Dihedral : 3.532 22.097 921 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.00 % Allowed : 16.07 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.28), residues: 859 helix: 1.11 (0.28), residues: 348 sheet: -0.96 (0.36), residues: 181 loop : -1.23 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS B 54 PHE 0.018 0.001 PHE L 6 TYR 0.014 0.001 TYR B 289 ARG 0.010 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 117 time to evaluate : 0.800 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 122 average time/residue: 0.2042 time to fit residues: 33.4602 Evaluate side-chains 112 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 107 time to evaluate : 1.076 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1145 time to fit residues: 2.5195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 76 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 77 optimal weight: 0.0570 chunk 82 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 196 ASN A 213 HIS A 269 ASN A 331 ASN L 5 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6754 Z= 0.248 Angle : 0.575 7.587 9193 Z= 0.298 Chirality : 0.042 0.156 1085 Planarity : 0.003 0.037 1148 Dihedral : 3.747 17.443 921 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.01 % Allowed : 16.79 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.29), residues: 859 helix: 1.36 (0.28), residues: 349 sheet: -0.73 (0.37), residues: 167 loop : -1.18 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 82 HIS 0.005 0.001 HIS B 54 PHE 0.012 0.001 PHE R 272 TYR 0.016 0.002 TYR A 296 ARG 0.011 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 119 time to evaluate : 0.696 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 125 average time/residue: 0.1945 time to fit residues: 32.1050 Evaluate side-chains 111 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 103 time to evaluate : 0.682 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0683 time to fit residues: 1.9289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 46 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 20 optimal weight: 0.0970 chunk 27 optimal weight: 0.9980 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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: 0.6714 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6754 Z= 0.197 Angle : 0.544 7.867 9193 Z= 0.282 Chirality : 0.041 0.179 1085 Planarity : 0.003 0.045 1148 Dihedral : 3.755 18.228 921 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.72 % Allowed : 18.22 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.29), residues: 859 helix: 1.62 (0.28), residues: 349 sheet: -0.74 (0.37), residues: 169 loop : -0.97 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 82 HIS 0.004 0.001 HIS B 54 PHE 0.010 0.001 PHE A 334 TYR 0.017 0.002 TYR B 59 ARG 0.011 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 118 time to evaluate : 0.770 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 123 average time/residue: 0.1815 time to fit residues: 30.1052 Evaluate side-chains 119 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 110 time to evaluate : 0.691 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0768 time to fit residues: 2.2447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 73 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 79 optimal weight: 0.0470 overall best weight: 1.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN L 5 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6754 Z= 0.318 Angle : 0.637 7.568 9193 Z= 0.333 Chirality : 0.044 0.158 1085 Planarity : 0.004 0.045 1148 Dihedral : 4.153 19.812 921 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.44 % Allowed : 18.36 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.29), residues: 859 helix: 1.48 (0.28), residues: 348 sheet: -0.96 (0.36), residues: 171 loop : -0.98 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP B 82 HIS 0.007 0.001 HIS B 54 PHE 0.022 0.002 PHE R 272 TYR 0.024 0.002 TYR B 59 ARG 0.011 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 115 time to evaluate : 0.722 Fit side-chains outliers start: 17 outliers final: 9 residues processed: 126 average time/residue: 0.1991 time to fit residues: 33.2929 Evaluate side-chains 114 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 105 time to evaluate : 0.757 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0720 time to fit residues: 2.1632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 60 optimal weight: 0.0170 chunk 69 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 32 optimal weight: 0.0770 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6754 Z= 0.188 Angle : 0.571 7.687 9193 Z= 0.291 Chirality : 0.042 0.167 1085 Planarity : 0.004 0.045 1148 Dihedral : 3.970 20.008 921 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.43 % Allowed : 21.38 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.29), residues: 859 helix: 1.56 (0.29), residues: 350 sheet: -0.87 (0.36), residues: 169 loop : -0.95 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 82 HIS 0.006 0.001 HIS B 183 PHE 0.023 0.001 PHE R 272 TYR 0.011 0.001 TYR B 145 ARG 0.009 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 113 time to evaluate : 0.822 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 114 average time/residue: 0.1932 time to fit residues: 29.5127 Evaluate side-chains 107 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 104 time to evaluate : 0.757 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0757 time to fit residues: 1.4263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 48 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 52 optimal weight: 0.0870 chunk 55 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 64 optimal weight: 0.0670 chunk 74 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6754 Z= 0.182 Angle : 0.570 7.455 9193 Z= 0.293 Chirality : 0.042 0.175 1085 Planarity : 0.004 0.052 1148 Dihedral : 3.921 18.133 921 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.86 % Allowed : 21.66 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.29), residues: 859 helix: 1.56 (0.29), residues: 349 sheet: -0.74 (0.38), residues: 159 loop : -1.00 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 82 HIS 0.005 0.001 HIS B 183 PHE 0.020 0.001 PHE R 272 TYR 0.011 0.001 TYR B 59 ARG 0.010 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 0.762 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 114 average time/residue: 0.1926 time to fit residues: 29.5846 Evaluate side-chains 110 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 106 time to evaluate : 0.799 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0818 time to fit residues: 1.5411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 50 optimal weight: 0.1980 chunk 80 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.4739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6754 Z= 0.198 Angle : 0.588 8.906 9193 Z= 0.296 Chirality : 0.043 0.148 1085 Planarity : 0.004 0.044 1148 Dihedral : 3.895 17.986 921 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.29 % Allowed : 22.53 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.29), residues: 859 helix: 1.52 (0.29), residues: 349 sheet: -0.69 (0.36), residues: 167 loop : -0.92 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B 82 HIS 0.004 0.001 HIS B 183 PHE 0.020 0.001 PHE A 189 TYR 0.012 0.001 TYR B 59 ARG 0.009 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 113 time to evaluate : 0.752 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 114 average time/residue: 0.2019 time to fit residues: 30.8414 Evaluate side-chains 106 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 0.741 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0693 time to fit residues: 1.3544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 0.5980 chunk 38 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.5030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6754 Z= 0.277 Angle : 0.649 8.589 9193 Z= 0.330 Chirality : 0.044 0.146 1085 Planarity : 0.004 0.049 1148 Dihedral : 4.137 18.126 921 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.43 % Allowed : 22.96 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.29), residues: 859 helix: 1.40 (0.29), residues: 348 sheet: -1.01 (0.36), residues: 161 loop : -1.00 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP B 82 HIS 0.006 0.001 HIS B 54 PHE 0.013 0.001 PHE R 272 TYR 0.015 0.002 TYR B 59 ARG 0.008 0.001 ARG A 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 105 time to evaluate : 0.680 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 107 average time/residue: 0.2125 time to fit residues: 29.9493 Evaluate side-chains 104 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 101 time to evaluate : 0.735 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0924 time to fit residues: 1.4830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 20 optimal weight: 4.9990 chunk 62 optimal weight: 0.0980 chunk 9 optimal weight: 0.5980 chunk 18 optimal weight: 0.4980 chunk 67 optimal weight: 0.7980 chunk 28 optimal weight: 0.0970 chunk 69 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 3 optimal weight: 9.9990 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.200927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.166986 restraints weight = 6912.709| |-----------------------------------------------------------------------------| r_work (start): 0.4199 rms_B_bonded: 2.14 r_work: 0.4068 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3911 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.4864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6754 Z= 0.164 Angle : 0.581 8.117 9193 Z= 0.293 Chirality : 0.042 0.150 1085 Planarity : 0.003 0.041 1148 Dihedral : 3.918 17.981 921 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.29 % Allowed : 23.10 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.29), residues: 859 helix: 1.52 (0.29), residues: 348 sheet: -0.88 (0.35), residues: 172 loop : -0.91 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP B 82 HIS 0.002 0.001 HIS B 311 PHE 0.020 0.001 PHE R 272 TYR 0.011 0.001 TYR B 59 ARG 0.008 0.001 ARG A 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2090.86 seconds wall clock time: 38 minutes 27.04 seconds (2307.04 seconds total)