Starting phenix.real_space_refine on Tue Sep 24 19:02:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz7_32905/09_2024/7wz7_32905_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz7_32905/09_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_32905/09_2024/7wz7_32905.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz7_32905/09_2024/7wz7_32905.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz7_32905/09_2024/7wz7_32905_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wz7_32905/09_2024/7wz7_32905_neut.cif" } 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. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 5.03, per 1000 atoms: 0.58 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 - 3.00 Amino acid : True - 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: 2.29 Conformation dependent library (CDL) restraints added in 1.0 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: 1.05 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: 2.94 Time building geometry restraints manager: 2.66 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: 0.00 - 2.11: 11516 2.11 - 4.22: 387 4.22 - 6.33: 61 6.33 - 8.43: 18 8.43 - 10.54: 7 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 3.040 nonbonded pdb=" O LEU A 291 " pdb=" OG1 THR A 347 " model vdw 2.257 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.266 3.040 nonbonded pdb=" O ARG A 314 " pdb=" OH TYR A 326 " model vdw 2.270 3.040 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.287 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 1.190 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 24.110 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.280 ------------------------------------------------------------------------------- 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 : 0.901 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: 0.9291 time to fit residues: 213.3776 Evaluate side-chains 192 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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: 0.0980 chunk 82 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN E 44 HIS R 820 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8855 Z= 0.252 Angle : 0.649 9.190 11989 Z= 0.334 Chirality : 0.045 0.190 1382 Planarity : 0.004 0.043 1502 Dihedral : 5.198 23.262 1185 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.20 % Allowed : 10.90 % Favored : 86.90 % 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: -0.14 (0.26), residues: 1086 helix: 1.44 (0.28), residues: 356 sheet: -0.70 (0.28), residues: 291 loop : -0.85 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 211 HIS 0.006 0.001 HIS A 345 PHE 0.021 0.002 PHE A 357 TYR 0.016 0.002 TYR C 178 ARG 0.007 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 215 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 194 time to evaluate : 0.870 Fit side-chains REVERT: A 233 LYS cc_start: 0.7740 (mmtt) cc_final: 0.7453 (mmtt) REVERT: A 235 PHE cc_start: 0.8028 (m-80) cc_final: 0.7404 (m-80) REVERT: B 130 GLU cc_start: 0.7377 (mp0) cc_final: 0.7079 (mp0) REVERT: B 325 MET cc_start: 0.6954 (mmt) cc_final: 0.6600 (mtt) REVERT: C 90 ASP cc_start: 0.6982 (m-30) cc_final: 0.6698 (m-30) REVERT: R 582 PHE cc_start: 0.7363 (m-80) cc_final: 0.7130 (m-80) REVERT: R 827 ASN cc_start: 0.7243 (m-40) cc_final: 0.6731 (m-40) REVERT: R 833 PHE cc_start: 0.7230 (m-10) cc_final: 0.7000 (m-80) outliers start: 21 outliers final: 8 residues processed: 201 average time/residue: 0.9288 time to fit residues: 201.9402 Evaluate side-chains 185 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 177 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 C residue 177 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 212 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.0370 chunk 30 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 33 optimal weight: 0.1980 chunk 79 optimal weight: 0.0060 overall best weight: 0.3474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN B 176 GLN E 18 GLN R 820 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8855 Z= 0.196 Angle : 0.590 8.195 11989 Z= 0.303 Chirality : 0.043 0.160 1382 Planarity : 0.004 0.039 1502 Dihedral : 4.851 23.107 1185 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.31 % Allowed : 14.05 % Favored : 83.65 % 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: 0.22 (0.26), residues: 1086 helix: 1.83 (0.28), residues: 358 sheet: -0.68 (0.29), residues: 289 loop : -0.60 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 211 HIS 0.006 0.001 HIS A 345 PHE 0.023 0.002 PHE A 357 TYR 0.014 0.001 TYR C 178 ARG 0.009 0.000 ARG R 685 *********************** 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 203 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 181 time to evaluate : 1.088 Fit side-chains REVERT: A 233 LYS cc_start: 0.7728 (mmtt) cc_final: 0.7446 (mmtt) REVERT: A 235 PHE cc_start: 0.7930 (m-10) cc_final: 0.7328 (m-80) REVERT: A 285 VAL cc_start: 0.6910 (t) cc_final: 0.6694 (m) REVERT: A 294 MET cc_start: 0.6746 (ptt) cc_final: 0.6488 (ptt) REVERT: A 343 PHE cc_start: 0.6972 (m-80) cc_final: 0.6747 (m-10) REVERT: B 38 ASP cc_start: 0.7664 (m-30) cc_final: 0.7394 (m-30) REVERT: B 129 ARG cc_start: 0.8086 (mmm-85) cc_final: 0.7598 (mmm-85) REVERT: B 130 GLU cc_start: 0.7300 (mp0) cc_final: 0.7010 (mp0) REVERT: B 325 MET cc_start: 0.6939 (mmt) cc_final: 0.6671 (mtt) REVERT: C 90 ASP cc_start: 0.6848 (m-30) cc_final: 0.6570 (m-30) REVERT: R 582 PHE cc_start: 0.7393 (m-80) cc_final: 0.7172 (m-80) REVERT: R 693 MET cc_start: 0.5904 (ptt) cc_final: 0.5649 (ptt) outliers start: 22 outliers final: 14 residues processed: 189 average time/residue: 0.9706 time to fit residues: 198.1999 Evaluate side-chains 191 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 177 time to evaluate : 0.995 ------------------------------------------------------------------------------- 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 241 ILE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 218 CYS 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 R residue 677 MET Chi-restraints excluded: chain R residue 763 LEU Chi-restraints excluded: chain R residue 811 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.0670 chunk 74 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 176 GLN R 820 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8855 Z= 0.346 Angle : 0.637 9.138 11989 Z= 0.329 Chirality : 0.045 0.161 1382 Planarity : 0.004 0.060 1502 Dihedral : 4.972 26.164 1185 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.14 % Allowed : 15.09 % Favored : 81.76 % 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: 1.72 (0.28), residues: 359 sheet: -0.80 (0.28), residues: 295 loop : -0.63 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 211 HIS 0.009 0.001 HIS A 345 PHE 0.027 0.002 PHE A 357 TYR 0.017 0.002 TYR C 178 ARG 0.010 0.001 ARG R 685 *********************** 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 217 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 187 time to evaluate : 0.865 Fit side-chains REVERT: A 233 LYS cc_start: 0.7744 (mmtt) cc_final: 0.7466 (mmtt) REVERT: A 235 PHE cc_start: 0.7966 (m-10) cc_final: 0.7452 (m-80) REVERT: A 266 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7301 (pp) REVERT: A 285 VAL cc_start: 0.6996 (t) cc_final: 0.6792 (m) REVERT: A 294 MET cc_start: 0.6798 (ptt) cc_final: 0.6490 (ptt) REVERT: A 350 ILE cc_start: 0.5422 (OUTLIER) cc_final: 0.4855 (pt) REVERT: B 38 ASP cc_start: 0.7711 (m-30) cc_final: 0.7435 (m-30) REVERT: B 130 GLU cc_start: 0.7390 (mp0) cc_final: 0.7087 (mp0) REVERT: B 325 MET cc_start: 0.6919 (mmt) cc_final: 0.6590 (mtt) REVERT: C 90 ASP cc_start: 0.7053 (m-30) cc_final: 0.6808 (m-30) REVERT: R 582 PHE cc_start: 0.7584 (m-80) cc_final: 0.7301 (m-80) REVERT: R 693 MET cc_start: 0.5914 (ptt) cc_final: 0.5608 (ptt) outliers start: 30 outliers final: 16 residues processed: 199 average time/residue: 1.0202 time to fit residues: 218.8836 Evaluate side-chains 199 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 181 time to evaluate : 1.093 ------------------------------------------------------------------------------- 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 266 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 274 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 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 R residue 763 LEU Chi-restraints excluded: chain R residue 811 ILE Chi-restraints excluded: chain R residue 821 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.3980 chunk 1 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 94 optimal weight: 0.1980 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 0.1980 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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: 0.6746 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8855 Z= 0.207 Angle : 0.583 9.284 11989 Z= 0.298 Chirality : 0.043 0.150 1382 Planarity : 0.004 0.047 1502 Dihedral : 4.752 23.580 1185 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.25 % Allowed : 15.62 % Favored : 81.13 % 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: 0.31 (0.26), residues: 1086 helix: 1.93 (0.27), residues: 359 sheet: -0.71 (0.29), residues: 289 loop : -0.52 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 211 HIS 0.006 0.001 HIS A 345 PHE 0.013 0.001 PHE A 282 TYR 0.013 0.001 TYR C 178 ARG 0.008 0.000 ARG R 685 *********************** 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 218 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 187 time to evaluate : 0.939 Fit side-chains REVERT: A 233 LYS cc_start: 0.7739 (mmtt) cc_final: 0.7396 (mmtt) REVERT: A 235 PHE cc_start: 0.7999 (m-10) cc_final: 0.7420 (m-80) REVERT: A 266 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7377 (pp) REVERT: A 270 MET cc_start: 0.6855 (ttt) cc_final: 0.6294 (tpp) REVERT: A 285 VAL cc_start: 0.6941 (t) cc_final: 0.6724 (m) REVERT: A 294 MET cc_start: 0.6811 (ptt) cc_final: 0.6462 (ptt) REVERT: A 350 ILE cc_start: 0.5224 (OUTLIER) cc_final: 0.4653 (pt) REVERT: B 38 ASP cc_start: 0.7677 (m-30) cc_final: 0.7405 (m-30) REVERT: B 130 GLU cc_start: 0.7238 (mp0) cc_final: 0.6993 (mp0) REVERT: B 325 MET cc_start: 0.6906 (mmt) cc_final: 0.6699 (mtt) REVERT: C 90 ASP cc_start: 0.6856 (m-30) cc_final: 0.6611 (m-30) REVERT: C 174 GLN cc_start: 0.7487 (tt0) cc_final: 0.7267 (pt0) REVERT: R 582 PHE cc_start: 0.7500 (m-80) cc_final: 0.7193 (m-80) REVERT: R 799 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8082 (tp) REVERT: R 833 PHE cc_start: 0.7163 (m-10) cc_final: 0.6552 (m-80) outliers start: 31 outliers final: 17 residues processed: 202 average time/residue: 0.8506 time to fit residues: 184.8474 Evaluate side-chains 202 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 182 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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 266 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 274 THR 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 C residue 234 GLU 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 Chi-restraints excluded: chain R residue 811 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 26 optimal weight: 0.1980 chunk 105 optimal weight: 0.9990 chunk 87 optimal weight: 0.0010 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 overall best weight: 0.4186 ------------------------------------------------------------------------------- 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 R 827 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.2661 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= 0.220 Angle : 0.592 9.593 11989 Z= 0.303 Chirality : 0.043 0.148 1382 Planarity : 0.004 0.038 1502 Dihedral : 4.682 24.658 1185 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.46 % Allowed : 16.56 % Favored : 79.98 % 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: 0.33 (0.26), residues: 1086 helix: 1.98 (0.27), residues: 359 sheet: -0.71 (0.29), residues: 290 loop : -0.53 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 211 HIS 0.006 0.001 HIS A 345 PHE 0.014 0.002 PHE B 241 TYR 0.014 0.001 TYR C 178 ARG 0.009 0.000 ARG B 129 *********************** 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 217 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 184 time to evaluate : 0.955 Fit side-chains REVERT: A 233 LYS cc_start: 0.7733 (mmtt) cc_final: 0.7397 (mmtt) REVERT: A 235 PHE cc_start: 0.8016 (m-10) cc_final: 0.7436 (m-80) REVERT: A 266 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7156 (pp) REVERT: A 270 MET cc_start: 0.6895 (ttt) cc_final: 0.6473 (tpp) REVERT: A 285 VAL cc_start: 0.6934 (t) cc_final: 0.6701 (m) REVERT: A 294 MET cc_start: 0.6876 (ptt) cc_final: 0.6489 (ptt) REVERT: A 350 ILE cc_start: 0.5212 (OUTLIER) cc_final: 0.4672 (pt) REVERT: B 38 ASP cc_start: 0.7658 (m-30) cc_final: 0.7388 (m-30) REVERT: B 130 GLU cc_start: 0.7212 (mp0) cc_final: 0.6955 (mp0) REVERT: C 90 ASP cc_start: 0.6933 (m-30) cc_final: 0.6604 (m-30) REVERT: R 582 PHE cc_start: 0.7529 (m-80) cc_final: 0.7173 (m-80) REVERT: R 630 ILE cc_start: 0.6555 (mt) cc_final: 0.6335 (mm) REVERT: R 799 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8089 (tp) outliers start: 33 outliers final: 14 residues processed: 201 average time/residue: 0.8909 time to fit residues: 193.3049 Evaluate side-chains 200 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 183 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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 241 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 275 SER 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 799 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.7980 chunk 60 optimal weight: 0.0870 chunk 77 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 105 optimal weight: 0.0970 chunk 65 optimal weight: 2.9990 chunk 64 optimal weight: 0.0980 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 266 HIS R 820 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.2855 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= 0.210 Angle : 0.590 10.519 11989 Z= 0.301 Chirality : 0.043 0.146 1382 Planarity : 0.004 0.038 1502 Dihedral : 4.615 25.315 1185 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.14 % Allowed : 16.98 % Favored : 79.87 % 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: 358 sheet: -0.58 (0.30), residues: 278 loop : -0.57 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 211 HIS 0.004 0.001 HIS A 345 PHE 0.014 0.002 PHE B 241 TYR 0.015 0.002 TYR C 178 ARG 0.007 0.000 ARG B 129 *********************** 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 210 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 180 time to evaluate : 0.674 Fit side-chains revert: symmetry clash REVERT: A 233 LYS cc_start: 0.7730 (mmtt) cc_final: 0.7399 (mmtt) REVERT: A 235 PHE cc_start: 0.8009 (m-10) cc_final: 0.7431 (m-80) REVERT: A 266 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7120 (pp) REVERT: A 270 MET cc_start: 0.6856 (ttt) cc_final: 0.6436 (tpp) REVERT: A 343 PHE cc_start: 0.6861 (m-80) cc_final: 0.6639 (m-10) REVERT: A 350 ILE cc_start: 0.5170 (OUTLIER) cc_final: 0.4648 (pt) REVERT: B 38 ASP cc_start: 0.7608 (m-30) cc_final: 0.7344 (m-30) REVERT: B 76 ASP cc_start: 0.6713 (m-30) cc_final: 0.6487 (m-30) REVERT: B 129 ARG cc_start: 0.8047 (mmm-85) cc_final: 0.7638 (mmm-85) REVERT: B 130 GLU cc_start: 0.7155 (mp0) cc_final: 0.6921 (mp0) REVERT: B 289 TYR cc_start: 0.7994 (m-80) cc_final: 0.7339 (m-80) REVERT: C 90 ASP cc_start: 0.6906 (m-30) cc_final: 0.6594 (m-30) REVERT: R 582 PHE cc_start: 0.7542 (m-80) cc_final: 0.7172 (m-80) REVERT: R 793 LEU cc_start: 0.7757 (tp) cc_final: 0.7498 (tm) REVERT: R 799 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8114 (tp) REVERT: R 827 ASN cc_start: 0.7315 (m-40) cc_final: 0.7074 (m-40) outliers start: 30 outliers final: 13 residues processed: 196 average time/residue: 1.0159 time to fit residues: 214.3368 Evaluate side-chains 194 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 178 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 241 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 200 PHE 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 799 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 100 optimal weight: 0.0470 chunk 91 optimal weight: 0.0980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN B 176 GLN B 295 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8855 Z= 0.258 Angle : 0.606 11.352 11989 Z= 0.312 Chirality : 0.043 0.152 1382 Planarity : 0.004 0.051 1502 Dihedral : 4.699 25.685 1185 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.52 % Allowed : 18.55 % Favored : 78.93 % 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: 2.14 (0.27), residues: 359 sheet: -0.55 (0.30), residues: 279 loop : -0.60 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 211 HIS 0.007 0.001 HIS B 266 PHE 0.018 0.002 PHE A 282 TYR 0.016 0.002 TYR C 178 ARG 0.010 0.001 ARG B 219 *********************** 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 205 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 181 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: A 233 LYS cc_start: 0.7736 (mmtt) cc_final: 0.7387 (mmtt) REVERT: A 235 PHE cc_start: 0.8012 (m-10) cc_final: 0.7540 (m-80) REVERT: A 270 MET cc_start: 0.6963 (ttt) cc_final: 0.6521 (tpp) REVERT: A 343 PHE cc_start: 0.6909 (m-80) cc_final: 0.6698 (m-10) REVERT: A 350 ILE cc_start: 0.5219 (OUTLIER) cc_final: 0.4716 (pt) REVERT: B 38 ASP cc_start: 0.7647 (m-30) cc_final: 0.7399 (m-30) REVERT: B 76 ASP cc_start: 0.6728 (m-30) cc_final: 0.6506 (m-30) REVERT: B 129 ARG cc_start: 0.8049 (mmm-85) cc_final: 0.7652 (mmm-85) REVERT: B 130 GLU cc_start: 0.7195 (mp0) cc_final: 0.6964 (mp0) REVERT: B 186 ASP cc_start: 0.7550 (p0) cc_final: 0.6873 (p0) REVERT: C 90 ASP cc_start: 0.6913 (m-30) cc_final: 0.6646 (m-30) REVERT: R 582 PHE cc_start: 0.7595 (m-80) cc_final: 0.7264 (m-80) REVERT: R 793 LEU cc_start: 0.7789 (tp) cc_final: 0.7508 (tm) REVERT: R 799 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8124 (tp) outliers start: 24 outliers final: 13 residues processed: 194 average time/residue: 0.9533 time to fit residues: 199.8321 Evaluate side-chains 189 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 174 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 241 ILE Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 200 PHE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain R residue 671 LEU Chi-restraints excluded: chain R residue 763 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: 1.9990 chunk 100 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 42 optimal weight: 0.1980 chunk 76 optimal weight: 0.3980 chunk 30 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 92 optimal weight: 0.0980 chunk 64 optimal weight: 0.7980 chunk 103 optimal weight: 0.4980 chunk 63 optimal weight: 0.7980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN B 125 ASN B 176 GLN B 295 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8855 Z= 0.218 Angle : 0.600 11.790 11989 Z= 0.306 Chirality : 0.043 0.158 1382 Planarity : 0.004 0.042 1502 Dihedral : 4.674 25.611 1185 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.10 % Allowed : 19.39 % Favored : 78.51 % 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: 0.50 (0.26), residues: 1086 helix: 2.19 (0.27), residues: 359 sheet: -0.47 (0.30), residues: 277 loop : -0.61 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 211 HIS 0.008 0.001 HIS R 820 PHE 0.019 0.002 PHE A 282 TYR 0.015 0.002 TYR C 178 ARG 0.009 0.001 ARG B 219 *********************** 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 200 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 180 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: A 233 LYS cc_start: 0.7741 (mmtt) cc_final: 0.7401 (mmtt) REVERT: A 235 PHE cc_start: 0.8014 (m-10) cc_final: 0.7389 (m-80) REVERT: A 270 MET cc_start: 0.6962 (ttt) cc_final: 0.6511 (tpp) REVERT: A 343 PHE cc_start: 0.6961 (m-80) cc_final: 0.6733 (m-10) REVERT: A 350 ILE cc_start: 0.5140 (OUTLIER) cc_final: 0.4643 (pt) REVERT: B 38 ASP cc_start: 0.7608 (m-30) cc_final: 0.7370 (m-30) REVERT: B 129 ARG cc_start: 0.8044 (mmm-85) cc_final: 0.7649 (mmm-85) REVERT: B 130 GLU cc_start: 0.7132 (mp0) cc_final: 0.6908 (mp0) REVERT: B 186 ASP cc_start: 0.7571 (p0) cc_final: 0.6838 (p0) REVERT: B 289 TYR cc_start: 0.7996 (m-80) cc_final: 0.7419 (m-80) REVERT: C 90 ASP cc_start: 0.6918 (m-30) cc_final: 0.6606 (m-30) REVERT: R 582 PHE cc_start: 0.7565 (m-80) cc_final: 0.7209 (m-80) REVERT: R 793 LEU cc_start: 0.7818 (tp) cc_final: 0.7525 (tm) REVERT: R 799 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8112 (tp) outliers start: 20 outliers final: 11 residues processed: 191 average time/residue: 0.9290 time to fit residues: 192.0040 Evaluate side-chains 189 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 176 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 350 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 200 PHE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain R residue 763 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: 0.9980 chunk 71 optimal weight: 0.9980 chunk 108 optimal weight: 0.0980 chunk 99 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 66 optimal weight: 0.4980 chunk 53 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 92 optimal weight: 0.0970 chunk 26 optimal weight: 0.5980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN B 176 GLN B 295 ASN C 159 ASN C 174 GLN R 827 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8855 Z= 0.219 Angle : 0.605 12.973 11989 Z= 0.309 Chirality : 0.043 0.159 1382 Planarity : 0.004 0.041 1502 Dihedral : 4.658 23.503 1185 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.10 % Allowed : 19.18 % Favored : 78.72 % 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: 0.52 (0.26), residues: 1086 helix: 2.23 (0.27), residues: 359 sheet: -0.42 (0.30), residues: 277 loop : -0.66 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 211 HIS 0.006 0.001 HIS R 820 PHE 0.023 0.002 PHE A 282 TYR 0.015 0.002 TYR C 178 ARG 0.009 0.001 ARG B 219 ********************** 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 199 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 179 time to evaluate : 0.849 Fit side-chains revert: symmetry clash REVERT: A 233 LYS cc_start: 0.7736 (mmtt) cc_final: 0.7396 (mmtt) REVERT: A 235 PHE cc_start: 0.7990 (m-10) cc_final: 0.7388 (m-80) REVERT: A 270 MET cc_start: 0.6988 (ttt) cc_final: 0.6516 (tpp) REVERT: A 343 PHE cc_start: 0.7005 (m-80) cc_final: 0.6790 (m-10) REVERT: A 350 ILE cc_start: 0.5173 (OUTLIER) cc_final: 0.4687 (pt) REVERT: B 38 ASP cc_start: 0.7582 (m-30) cc_final: 0.7339 (m-30) REVERT: B 130 GLU cc_start: 0.7127 (mp0) cc_final: 0.6912 (mp0) REVERT: B 289 TYR cc_start: 0.7987 (m-80) cc_final: 0.7393 (m-80) REVERT: C 90 ASP cc_start: 0.6884 (m-30) cc_final: 0.6586 (m-30) REVERT: R 582 PHE cc_start: 0.7570 (m-80) cc_final: 0.7202 (m-80) REVERT: R 793 LEU cc_start: 0.7811 (tp) cc_final: 0.7515 (tm) REVERT: R 799 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8228 (tp) outliers start: 20 outliers final: 13 residues processed: 189 average time/residue: 0.9315 time to fit residues: 190.1471 Evaluate side-chains 187 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 172 time to evaluate : 0.839 ------------------------------------------------------------------------------- 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 350 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 200 PHE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain R residue 763 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: 2.9990 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 62 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN B 176 GLN B 295 ASN C 159 ASN C 174 GLN ** R 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.180303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.152115 restraints weight = 12363.488| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 2.34 r_work: 0.3844 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8855 Z= 0.298 Angle : 0.637 12.646 11989 Z= 0.324 Chirality : 0.044 0.162 1382 Planarity : 0.004 0.043 1502 Dihedral : 4.749 25.661 1185 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.99 % Allowed : 19.39 % 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: 0.46 (0.26), residues: 1086 helix: 2.23 (0.27), residues: 356 sheet: -0.47 (0.30), residues: 283 loop : -0.71 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 211 HIS 0.007 0.001 HIS R 820 PHE 0.020 0.002 PHE R 823 TYR 0.017 0.002 TYR C 178 ARG 0.010 0.001 ARG B 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3695.28 seconds wall clock time: 65 minutes 41.84 seconds (3941.84 seconds total)