Starting phenix.real_space_refine on Sat May 10 21:14:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c7u_45294/05_2025/9c7u_45294_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c7u_45294/05_2025/9c7u_45294.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c7u_45294/05_2025/9c7u_45294.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c7u_45294/05_2025/9c7u_45294.map" model { file = "/net/cci-nas-00/data/ceres_data/9c7u_45294/05_2025/9c7u_45294_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c7u_45294/05_2025/9c7u_45294_neut.cif" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 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 27 5.16 5 C 4356 2.51 5 N 1189 2.21 5 O 1276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6848 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3979 Classifications: {'peptide': 505} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 17, 'TRANS': 487} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 1482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1482 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 10, 'TRANS': 175} Chain: "C" Number of atoms: 1373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1373 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 3, 'TRANS': 201} Chain breaks: 3 Unresolved non-hydrogen bonds: 263 Unresolved non-hydrogen angles: 338 Unresolved non-hydrogen dihedrals: 226 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 9, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 137 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.34, per 1000 atoms: 0.93 Number of scatterers: 6848 At special positions: 0 Unit cell: (61.568, 79.872, 160.576, 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 27 16.00 O 1276 8.00 N 1189 7.00 C 4356 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 692 " - pdb=" SG CYS B 716 " distance=2.03 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 428 " Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 1.1 seconds 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1692 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 7 sheets defined 45.5% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 through 92' Processing helix chain 'A' and resid 93 through 103 Processing helix chain 'A' and resid 120 through 136 removed outlier: 3.637A pdb=" N GLU A 131 " --> pdb=" O PHE A 127 " (cutoff:3.500A) Proline residue: A 132 - end of helix Processing helix chain 'A' and resid 149 through 165 removed outlier: 3.591A pdb=" N ALA A 164 " --> pdb=" O GLN A 160 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 180 Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 241 through 261 removed outlier: 3.809A pdb=" N SER A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYR A 261 " --> pdb=" O ARG A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 265 Processing helix chain 'A' and resid 282 through 292 Processing helix chain 'A' and resid 332 through 348 Processing helix chain 'A' and resid 371 through 378 removed outlier: 4.031A pdb=" N PHE A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG A 378 " --> pdb=" O ARG A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 406 Processing helix chain 'A' and resid 407 through 427 Processing helix chain 'A' and resid 429 through 433 removed outlier: 4.044A pdb=" N GLY A 433 " --> pdb=" O THR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 462 removed outlier: 4.233A pdb=" N GLN A 462 " --> pdb=" O TRP A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 485 Processing helix chain 'A' and resid 521 through 553 removed outlier: 3.747A pdb=" N ASP A 525 " --> pdb=" O PRO A 521 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLN A 544 " --> pdb=" O TYR A 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 695 removed outlier: 4.138A pdb=" N ILE B 694 " --> pdb=" O ASP B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 775 No H-bonds generated for 'chain 'B' and resid 773 through 775' Processing helix chain 'C' and resid 3 through 24 removed outlier: 3.837A pdb=" N PHE C 15 " --> pdb=" O ALA C 11 " (cutoff:3.500A) Proline residue: C 16 - end of helix Processing helix chain 'C' and resid 25 through 29 Processing helix chain 'C' and resid 31 through 56 Processing helix chain 'C' and resid 69 through 91 removed outlier: 3.860A pdb=" N ASN C 91 " --> pdb=" O VAL C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 113 removed outlier: 3.760A pdb=" N GLY C 105 " --> pdb=" O VAL C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 122 Processing helix chain 'C' and resid 130 through 157 removed outlier: 3.522A pdb=" N LEU C 143 " --> pdb=" O SER C 139 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL C 144 " --> pdb=" O ASN C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 177 Processing helix chain 'C' and resid 178 through 190 Processing helix chain 'C' and resid 194 through 220 Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 47 removed outlier: 3.538A pdb=" N HIS A 44 " --> pdb=" O ALA A 516 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A 70 " --> pdb=" O MET A 186 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 50 removed outlier: 6.229A pdb=" N VAL A 108 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ALA A 146 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE A 110 " --> pdb=" O ALA A 146 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 353 through 358 removed outlier: 3.768A pdb=" N SER A 355 " --> pdb=" O LEU A 320 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 322 " --> pdb=" O SER A 355 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N VAL A 308 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N LEU A 385 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N CYS A 310 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU A 309 " --> pdb=" O THR A 218 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL A 220 " --> pdb=" O LEU A 309 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N LEU A 311 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL A 222 " --> pdb=" O LEU A 311 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE A 219 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N PHE A 273 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE A 221 " --> pdb=" O PHE A 273 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N SER A 275 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE A 201 " --> pdb=" O HIS A 494 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N HIS A 494 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N SER A 203 " --> pdb=" O GLN A 492 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLN A 492 " --> pdb=" O SER A 203 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLU A 205 " --> pdb=" O VAL A 490 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL A 490 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 669 through 672 removed outlier: 6.558A pdb=" N THR B 670 " --> pdb=" O ILE B 752 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL B 754 " --> pdb=" O THR B 670 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N SER B 672 " --> pdb=" O VAL B 754 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N ARG B 756 " --> pdb=" O SER B 672 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 698 through 700 removed outlier: 3.919A pdb=" N GLU B 685 " --> pdb=" O GLN B 721 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR B 718 " --> pdb=" O ILE B 740 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE B 740 " --> pdb=" O TYR B 718 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL B 720 " --> pdb=" O ARG B 738 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG B 738 " --> pdb=" O VAL B 720 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 777 through 779 311 hydrogen bonds defined for protein. 888 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.88 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2282 1.34 - 1.46: 1383 1.46 - 1.58: 3276 1.58 - 1.69: 0 1.69 - 1.81: 47 Bond restraints: 6988 Sorted by residual: bond pdb=" C5 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.23e+00 bond pdb=" N ASP A 525 " pdb=" CA ASP A 525 " ideal model delta sigma weight residual 1.458 1.445 0.013 1.30e-02 5.92e+03 9.55e-01 bond pdb=" C3 NAG A 601 " pdb=" O3 NAG A 601 " ideal model delta sigma weight residual 1.403 1.422 -0.019 2.00e-02 2.50e+03 9.36e-01 bond pdb=" CA GLU A 431 " pdb=" CB GLU A 431 " ideal model delta sigma weight residual 1.524 1.538 -0.014 1.51e-02 4.39e+03 8.76e-01 bond pdb=" CB ILE A 155 " pdb=" CG2 ILE A 155 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.37e-01 ... (remaining 6983 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 9342 1.93 - 3.86: 137 3.86 - 5.80: 19 5.80 - 7.73: 6 7.73 - 9.66: 3 Bond angle restraints: 9507 Sorted by residual: angle pdb=" CA GLU A 431 " pdb=" CB GLU A 431 " pdb=" CG GLU A 431 " ideal model delta sigma weight residual 114.10 122.25 -8.15 2.00e+00 2.50e-01 1.66e+01 angle pdb=" CB MET A 456 " pdb=" CG MET A 456 " pdb=" SD MET A 456 " ideal model delta sigma weight residual 112.70 122.36 -9.66 3.00e+00 1.11e-01 1.04e+01 angle pdb=" CB ARG A 339 " pdb=" CG ARG A 339 " pdb=" CD ARG A 339 " ideal model delta sigma weight residual 111.30 117.24 -5.94 2.30e+00 1.89e-01 6.66e+00 angle pdb=" N PHE C 4 " pdb=" CA PHE C 4 " pdb=" C PHE C 4 " ideal model delta sigma weight residual 112.54 109.44 3.10 1.22e+00 6.72e-01 6.44e+00 angle pdb=" C GLU A 431 " pdb=" CA GLU A 431 " pdb=" CB GLU A 431 " ideal model delta sigma weight residual 111.40 114.64 -3.24 1.29e+00 6.01e-01 6.31e+00 ... (remaining 9502 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 3563 17.86 - 35.71: 457 35.71 - 53.57: 114 53.57 - 71.43: 22 71.43 - 89.28: 5 Dihedral angle restraints: 4161 sinusoidal: 1545 harmonic: 2616 Sorted by residual: dihedral pdb=" CA SER A 397 " pdb=" C SER A 397 " pdb=" N SER A 398 " pdb=" CA SER A 398 " ideal model delta harmonic sigma weight residual 180.00 158.66 21.34 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA ILE A 130 " pdb=" C ILE A 130 " pdb=" N GLU A 131 " pdb=" CA GLU A 131 " ideal model delta harmonic sigma weight residual 180.00 -161.12 -18.88 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA THR A 74 " pdb=" C THR A 74 " pdb=" N MET A 75 " pdb=" CA MET A 75 " ideal model delta harmonic sigma weight residual -180.00 -161.41 -18.59 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 4158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 862 0.046 - 0.092: 180 0.092 - 0.138: 53 0.138 - 0.184: 0 0.184 - 0.230: 1 Chirality restraints: 1096 Sorted by residual: chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 428 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA THR A 313 " pdb=" N THR A 313 " pdb=" C THR A 313 " pdb=" CB THR A 313 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.00e-01 chirality pdb=" CA VAL B 815 " pdb=" N VAL B 815 " pdb=" C VAL B 815 " pdb=" CB VAL B 815 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.98e-01 ... (remaining 1093 not shown) Planarity restraints: 1228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 4 " -0.018 2.00e-02 2.50e+03 1.86e-02 6.06e+00 pdb=" CG PHE C 4 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE C 4 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE C 4 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE C 4 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE C 4 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 4 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 434 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO A 435 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 435 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 435 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 778 " -0.013 2.00e-02 2.50e+03 9.88e-03 2.44e+00 pdb=" CG TRP B 778 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP B 778 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP B 778 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 778 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 778 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 778 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 778 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 778 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 778 " -0.003 2.00e-02 2.50e+03 ... (remaining 1225 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 193 2.69 - 3.24: 6982 3.24 - 3.80: 10900 3.80 - 4.35: 13433 4.35 - 4.90: 22381 Nonbonded interactions: 53889 Sorted by model distance: nonbonded pdb=" O LEU A 258 " pdb=" OG1 THR A 264 " model vdw 2.138 3.040 nonbonded pdb=" OG SER A 256 " pdb=" O TYR A 486 " model vdw 2.255 3.040 nonbonded pdb=" N GLU C 127 " pdb=" OE1 GLU C 127 " model vdw 2.261 3.120 nonbonded pdb=" OD1 ASP A 525 " pdb=" ND2 ASN C 8 " model vdw 2.263 3.120 nonbonded pdb=" OD1 ASN B 813 " pdb=" OG1 THR B 837 " model vdw 2.264 3.040 ... (remaining 53884 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.640 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 21.210 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 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 : 0.003 0.036 6990 Z= 0.149 Angle : 0.614 9.660 9512 Z= 0.326 Chirality : 0.041 0.230 1096 Planarity : 0.004 0.043 1227 Dihedral : 16.991 89.285 2466 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 0.29 % Allowed : 33.28 % Favored : 66.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.30), residues: 882 helix: 2.11 (0.27), residues: 367 sheet: -2.40 (0.42), residues: 157 loop : -2.42 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 778 HIS 0.005 0.001 HIS B 844 PHE 0.043 0.002 PHE C 4 TYR 0.020 0.001 TYR C 216 ARG 0.003 0.000 ARG A 464 Details of bonding type rmsd link_NAG-ASN : bond 0.00430 ( 1) link_NAG-ASN : angle 3.01834 ( 3) hydrogen bonds : bond 0.13090 ( 311) hydrogen bonds : angle 5.29115 ( 888) SS BOND : bond 0.00152 ( 1) SS BOND : angle 0.22643 ( 2) covalent geometry : bond 0.00326 ( 6988) covalent geometry : angle 0.61135 ( 9507) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 106 time to evaluate : 0.737 Fit side-chains revert: symmetry clash REVERT: A 450 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7743 (pt0) outliers start: 2 outliers final: 1 residues processed: 108 average time/residue: 0.1622 time to fit residues: 24.8003 Evaluate side-chains 102 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 100 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain B residue 792 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 35 optimal weight: 0.0020 chunk 68 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 overall best weight: 0.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN ** B 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.142907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.101968 restraints weight = 10435.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.105147 restraints weight = 5922.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.107121 restraints weight = 4204.970| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.0754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6990 Z= 0.204 Angle : 0.605 8.226 9512 Z= 0.314 Chirality : 0.044 0.225 1096 Planarity : 0.004 0.043 1227 Dihedral : 6.133 84.208 996 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.32 % Favored : 89.68 % Rotamer: Outliers : 5.38 % Allowed : 28.20 % Favored : 66.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.30), residues: 882 helix: 2.05 (0.27), residues: 362 sheet: -2.29 (0.43), residues: 149 loop : -2.38 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 778 HIS 0.005 0.001 HIS B 844 PHE 0.015 0.002 PHE C 4 TYR 0.010 0.001 TYR C 29 ARG 0.002 0.000 ARG A 413 Details of bonding type rmsd link_NAG-ASN : bond 0.00478 ( 1) link_NAG-ASN : angle 3.09331 ( 3) hydrogen bonds : bond 0.03412 ( 311) hydrogen bonds : angle 4.38444 ( 888) SS BOND : bond 0.00137 ( 1) SS BOND : angle 0.21105 ( 2) covalent geometry : bond 0.00478 ( 6988) covalent geometry : angle 0.60302 ( 9507) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 115 time to evaluate : 0.774 Fit side-chains revert: symmetry clash REVERT: A 456 MET cc_start: 0.8442 (mmm) cc_final: 0.8215 (mmm) REVERT: B 731 GLU cc_start: 0.8470 (tm-30) cc_final: 0.7776 (tt0) outliers start: 37 outliers final: 24 residues processed: 141 average time/residue: 0.1640 time to fit residues: 32.1603 Evaluate side-chains 123 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain B residue 690 ASN Chi-restraints excluded: chain B residue 719 HIS Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 819 ASP Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 208 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 22 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 82 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.142781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.104418 restraints weight = 10630.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.106695 restraints weight = 6401.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.108120 restraints weight = 4634.692| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6990 Z= 0.191 Angle : 0.596 10.962 9512 Z= 0.308 Chirality : 0.044 0.216 1096 Planarity : 0.004 0.043 1227 Dihedral : 4.984 40.183 990 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.43 % Favored : 89.57 % Rotamer: Outliers : 6.10 % Allowed : 29.22 % Favored : 64.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.30), residues: 882 helix: 2.00 (0.27), residues: 363 sheet: -2.44 (0.41), residues: 152 loop : -2.42 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 778 HIS 0.005 0.001 HIS B 844 PHE 0.010 0.002 PHE B 801 TYR 0.011 0.001 TYR A 261 ARG 0.002 0.000 ARG A 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00373 ( 1) link_NAG-ASN : angle 3.05149 ( 3) hydrogen bonds : bond 0.03250 ( 311) hydrogen bonds : angle 4.29840 ( 888) SS BOND : bond 0.00219 ( 1) SS BOND : angle 0.40243 ( 2) covalent geometry : bond 0.00448 ( 6988) covalent geometry : angle 0.59411 ( 9507) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 104 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 356 MET cc_start: 0.8031 (ttp) cc_final: 0.7756 (ttp) REVERT: A 456 MET cc_start: 0.8421 (mmm) cc_final: 0.8147 (mmm) REVERT: B 704 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8199 (pp20) REVERT: C 21 TYR cc_start: 0.5808 (OUTLIER) cc_final: 0.5119 (t80) outliers start: 42 outliers final: 27 residues processed: 133 average time/residue: 0.1580 time to fit residues: 29.5154 Evaluate side-chains 126 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 719 HIS Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 813 ASN Chi-restraints excluded: chain B residue 819 ASP Chi-restraints excluded: chain C residue 21 TYR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain C residue 208 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 84 optimal weight: 20.0000 chunk 30 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 56 optimal weight: 0.0060 chunk 9 optimal weight: 2.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.142157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.101460 restraints weight = 10667.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.104641 restraints weight = 5963.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.106678 restraints weight = 4207.714| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6990 Z= 0.191 Angle : 0.596 11.139 9512 Z= 0.305 Chirality : 0.044 0.211 1096 Planarity : 0.004 0.042 1227 Dihedral : 4.835 28.442 990 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 7.70 % Allowed : 29.22 % Favored : 63.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.30), residues: 882 helix: 1.85 (0.27), residues: 368 sheet: -2.34 (0.43), residues: 141 loop : -2.39 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 195 HIS 0.005 0.001 HIS B 844 PHE 0.014 0.002 PHE B 836 TYR 0.013 0.001 TYR C 29 ARG 0.002 0.000 ARG A 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00313 ( 1) link_NAG-ASN : angle 2.88262 ( 3) hydrogen bonds : bond 0.03168 ( 311) hydrogen bonds : angle 4.23784 ( 888) SS BOND : bond 0.00204 ( 1) SS BOND : angle 0.38846 ( 2) covalent geometry : bond 0.00451 ( 6988) covalent geometry : angle 0.59362 ( 9507) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 105 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 456 MET cc_start: 0.8456 (mmm) cc_final: 0.8156 (mmm) REVERT: C 21 TYR cc_start: 0.6131 (OUTLIER) cc_final: 0.5297 (t80) outliers start: 53 outliers final: 40 residues processed: 142 average time/residue: 0.1487 time to fit residues: 29.7837 Evaluate side-chains 140 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 99 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain B residue 719 HIS Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 792 GLN Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 813 ASN Chi-restraints excluded: chain B residue 819 ASP Chi-restraints excluded: chain C residue 21 TYR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 215 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 27 optimal weight: 0.0470 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 GLN ** B 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.141561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.101058 restraints weight = 10599.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.104209 restraints weight = 5951.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.106134 restraints weight = 4215.341| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6990 Z= 0.194 Angle : 0.579 7.645 9512 Z= 0.302 Chirality : 0.043 0.197 1096 Planarity : 0.004 0.042 1227 Dihedral : 4.746 21.044 990 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 7.99 % Allowed : 28.05 % Favored : 63.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.30), residues: 882 helix: 1.85 (0.27), residues: 368 sheet: -2.52 (0.41), residues: 148 loop : -2.36 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 778 HIS 0.005 0.001 HIS B 844 PHE 0.012 0.002 PHE C 128 TYR 0.010 0.001 TYR A 261 ARG 0.001 0.000 ARG A 64 Details of bonding type rmsd link_NAG-ASN : bond 0.00279 ( 1) link_NAG-ASN : angle 2.72208 ( 3) hydrogen bonds : bond 0.03122 ( 311) hydrogen bonds : angle 4.20328 ( 888) SS BOND : bond 0.00233 ( 1) SS BOND : angle 0.42300 ( 2) covalent geometry : bond 0.00457 ( 6988) covalent geometry : angle 0.57681 ( 9507) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 102 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 356 MET cc_start: 0.8102 (ttp) cc_final: 0.7845 (ttp) REVERT: A 456 MET cc_start: 0.8494 (mmm) cc_final: 0.8178 (mmm) REVERT: B 786 ASN cc_start: 0.7423 (OUTLIER) cc_final: 0.6983 (p0) REVERT: C 21 TYR cc_start: 0.6226 (OUTLIER) cc_final: 0.5333 (t80) REVERT: C 195 TRP cc_start: 0.7441 (m-10) cc_final: 0.7135 (m-10) outliers start: 55 outliers final: 39 residues processed: 144 average time/residue: 0.1516 time to fit residues: 31.0563 Evaluate side-chains 139 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 98 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain B residue 719 HIS Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 786 ASN Chi-restraints excluded: chain B residue 792 GLN Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 813 ASN Chi-restraints excluded: chain B residue 819 ASP Chi-restraints excluded: chain C residue 21 TYR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 215 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 43 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 56 optimal weight: 0.2980 chunk 45 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 GLN ** B 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.142736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.102108 restraints weight = 10633.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.105406 restraints weight = 5970.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.107505 restraints weight = 4160.681| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6990 Z= 0.158 Angle : 0.556 6.448 9512 Z= 0.291 Chirality : 0.043 0.200 1096 Planarity : 0.004 0.042 1227 Dihedral : 4.665 21.011 990 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 7.41 % Allowed : 29.07 % Favored : 63.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.30), residues: 882 helix: 1.93 (0.27), residues: 368 sheet: -2.50 (0.41), residues: 153 loop : -2.32 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 778 HIS 0.007 0.001 HIS B 842 PHE 0.039 0.002 PHE B 836 TYR 0.013 0.001 TYR A 261 ARG 0.002 0.000 ARG C 115 Details of bonding type rmsd link_NAG-ASN : bond 0.00332 ( 1) link_NAG-ASN : angle 2.58254 ( 3) hydrogen bonds : bond 0.03033 ( 311) hydrogen bonds : angle 4.09546 ( 888) SS BOND : bond 0.00200 ( 1) SS BOND : angle 0.39292 ( 2) covalent geometry : bond 0.00370 ( 6988) covalent geometry : angle 0.55438 ( 9507) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 107 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 PHE cc_start: 0.9077 (OUTLIER) cc_final: 0.8814 (p90) REVERT: A 356 MET cc_start: 0.8106 (ttp) cc_final: 0.7832 (ttp) REVERT: A 456 MET cc_start: 0.8444 (mmm) cc_final: 0.8152 (mmm) REVERT: B 786 ASN cc_start: 0.7389 (OUTLIER) cc_final: 0.6947 (p0) REVERT: C 21 TYR cc_start: 0.6264 (OUTLIER) cc_final: 0.5306 (t80) REVERT: C 195 TRP cc_start: 0.7293 (m-10) cc_final: 0.7006 (m-10) outliers start: 51 outliers final: 40 residues processed: 143 average time/residue: 0.1446 time to fit residues: 29.4295 Evaluate side-chains 144 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 101 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 719 HIS Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 786 ASN Chi-restraints excluded: chain B residue 792 GLN Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 813 ASN Chi-restraints excluded: chain B residue 819 ASP Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain C residue 21 TYR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 215 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 80 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 41 optimal weight: 0.0980 chunk 2 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 28 optimal weight: 0.4980 chunk 83 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS ** B 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.143069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.104663 restraints weight = 10509.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.106422 restraints weight = 6037.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.107588 restraints weight = 4560.801| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6990 Z= 0.152 Angle : 0.575 10.602 9512 Z= 0.300 Chirality : 0.043 0.278 1096 Planarity : 0.004 0.040 1227 Dihedral : 4.592 20.916 990 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 7.27 % Allowed : 29.80 % Favored : 62.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.30), residues: 882 helix: 1.98 (0.27), residues: 369 sheet: -2.39 (0.43), residues: 143 loop : -2.36 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 778 HIS 0.006 0.001 HIS B 844 PHE 0.030 0.002 PHE B 836 TYR 0.011 0.001 TYR A 261 ARG 0.002 0.000 ARG C 115 Details of bonding type rmsd link_NAG-ASN : bond 0.00362 ( 1) link_NAG-ASN : angle 2.73605 ( 3) hydrogen bonds : bond 0.02973 ( 311) hydrogen bonds : angle 4.06604 ( 888) SS BOND : bond 0.00195 ( 1) SS BOND : angle 0.38393 ( 2) covalent geometry : bond 0.00356 ( 6988) covalent geometry : angle 0.57350 ( 9507) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 104 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 PHE cc_start: 0.9082 (OUTLIER) cc_final: 0.8753 (p90) REVERT: A 356 MET cc_start: 0.8073 (ttp) cc_final: 0.7767 (ttp) REVERT: A 456 MET cc_start: 0.8450 (mmm) cc_final: 0.8151 (mmm) REVERT: B 786 ASN cc_start: 0.7347 (OUTLIER) cc_final: 0.6903 (p0) REVERT: C 21 TYR cc_start: 0.6186 (OUTLIER) cc_final: 0.5248 (t80) REVERT: C 195 TRP cc_start: 0.7143 (m-10) cc_final: 0.6895 (m-10) outliers start: 50 outliers final: 41 residues processed: 140 average time/residue: 0.1418 time to fit residues: 28.8571 Evaluate side-chains 146 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 102 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 719 HIS Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 786 ASN Chi-restraints excluded: chain B residue 792 GLN Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 812 GLU Chi-restraints excluded: chain B residue 813 ASN Chi-restraints excluded: chain B residue 819 ASP Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain C residue 21 TYR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 215 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 75 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 82 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.142478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.104548 restraints weight = 10648.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.106120 restraints weight = 6472.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.107921 restraints weight = 4327.889| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6990 Z= 0.180 Angle : 0.608 13.948 9512 Z= 0.310 Chirality : 0.044 0.225 1096 Planarity : 0.004 0.040 1227 Dihedral : 4.611 21.004 990 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer: Outliers : 7.70 % Allowed : 29.36 % Favored : 62.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.30), residues: 882 helix: 1.97 (0.27), residues: 368 sheet: -2.53 (0.42), residues: 148 loop : -2.34 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 778 HIS 0.005 0.001 HIS B 844 PHE 0.030 0.002 PHE B 836 TYR 0.012 0.001 TYR A 261 ARG 0.002 0.000 ARG A 339 Details of bonding type rmsd link_NAG-ASN : bond 0.00400 ( 1) link_NAG-ASN : angle 2.72507 ( 3) hydrogen bonds : bond 0.03049 ( 311) hydrogen bonds : angle 4.09594 ( 888) SS BOND : bond 0.00210 ( 1) SS BOND : angle 0.38826 ( 2) covalent geometry : bond 0.00424 ( 6988) covalent geometry : angle 0.60656 ( 9507) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 105 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 PHE cc_start: 0.9102 (OUTLIER) cc_final: 0.8691 (p90) REVERT: A 356 MET cc_start: 0.8149 (ttp) cc_final: 0.7802 (ttp) REVERT: A 456 MET cc_start: 0.8511 (mmm) cc_final: 0.8195 (mmm) REVERT: B 731 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.7832 (tt0) REVERT: B 786 ASN cc_start: 0.7385 (OUTLIER) cc_final: 0.6922 (p0) REVERT: C 21 TYR cc_start: 0.6296 (OUTLIER) cc_final: 0.5365 (t80) outliers start: 53 outliers final: 39 residues processed: 145 average time/residue: 0.1795 time to fit residues: 37.1374 Evaluate side-chains 145 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 102 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 719 HIS Chi-restraints excluded: chain B residue 731 GLU Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 786 ASN Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 812 GLU Chi-restraints excluded: chain B residue 813 ASN Chi-restraints excluded: chain B residue 819 ASP Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain C residue 21 TYR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 215 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 30 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 12 optimal weight: 0.0470 chunk 58 optimal weight: 0.0970 chunk 69 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 17 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 53 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 792 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.145142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.105947 restraints weight = 10590.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.108083 restraints weight = 6419.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.109470 restraints weight = 4749.377| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6990 Z= 0.128 Angle : 0.591 13.717 9512 Z= 0.298 Chirality : 0.043 0.267 1096 Planarity : 0.004 0.043 1227 Dihedral : 4.513 20.733 990 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 5.81 % Allowed : 30.67 % Favored : 63.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.30), residues: 882 helix: 2.07 (0.27), residues: 369 sheet: -2.28 (0.43), residues: 143 loop : -2.32 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 778 HIS 0.006 0.001 HIS B 844 PHE 0.033 0.002 PHE B 836 TYR 0.011 0.001 TYR A 486 ARG 0.009 0.000 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00506 ( 1) link_NAG-ASN : angle 2.80985 ( 3) hydrogen bonds : bond 0.02916 ( 311) hydrogen bonds : angle 3.97770 ( 888) SS BOND : bond 0.00155 ( 1) SS BOND : angle 0.34584 ( 2) covalent geometry : bond 0.00298 ( 6988) covalent geometry : angle 0.58940 ( 9507) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 109 time to evaluate : 0.793 Fit side-chains revert: symmetry clash REVERT: A 228 PHE cc_start: 0.9052 (OUTLIER) cc_final: 0.8682 (p90) REVERT: A 356 MET cc_start: 0.7968 (ttp) cc_final: 0.7659 (ttp) REVERT: A 456 MET cc_start: 0.8423 (mmm) cc_final: 0.8137 (mmm) REVERT: B 731 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.7809 (tt0) REVERT: B 786 ASN cc_start: 0.7202 (OUTLIER) cc_final: 0.6757 (p0) REVERT: B 812 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7040 (mm-30) REVERT: C 21 TYR cc_start: 0.6215 (OUTLIER) cc_final: 0.5308 (t80) REVERT: C 115 ARG cc_start: 0.7590 (ttm-80) cc_final: 0.6941 (ttm-80) outliers start: 40 outliers final: 30 residues processed: 138 average time/residue: 0.1605 time to fit residues: 30.8416 Evaluate side-chains 133 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 98 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 719 HIS Chi-restraints excluded: chain B residue 731 GLU Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 786 ASN Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 812 GLU Chi-restraints excluded: chain B residue 813 ASN Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain C residue 21 TYR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 208 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 62 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 7 optimal weight: 0.4980 chunk 3 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 33 optimal weight: 0.0970 chunk 49 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 chunk 82 optimal weight: 9.9990 chunk 35 optimal weight: 0.0570 chunk 56 optimal weight: 0.2980 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS ** B 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.146074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.106940 restraints weight = 10753.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.110062 restraints weight = 6853.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.111533 restraints weight = 4211.136| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6990 Z= 0.120 Angle : 0.578 11.337 9512 Z= 0.295 Chirality : 0.043 0.305 1096 Planarity : 0.004 0.040 1227 Dihedral : 4.382 21.593 990 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 5.09 % Allowed : 31.40 % Favored : 63.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.30), residues: 882 helix: 2.17 (0.27), residues: 368 sheet: -2.28 (0.41), residues: 152 loop : -2.30 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 778 HIS 0.006 0.001 HIS B 844 PHE 0.023 0.002 PHE B 836 TYR 0.011 0.001 TYR A 486 ARG 0.007 0.000 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00539 ( 1) link_NAG-ASN : angle 2.79860 ( 3) hydrogen bonds : bond 0.02881 ( 311) hydrogen bonds : angle 3.86782 ( 888) SS BOND : bond 0.00145 ( 1) SS BOND : angle 0.31101 ( 2) covalent geometry : bond 0.00274 ( 6988) covalent geometry : angle 0.57628 ( 9507) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 107 time to evaluate : 0.800 Fit side-chains revert: symmetry clash REVERT: A 228 PHE cc_start: 0.9062 (OUTLIER) cc_final: 0.8756 (p90) REVERT: A 356 MET cc_start: 0.7851 (ttp) cc_final: 0.7526 (ttp) REVERT: A 456 MET cc_start: 0.8426 (mmm) cc_final: 0.8133 (mmm) REVERT: B 731 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7749 (tt0) REVERT: B 786 ASN cc_start: 0.7143 (OUTLIER) cc_final: 0.6711 (p0) REVERT: B 812 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7013 (mm-30) REVERT: C 21 TYR cc_start: 0.6279 (OUTLIER) cc_final: 0.5401 (t80) REVERT: C 115 ARG cc_start: 0.7542 (ttm-80) cc_final: 0.7040 (ttm-80) outliers start: 35 outliers final: 27 residues processed: 131 average time/residue: 0.1613 time to fit residues: 30.3963 Evaluate side-chains 132 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 100 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 719 HIS Chi-restraints excluded: chain B residue 731 GLU Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 786 ASN Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 812 GLU Chi-restraints excluded: chain B residue 813 ASN Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain C residue 21 TYR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 208 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 30 optimal weight: 0.4980 chunk 65 optimal weight: 0.3980 chunk 41 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 76 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.144782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.103970 restraints weight = 10618.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.107196 restraints weight = 6043.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.109227 restraints weight = 4283.907| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6990 Z= 0.150 Angle : 0.590 11.327 9512 Z= 0.301 Chirality : 0.043 0.281 1096 Planarity : 0.004 0.040 1227 Dihedral : 4.392 20.863 990 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 5.38 % Allowed : 31.10 % Favored : 63.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.30), residues: 882 helix: 2.08 (0.27), residues: 375 sheet: -2.21 (0.42), residues: 150 loop : -2.31 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 778 HIS 0.006 0.001 HIS B 842 PHE 0.025 0.002 PHE B 836 TYR 0.020 0.001 TYR C 216 ARG 0.007 0.000 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00462 ( 1) link_NAG-ASN : angle 2.78536 ( 3) hydrogen bonds : bond 0.02924 ( 311) hydrogen bonds : angle 3.90752 ( 888) SS BOND : bond 0.00188 ( 1) SS BOND : angle 0.32602 ( 2) covalent geometry : bond 0.00352 ( 6988) covalent geometry : angle 0.58809 ( 9507) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2559.61 seconds wall clock time: 45 minutes 30.45 seconds (2730.45 seconds total)