Starting phenix.real_space_refine on Mon Mar 11 16:49:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz7_32905/03_2024/7wz7_32905_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz7_32905/03_2024/7wz7_32905.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz7_32905/03_2024/7wz7_32905.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz7_32905/03_2024/7wz7_32905.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz7_32905/03_2024/7wz7_32905_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz7_32905/03_2024/7wz7_32905_neut.pdb" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 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 57 5.16 5 C 5553 2.51 5 N 1487 2.21 5 O 1579 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8676 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1734 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 205} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 1776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1776 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "E" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2130 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 9, 'TRANS': 262} Chain breaks: 2 Time building chain proxies: 4.84, per 1000 atoms: 0.56 Number of scatterers: 8676 At special positions: 0 Unit cell: (93.96, 117.72, 131.76, 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 57 16.00 O 1579 8.00 N 1487 7.00 C 5553 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 147 " - pdb=" SG CYS C 217 " distance=2.05 Simple disulfide: pdb=" SG CYS R 657 " - pdb=" SG CYS R 733 " distance=2.04 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: 3.33 Conformation dependent library (CDL) restraints added in 1.6 seconds 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2070 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 12 sheets defined 38.7% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 15 through 38 Processing helix chain 'A' and resid 49 through 66 removed outlier: 3.673A pdb=" N ASN A 66 " --> pdb=" O ILE A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.863A pdb=" N ASN A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 319 through 333 removed outlier: 3.767A pdb=" N VAL A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 375 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 53 through 56 removed outlier: 4.168A pdb=" N GLY C 56 " --> pdb=" O SER C 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 53 through 56' Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.923A pdb=" N THR C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 24 removed outlier: 3.624A pdb=" N ASN E 24 " --> pdb=" O LYS E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 44 Processing helix chain 'E' and resid 45 through 48 removed outlier: 3.574A pdb=" N ASP E 48 " --> pdb=" O ALA E 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 45 through 48' Processing helix chain 'E' and resid 55 through 59 Processing helix chain 'R' and resid 568 through 573 Processing helix chain 'R' and resid 578 through 580 No H-bonds generated for 'chain 'R' and resid 578 through 580' Processing helix chain 'R' and resid 581 through 611 removed outlier: 4.495A pdb=" N TRP R 587 " --> pdb=" O PRO R 583 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA R 608 " --> pdb=" O LEU R 604 " (cutoff:3.500A) Processing helix chain 'R' and resid 617 through 646 removed outlier: 3.740A pdb=" N THR R 646 " --> pdb=" O ILE R 642 " (cutoff:3.500A) Processing helix chain 'R' and resid 655 through 688 Processing helix chain 'R' and resid 694 through 707 Processing helix chain 'R' and resid 707 through 722 Processing helix chain 'R' and resid 744 through 768 Proline residue: R 750 - end of helix Processing helix chain 'R' and resid 785 through 801 Proline residue: R 798 - end of helix Processing helix chain 'R' and resid 802 through 805 Processing helix chain 'R' and resid 806 through 813 Processing helix chain 'R' and resid 814 through 817 removed outlier: 3.962A pdb=" N LEU R 817 " --> pdb=" O SER R 814 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 814 through 817' Processing helix chain 'R' and resid 818 through 828 Processing helix chain 'R' and resid 829 through 837 Processing helix chain 'R' and resid 842 through 854 Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 213 removed outlier: 6.632A pdb=" N LYS A 42 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N LEU A 245 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU A 44 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N MET A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N LEU A 46 " --> pdb=" O MET A 247 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N HIS A 345 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 289 " --> pdb=" O HIS A 345 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.522A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.652A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.039A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.594A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 6.630A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.614A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.620A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.181A pdb=" N GLY C 10 " --> pdb=" O THR C 118 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N MET C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TYR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 128 through 130 Processing sheet with id=AB3, first strand: chain 'C' and resid 134 through 136 removed outlier: 3.652A pdb=" N GLU C 234 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU C 166 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU C 175 " --> pdb=" O LEU C 166 " (cutoff:3.500A) 443 hydrogen bonds defined for protein. 1239 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: 2.91 Time building geometry restraints manager: 3.62 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: 2793 1.34 - 1.46: 2168 1.46 - 1.59: 3808 1.59 - 1.71: 0 1.71 - 1.83: 86 Bond restraints: 8855 Sorted by residual: bond pdb=" N TYR C 223 " pdb=" CA TYR C 223 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.14e-02 7.69e+03 1.11e+01 bond pdb=" CA ALA B 309 " pdb=" C ALA B 309 " ideal model delta sigma weight residual 1.524 1.485 0.039 1.31e-02 5.83e+03 8.72e+00 bond pdb=" N LYS R 728 " pdb=" CA LYS R 728 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.15e-02 7.56e+03 7.32e+00 bond pdb=" N SER C 52 " pdb=" CA SER C 52 " ideal model delta sigma weight residual 1.454 1.424 0.030 1.16e-02 7.43e+03 6.72e+00 bond pdb=" CA LYS R 728 " pdb=" C LYS R 728 " ideal model delta sigma weight residual 1.524 1.491 0.033 1.31e-02 5.83e+03 6.35e+00 ... (remaining 8850 not shown) Histogram of bond angle deviations from ideal: 97.94 - 105.20: 133 105.20 - 112.47: 4646 112.47 - 119.73: 2921 119.73 - 127.00: 4186 127.00 - 134.26: 103 Bond angle restraints: 11989 Sorted by residual: angle pdb=" N SER A 13 " pdb=" CA SER A 13 " pdb=" C SER A 13 " ideal model delta sigma weight residual 107.28 117.82 -10.54 1.75e+00 3.27e-01 3.63e+01 angle pdb=" C SER A 339 " pdb=" CA SER A 339 " pdb=" CB SER A 339 " ideal model delta sigma weight residual 109.83 115.12 -5.29 9.90e-01 1.02e+00 2.86e+01 angle pdb=" N GLY B 202 " pdb=" CA GLY B 202 " pdb=" C GLY B 202 " ideal model delta sigma weight residual 111.04 102.18 8.86 1.77e+00 3.19e-01 2.51e+01 angle pdb=" C TYR C 223 " pdb=" CA TYR C 223 " pdb=" CB TYR C 223 " ideal model delta sigma weight residual 109.56 117.59 -8.03 1.64e+00 3.72e-01 2.40e+01 angle pdb=" C SER A 13 " pdb=" CA SER A 13 " pdb=" CB SER A 13 " ideal model delta sigma weight residual 111.51 105.11 6.40 1.38e+00 5.25e-01 2.15e+01 ... (remaining 11984 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.49: 4866 15.49 - 30.98: 290 30.98 - 46.48: 66 46.48 - 61.97: 21 61.97 - 77.46: 2 Dihedral angle restraints: 5245 sinusoidal: 2049 harmonic: 3196 Sorted by residual: dihedral pdb=" CB CYS R 657 " pdb=" SG CYS R 657 " pdb=" SG CYS R 733 " pdb=" CB CYS R 733 " ideal model delta sinusoidal sigma weight residual -86.00 -126.67 40.67 1 1.00e+01 1.00e-02 2.32e+01 dihedral pdb=" CA GLY B 202 " pdb=" C GLY B 202 " pdb=" N ALA B 203 " pdb=" CA ALA B 203 " ideal model delta harmonic sigma weight residual -180.00 -159.30 -20.70 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA SER A 13 " pdb=" C SER A 13 " pdb=" N ALA A 14 " pdb=" CA ALA A 14 " ideal model delta harmonic sigma weight residual 180.00 160.02 19.98 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 5242 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1072 0.064 - 0.129: 273 0.129 - 0.193: 28 0.193 - 0.257: 6 0.257 - 0.321: 3 Chirality restraints: 1382 Sorted by residual: chirality pdb=" CA PRO B 236 " pdb=" N PRO B 236 " pdb=" C PRO B 236 " pdb=" CB PRO B 236 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CA LEU B 308 " pdb=" N LEU B 308 " pdb=" C LEU B 308 " pdb=" CB LEU B 308 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CG LEU B 55 " pdb=" CB LEU B 55 " pdb=" CD1 LEU B 55 " pdb=" CD2 LEU B 55 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 1379 not shown) Planarity restraints: 1502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 817 " 0.014 2.00e-02 2.50e+03 2.79e-02 7.78e+00 pdb=" C LEU R 817 " -0.048 2.00e-02 2.50e+03 pdb=" O LEU R 817 " 0.018 2.00e-02 2.50e+03 pdb=" N ALA R 818 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 196 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.79e+00 pdb=" C SER C 196 " 0.045 2.00e-02 2.50e+03 pdb=" O SER C 196 " -0.017 2.00e-02 2.50e+03 pdb=" N GLY C 197 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 62 " 0.019 2.00e-02 2.50e+03 1.87e-02 5.25e+00 pdb=" CG HIS B 62 " -0.040 2.00e-02 2.50e+03 pdb=" ND1 HIS B 62 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 HIS B 62 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS B 62 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS B 62 " 0.008 2.00e-02 2.50e+03 ... (remaining 1499 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1700 2.76 - 3.30: 8447 3.30 - 3.83: 14526 3.83 - 4.37: 17482 4.37 - 4.90: 30504 Nonbonded interactions: 72659 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.230 2.440 nonbonded pdb=" O LEU A 291 " pdb=" OG1 THR A 347 " model vdw 2.257 2.440 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.266 2.440 nonbonded pdb=" O ARG A 314 " pdb=" OH TYR A 326 " model vdw 2.270 2.440 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.287 2.440 ... (remaining 72654 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 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: 0.000 Extract box with map and model: 3.850 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.320 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:11.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 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 : 0.010 0.076 8855 Z= 0.664 Angle : 0.954 10.542 11989 Z= 0.541 Chirality : 0.057 0.321 1382 Planarity : 0.005 0.046 1502 Dihedral : 11.502 77.459 3169 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.69 (0.25), residues: 1086 helix: 0.60 (0.28), residues: 361 sheet: -0.86 (0.27), residues: 302 loop : -0.93 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 99 HIS 0.018 0.002 HIS B 62 PHE 0.034 0.004 PHE B 151 TYR 0.032 0.004 TYR B 105 ARG 0.009 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: A 43 ILE cc_start: 0.7002 (mt) cc_final: 0.6552 (tt) REVERT: A 235 PHE cc_start: 0.8013 (m-80) cc_final: 0.7514 (m-80) REVERT: A 285 VAL cc_start: 0.7074 (t) cc_final: 0.6797 (m) REVERT: C 180 MET cc_start: 0.6158 (ttm) cc_final: 0.5955 (tpp) REVERT: R 833 PHE cc_start: 0.7256 (m-10) cc_final: 0.7027 (m-80) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.9823 time to fit residues: 225.4520 Evaluate side-chains 192 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.0970 chunk 82 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 55 optimal weight: 0.0770 chunk 44 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 33 optimal weight: 0.1980 chunk 51 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN B 75 GLN E 44 HIS R 820 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8855 Z= 0.218 Angle : 0.619 8.880 11989 Z= 0.318 Chirality : 0.044 0.185 1382 Planarity : 0.004 0.043 1502 Dihedral : 5.133 23.656 1185 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.31 % Allowed : 11.32 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.26), residues: 1086 helix: 1.44 (0.28), residues: 359 sheet: -0.67 (0.28), residues: 289 loop : -0.80 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 211 HIS 0.007 0.001 HIS A 345 PHE 0.019 0.002 PHE R 806 TYR 0.015 0.002 TYR C 178 ARG 0.009 0.000 ARG R 685 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 199 time to evaluate : 1.019 Fit side-chains REVERT: A 233 LYS cc_start: 0.7723 (mmtt) cc_final: 0.7448 (mmtt) REVERT: A 235 PHE cc_start: 0.8010 (m-80) cc_final: 0.7465 (m-80) REVERT: B 130 GLU cc_start: 0.7405 (mp0) cc_final: 0.7153 (mp0) REVERT: B 230 ASN cc_start: 0.7591 (m-40) cc_final: 0.7309 (m110) REVERT: B 268 ASN cc_start: 0.7690 (p0) cc_final: 0.7429 (p0) REVERT: B 325 MET cc_start: 0.6858 (mmt) cc_final: 0.6455 (mtt) REVERT: R 582 PHE cc_start: 0.7360 (m-80) cc_final: 0.7136 (m-80) REVERT: R 833 PHE cc_start: 0.7238 (m-10) cc_final: 0.7022 (m-80) outliers start: 22 outliers final: 11 residues processed: 206 average time/residue: 0.9778 time to fit residues: 217.3678 Evaluate side-chains 199 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 188 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain R residue 677 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 99 optimal weight: 0.4980 chunk 107 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 295 ASN R 820 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8855 Z= 0.281 Angle : 0.615 8.162 11989 Z= 0.314 Chirality : 0.045 0.286 1382 Planarity : 0.004 0.042 1502 Dihedral : 4.994 25.390 1185 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.83 % Allowed : 14.36 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.05 (0.26), residues: 1086 helix: 1.69 (0.28), residues: 359 sheet: -0.80 (0.28), residues: 295 loop : -0.68 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 211 HIS 0.007 0.001 HIS A 345 PHE 0.025 0.002 PHE A 357 TYR 0.017 0.002 TYR C 178 ARG 0.005 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 188 time to evaluate : 0.969 Fit side-chains REVERT: A 233 LYS cc_start: 0.7729 (mmtt) cc_final: 0.7447 (mmtt) REVERT: A 235 PHE cc_start: 0.7956 (m-10) cc_final: 0.7356 (m-80) REVERT: A 294 MET cc_start: 0.6722 (ptt) cc_final: 0.6489 (ptt) REVERT: A 343 PHE cc_start: 0.6970 (m-80) cc_final: 0.6753 (m-10) REVERT: B 130 GLU cc_start: 0.7438 (mp0) cc_final: 0.7178 (mp0) REVERT: B 230 ASN cc_start: 0.7608 (m-40) cc_final: 0.7375 (m110) REVERT: R 582 PHE cc_start: 0.7459 (m-80) cc_final: 0.7232 (m-80) outliers start: 27 outliers final: 14 residues processed: 196 average time/residue: 0.9778 time to fit residues: 206.6556 Evaluate side-chains 195 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 181 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain R residue 581 ILE Chi-restraints excluded: chain R residue 677 MET Chi-restraints excluded: chain R residue 763 LEU Chi-restraints excluded: chain R residue 811 ILE Chi-restraints excluded: chain R residue 822 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 176 GLN R 820 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 8855 Z= 0.301 Angle : 0.615 8.399 11989 Z= 0.313 Chirality : 0.044 0.203 1382 Planarity : 0.004 0.041 1502 Dihedral : 4.946 25.562 1185 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.25 % Allowed : 14.57 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.08 (0.26), residues: 1086 helix: 1.75 (0.28), residues: 360 sheet: -0.85 (0.28), residues: 294 loop : -0.64 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 211 HIS 0.005 0.001 HIS A 345 PHE 0.019 0.002 PHE A 357 TYR 0.017 0.002 TYR C 178 ARG 0.006 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 181 time to evaluate : 0.962 Fit side-chains REVERT: A 233 LYS cc_start: 0.7734 (mmtt) cc_final: 0.7390 (mmtt) REVERT: A 235 PHE cc_start: 0.7911 (m-10) cc_final: 0.7373 (m-80) REVERT: A 266 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7354 (pp) REVERT: A 270 MET cc_start: 0.6860 (ttt) cc_final: 0.6464 (tpp) REVERT: A 294 MET cc_start: 0.6784 (ptt) cc_final: 0.6473 (ptt) REVERT: A 350 ILE cc_start: 0.5175 (OUTLIER) cc_final: 0.4696 (pt) REVERT: B 130 GLU cc_start: 0.7420 (mp0) cc_final: 0.7152 (mp0) REVERT: C 65 LYS cc_start: 0.7826 (tppt) cc_final: 0.7618 (tttm) REVERT: R 582 PHE cc_start: 0.7577 (m-80) cc_final: 0.7309 (m-80) REVERT: R 833 PHE cc_start: 0.7114 (m-80) cc_final: 0.6561 (m-80) outliers start: 31 outliers final: 17 residues processed: 193 average time/residue: 1.0232 time to fit residues: 212.4029 Evaluate side-chains 201 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 182 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain R residue 763 LEU Chi-restraints excluded: chain R residue 811 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN B 75 GLN B 176 GLN B 230 ASN R 820 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8855 Z= 0.290 Angle : 0.608 9.080 11989 Z= 0.309 Chirality : 0.044 0.154 1382 Planarity : 0.004 0.043 1502 Dihedral : 4.869 25.654 1185 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.46 % Allowed : 14.99 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.13 (0.26), residues: 1086 helix: 1.76 (0.28), residues: 360 sheet: -0.67 (0.29), residues: 279 loop : -0.72 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 211 HIS 0.008 0.001 HIS A 345 PHE 0.022 0.002 PHE A 357 TYR 0.017 0.002 TYR C 178 ARG 0.006 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 178 time to evaluate : 0.892 Fit side-chains REVERT: A 233 LYS cc_start: 0.7737 (mmtt) cc_final: 0.7356 (mmtt) REVERT: A 235 PHE cc_start: 0.7984 (m-10) cc_final: 0.7398 (m-80) REVERT: A 266 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7294 (pp) REVERT: A 270 MET cc_start: 0.6904 (ttt) cc_final: 0.6437 (tpp) REVERT: A 294 MET cc_start: 0.6792 (ptt) cc_final: 0.6430 (ptt) REVERT: A 338 ARG cc_start: 0.7614 (tpp-160) cc_final: 0.7413 (tpp-160) REVERT: B 130 GLU cc_start: 0.7405 (mp0) cc_final: 0.7140 (mp0) REVERT: B 228 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7553 (m-30) REVERT: R 582 PHE cc_start: 0.7564 (m-80) cc_final: 0.7263 (m-80) REVERT: R 799 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8118 (tp) REVERT: R 833 PHE cc_start: 0.7120 (m-80) cc_final: 0.6564 (m-80) outliers start: 33 outliers final: 16 residues processed: 193 average time/residue: 1.0096 time to fit residues: 209.8548 Evaluate side-chains 200 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 181 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain R residue 745 LEU Chi-restraints excluded: chain R residue 763 LEU Chi-restraints excluded: chain R residue 799 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 105 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 48 optimal weight: 0.0980 chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 230 ASN C 171 GLN R 820 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8855 Z= 0.243 Angle : 0.588 8.906 11989 Z= 0.300 Chirality : 0.043 0.149 1382 Planarity : 0.004 0.042 1502 Dihedral : 4.747 25.090 1185 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.35 % Allowed : 16.25 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.26 (0.26), residues: 1086 helix: 1.94 (0.27), residues: 360 sheet: -0.66 (0.29), residues: 279 loop : -0.68 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 211 HIS 0.008 0.001 HIS A 345 PHE 0.013 0.002 PHE B 241 TYR 0.015 0.002 TYR C 178 ARG 0.007 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 179 time to evaluate : 0.999 Fit side-chains REVERT: A 233 LYS cc_start: 0.7731 (mmtt) cc_final: 0.7366 (mmtt) REVERT: A 235 PHE cc_start: 0.7975 (m-10) cc_final: 0.7475 (m-80) REVERT: A 266 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7261 (pp) REVERT: A 270 MET cc_start: 0.6940 (ttt) cc_final: 0.6458 (tpp) REVERT: A 294 MET cc_start: 0.6846 (ptt) cc_final: 0.6460 (ptt) REVERT: B 38 ASP cc_start: 0.7658 (m-30) cc_final: 0.7403 (m-30) REVERT: B 130 GLU cc_start: 0.7332 (mp0) cc_final: 0.7077 (mp0) REVERT: B 228 ASP cc_start: 0.7911 (OUTLIER) cc_final: 0.7565 (m-30) REVERT: C 180 MET cc_start: 0.5843 (OUTLIER) cc_final: 0.5337 (ttp) REVERT: R 582 PHE cc_start: 0.7554 (m-80) cc_final: 0.7190 (m-80) REVERT: R 793 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7566 (tp) REVERT: R 799 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8122 (tp) REVERT: R 833 PHE cc_start: 0.7146 (m-80) cc_final: 0.6572 (m-80) outliers start: 32 outliers final: 17 residues processed: 194 average time/residue: 1.0495 time to fit residues: 219.2175 Evaluate side-chains 201 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 179 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain R residue 670 SER Chi-restraints excluded: chain R residue 745 LEU Chi-restraints excluded: chain R residue 763 LEU Chi-restraints excluded: chain R residue 793 LEU Chi-restraints excluded: chain R residue 799 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.0870 chunk 60 optimal weight: 0.0030 chunk 77 optimal weight: 8.9990 chunk 59 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 64 optimal weight: 0.2980 chunk 48 optimal weight: 0.4980 chunk 41 optimal weight: 0.4980 overall best weight: 0.2768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN R 820 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8855 Z= 0.187 Angle : 0.572 9.509 11989 Z= 0.289 Chirality : 0.042 0.145 1382 Planarity : 0.003 0.038 1502 Dihedral : 4.555 23.028 1185 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.14 % Allowed : 17.19 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.36 (0.26), residues: 1086 helix: 2.11 (0.27), residues: 361 sheet: -0.62 (0.30), residues: 266 loop : -0.70 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 211 HIS 0.005 0.001 HIS A 345 PHE 0.018 0.001 PHE A 343 TYR 0.013 0.001 TYR C 178 ARG 0.007 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 172 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: A 233 LYS cc_start: 0.7737 (mmtt) cc_final: 0.7361 (mmtt) REVERT: A 235 PHE cc_start: 0.8018 (m-10) cc_final: 0.7326 (m-80) REVERT: A 266 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7281 (pp) REVERT: A 270 MET cc_start: 0.6931 (ttt) cc_final: 0.6433 (tpp) REVERT: B 38 ASP cc_start: 0.7609 (m-30) cc_final: 0.7366 (m-30) REVERT: B 130 GLU cc_start: 0.7250 (mp0) cc_final: 0.7009 (mp0) REVERT: B 228 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7509 (m-30) REVERT: C 180 MET cc_start: 0.5774 (OUTLIER) cc_final: 0.5271 (ttp) REVERT: R 582 PHE cc_start: 0.7519 (m-80) cc_final: 0.7127 (m-80) REVERT: R 793 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7549 (tp) REVERT: R 799 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8106 (tp) REVERT: R 827 ASN cc_start: 0.7281 (m-40) cc_final: 0.7063 (m-40) REVERT: R 833 PHE cc_start: 0.7113 (m-80) cc_final: 0.6519 (m-80) outliers start: 30 outliers final: 16 residues processed: 184 average time/residue: 1.0171 time to fit residues: 202.0566 Evaluate side-chains 187 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 166 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain R residue 698 MET Chi-restraints excluded: chain R residue 745 LEU Chi-restraints excluded: chain R residue 763 LEU Chi-restraints excluded: chain R residue 793 LEU Chi-restraints excluded: chain R residue 799 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 66 optimal weight: 0.0670 chunk 71 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 chunk 91 optimal weight: 0.5980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8855 Z= 0.247 Angle : 0.594 11.249 11989 Z= 0.300 Chirality : 0.043 0.146 1382 Planarity : 0.004 0.039 1502 Dihedral : 4.641 24.381 1185 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.35 % Allowed : 17.51 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.39 (0.26), residues: 1086 helix: 2.12 (0.27), residues: 362 sheet: -0.56 (0.29), residues: 277 loop : -0.69 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 211 HIS 0.005 0.001 HIS A 345 PHE 0.020 0.002 PHE A 343 TYR 0.015 0.002 TYR B 85 ARG 0.007 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 171 time to evaluate : 0.998 Fit side-chains revert: symmetry clash REVERT: A 233 LYS cc_start: 0.7729 (mmtt) cc_final: 0.7359 (mmtt) REVERT: A 235 PHE cc_start: 0.7950 (m-10) cc_final: 0.7345 (m-80) REVERT: A 266 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7308 (pp) REVERT: A 270 MET cc_start: 0.6960 (ttt) cc_final: 0.6437 (tpp) REVERT: B 38 ASP cc_start: 0.7644 (m-30) cc_final: 0.7385 (m-30) REVERT: B 130 GLU cc_start: 0.7272 (mp0) cc_final: 0.7030 (mp0) REVERT: B 228 ASP cc_start: 0.7903 (OUTLIER) cc_final: 0.7554 (m-30) REVERT: C 180 MET cc_start: 0.5816 (OUTLIER) cc_final: 0.5280 (ttp) REVERT: R 582 PHE cc_start: 0.7568 (m-80) cc_final: 0.7235 (m-80) REVERT: R 793 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7552 (tp) REVERT: R 799 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8108 (tp) REVERT: R 833 PHE cc_start: 0.7120 (m-80) cc_final: 0.6515 (m-80) outliers start: 32 outliers final: 20 residues processed: 187 average time/residue: 1.0314 time to fit residues: 207.4127 Evaluate side-chains 194 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 169 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain R residue 763 LEU Chi-restraints excluded: chain R residue 793 LEU Chi-restraints excluded: chain R residue 799 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 58 optimal weight: 0.0980 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 chunk 64 optimal weight: 0.0670 chunk 103 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN B 176 GLN ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8855 Z= 0.229 Angle : 0.592 11.988 11989 Z= 0.298 Chirality : 0.043 0.152 1382 Planarity : 0.004 0.038 1502 Dihedral : 4.655 23.949 1185 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.62 % Allowed : 18.76 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.45 (0.26), residues: 1086 helix: 2.15 (0.27), residues: 362 sheet: -0.51 (0.29), residues: 279 loop : -0.66 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 211 HIS 0.005 0.001 HIS R 820 PHE 0.024 0.002 PHE A 343 TYR 0.015 0.002 TYR B 85 ARG 0.007 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 174 time to evaluate : 0.892 Fit side-chains revert: symmetry clash REVERT: A 233 LYS cc_start: 0.7729 (mmtt) cc_final: 0.7356 (mmtt) REVERT: A 235 PHE cc_start: 0.7944 (m-10) cc_final: 0.7324 (m-80) REVERT: A 270 MET cc_start: 0.6964 (ttt) cc_final: 0.6427 (tpp) REVERT: B 38 ASP cc_start: 0.7639 (m-30) cc_final: 0.7393 (m-30) REVERT: B 129 ARG cc_start: 0.8121 (mtp85) cc_final: 0.7795 (mmm-85) REVERT: B 130 GLU cc_start: 0.7245 (mp0) cc_final: 0.7018 (mp0) REVERT: B 228 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7539 (m-30) REVERT: B 262 MET cc_start: 0.6008 (ttm) cc_final: 0.5801 (ttm) REVERT: C 180 MET cc_start: 0.5821 (OUTLIER) cc_final: 0.5251 (ttp) REVERT: R 582 PHE cc_start: 0.7568 (m-80) cc_final: 0.7203 (m-80) REVERT: R 799 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8130 (tp) REVERT: R 833 PHE cc_start: 0.7100 (m-80) cc_final: 0.6458 (m-80) outliers start: 25 outliers final: 17 residues processed: 188 average time/residue: 0.9626 time to fit residues: 195.7929 Evaluate side-chains 192 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 172 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain R residue 763 LEU Chi-restraints excluded: chain R residue 793 LEU Chi-restraints excluded: chain R residue 799 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 99 optimal weight: 0.1980 chunk 86 optimal weight: 0.0170 chunk 8 optimal weight: 0.9980 chunk 66 optimal weight: 0.0770 chunk 53 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 92 optimal weight: 0.3980 chunk 26 optimal weight: 2.9990 overall best weight: 0.2976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 176 GLN ** R 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8855 Z= 0.188 Angle : 0.577 11.618 11989 Z= 0.289 Chirality : 0.042 0.164 1382 Planarity : 0.004 0.037 1502 Dihedral : 4.525 23.197 1185 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.52 % Allowed : 19.50 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.58 (0.27), residues: 1086 helix: 2.31 (0.27), residues: 362 sheet: -0.44 (0.30), residues: 279 loop : -0.63 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 211 HIS 0.003 0.001 HIS B 183 PHE 0.022 0.002 PHE A 282 TYR 0.013 0.001 TYR C 102 ARG 0.007 0.000 ARG A 34 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 176 time to evaluate : 1.006 Fit side-chains revert: symmetry clash REVERT: A 233 LYS cc_start: 0.7738 (mmtt) cc_final: 0.7348 (mmtt) REVERT: A 235 PHE cc_start: 0.7935 (m-10) cc_final: 0.7342 (m-80) REVERT: B 38 ASP cc_start: 0.7520 (m-30) cc_final: 0.7277 (m-30) REVERT: B 129 ARG cc_start: 0.8127 (mtp85) cc_final: 0.7795 (mmm-85) REVERT: B 228 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7423 (m-30) REVERT: C 180 MET cc_start: 0.5764 (OUTLIER) cc_final: 0.5176 (ttp) REVERT: R 582 PHE cc_start: 0.7511 (m-80) cc_final: 0.7165 (m-80) REVERT: R 799 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8189 (tp) outliers start: 24 outliers final: 17 residues processed: 189 average time/residue: 0.9303 time to fit residues: 190.4904 Evaluate side-chains 191 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 171 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain R residue 763 LEU Chi-restraints excluded: chain R residue 793 LEU Chi-restraints excluded: chain R residue 799 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 0.0870 chunk 86 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 176 GLN ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 827 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.180424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.151873 restraints weight = 12329.292| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 2.33 r_work: 0.3848 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 8855 Z= 0.311 Angle : 0.643 12.910 11989 Z= 0.324 Chirality : 0.045 0.159 1382 Planarity : 0.004 0.038 1502 Dihedral : 4.733 25.129 1185 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.41 % Allowed : 20.34 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.42 (0.26), residues: 1086 helix: 2.11 (0.27), residues: 364 sheet: -0.52 (0.29), residues: 281 loop : -0.68 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 804 HIS 0.007 0.001 HIS C 220 PHE 0.033 0.002 PHE A 282 TYR 0.020 0.002 TYR B 85 ARG 0.007 0.001 ARG B 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3811.39 seconds wall clock time: 68 minutes 29.91 seconds (4109.91 seconds total)