Starting phenix.real_space_refine on Thu Nov 14 17:31:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c7u_45294/11_2024/9c7u_45294_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c7u_45294/11_2024/9c7u_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c7u_45294/11_2024/9c7u_45294.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c7u_45294/11_2024/9c7u_45294.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c7u_45294/11_2024/9c7u_45294_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c7u_45294/11_2024/9c7u_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-5513/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: 5.69, per 1000 atoms: 0.83 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: 1.49 Conformation dependent library (CDL) restraints added in 953.2 milliseconds 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: 0.69 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: 2.03 Time building geometry restraints manager: 1.78 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: 5.290 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: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 20.940 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.610 ------------------------------------------------------------------------------- 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 6988 Z= 0.219 Angle : 0.611 9.660 9507 Z= 0.325 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 *********************** 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 : 0.790 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: 0.1599 time to fit residues: 24.4586 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 : 0.821 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 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 6988 Z= 0.317 Angle : 0.603 8.226 9507 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 *********************** 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 : 0.783 Fit side-chains revert: symmetry clash REVERT: A 456 MET cc_start: 0.8436 (mmm) cc_final: 0.8207 (mmm) REVERT: B 731 GLU cc_start: 0.8400 (tm-30) cc_final: 0.7773 (tt0) outliers start: 37 outliers final: 24 residues processed: 141 average time/residue: 0.1662 time to fit residues: 32.7506 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 : 0.764 ------------------------------------------------------------------------------- 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 44 optimal weight: 0.0040 chunk 24 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 79 optimal weight: 0.6980 chunk 27 optimal weight: 0.0980 chunk 64 optimal weight: 0.6980 overall best weight: 0.4792 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6988 Z= 0.201 Angle : 0.560 10.906 9507 Z= 0.289 Chirality : 0.042 0.218 1096 Planarity : 0.004 0.042 1227 Dihedral : 4.913 41.782 990 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 5.23 % Allowed : 29.65 % Favored : 65.12 % 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: 2.10 (0.27), residues: 363 sheet: -2.32 (0.40), residues: 165 loop : -2.39 (0.33), residues: 354 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 0.011 0.001 PHE A 441 TYR 0.009 0.001 TYR A 156 ARG 0.002 0.000 ARG A 114 *********************** 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 145 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 109 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 356 MET cc_start: 0.7881 (ttp) cc_final: 0.7657 (ttp) REVERT: A 456 MET cc_start: 0.8328 (mmm) cc_final: 0.8066 (mmm) REVERT: B 704 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8208 (pp20) REVERT: C 21 TYR cc_start: 0.5828 (OUTLIER) cc_final: 0.5148 (t80) outliers start: 36 outliers final: 25 residues processed: 134 average time/residue: 0.1640 time to fit residues: 30.7233 Evaluate side-chains 127 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.745 ------------------------------------------------------------------------------- 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 201 ILE Chi-restraints excluded: chain A residue 222 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 408 SER 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 704 GLU Chi-restraints excluded: chain B residue 719 HIS 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 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 79 optimal weight: 0.3980 chunk 60 optimal weight: 0.0770 chunk 41 optimal weight: 0.8980 chunk 8 optimal weight: 0.0010 chunk 38 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 80 optimal weight: 0.6980 chunk 85 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 overall best weight: 0.3544 ------------------------------------------------------------------------------- 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** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6988 Z= 0.174 Angle : 0.546 11.563 9507 Z= 0.280 Chirality : 0.042 0.216 1096 Planarity : 0.004 0.039 1227 Dihedral : 4.636 30.408 990 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 5.67 % Allowed : 30.23 % Favored : 64.10 % 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: -0.61 (0.30), residues: 882 helix: 2.07 (0.27), residues: 368 sheet: -2.23 (0.41), residues: 159 loop : -2.28 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 778 HIS 0.005 0.000 HIS B 844 PHE 0.014 0.001 PHE B 836 TYR 0.008 0.001 TYR A 486 ARG 0.002 0.000 ARG A 50 *********************** 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 152 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 113 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: A 356 MET cc_start: 0.7833 (ttp) cc_final: 0.7535 (ttp) REVERT: A 456 MET cc_start: 0.8286 (mmm) cc_final: 0.8007 (mmm) REVERT: B 812 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7021 (mm-30) REVERT: C 21 TYR cc_start: 0.6006 (OUTLIER) cc_final: 0.5249 (t80) outliers start: 39 outliers final: 26 residues processed: 141 average time/residue: 0.1582 time to fit residues: 32.2614 Evaluate side-chains 129 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.970 ------------------------------------------------------------------------------- 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 152 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 222 VAL 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 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 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 763 LEU 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 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 153 VAL Chi-restraints excluded: chain C residue 208 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 58 optimal weight: 0.0870 chunk 0 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 21 optimal weight: 0.0270 chunk 28 optimal weight: 0.4980 overall best weight: 0.5016 ------------------------------------------------------------------------------- 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** B 792 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6988 Z= 0.200 Angle : 0.536 6.823 9507 Z= 0.280 Chirality : 0.042 0.205 1096 Planarity : 0.004 0.037 1227 Dihedral : 4.465 20.746 990 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 6.98 % Allowed : 28.34 % 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: -0.53 (0.30), residues: 882 helix: 2.10 (0.27), residues: 368 sheet: -2.10 (0.42), residues: 157 loop : -2.23 (0.33), residues: 357 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 0.013 0.002 PHE C 128 TYR 0.018 0.001 TYR C 216 ARG 0.002 0.000 ARG A 379 *********************** 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 155 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 107 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 356 MET cc_start: 0.7862 (ttp) cc_final: 0.7519 (ttp) REVERT: A 456 MET cc_start: 0.8326 (mmm) cc_final: 0.8016 (mmm) REVERT: B 786 ASN cc_start: 0.7443 (OUTLIER) cc_final: 0.6816 (p0) REVERT: B 812 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.7052 (mm-30) REVERT: C 21 TYR cc_start: 0.6051 (OUTLIER) cc_final: 0.5211 (t80) REVERT: C 135 MET cc_start: 0.7708 (mtp) cc_final: 0.7183 (mtm) outliers start: 48 outliers final: 33 residues processed: 141 average time/residue: 0.1469 time to fit residues: 30.0893 Evaluate side-chains 137 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 101 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU 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 201 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 367 VAL 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 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 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 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 76 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 49 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 85 optimal weight: 0.0030 chunk 70 optimal weight: 0.6980 chunk 39 optimal weight: 0.1980 chunk 7 optimal weight: 0.0970 chunk 28 optimal weight: 0.4980 chunk 44 optimal weight: 0.0040 chunk 82 optimal weight: 0.7980 overall best weight: 0.1600 ------------------------------------------------------------------------------- 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** B 792 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6988 Z= 0.154 Angle : 0.546 8.122 9507 Z= 0.282 Chirality : 0.042 0.284 1096 Planarity : 0.004 0.045 1227 Dihedral : 4.355 20.641 990 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 5.23 % Allowed : 30.38 % Favored : 64.39 % 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: -0.41 (0.30), residues: 882 helix: 2.24 (0.27), residues: 368 sheet: -2.04 (0.43), residues: 152 loop : -2.22 (0.33), 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 0.040 0.001 PHE B 836 TYR 0.017 0.001 TYR C 216 ARG 0.002 0.000 ARG C 115 *********************** 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 151 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 115 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 356 MET cc_start: 0.7751 (ttp) cc_final: 0.7448 (ttp) REVERT: A 456 MET cc_start: 0.8324 (mmm) cc_final: 0.8017 (mmm) REVERT: B 786 ASN cc_start: 0.7421 (OUTLIER) cc_final: 0.6799 (p0) REVERT: B 812 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.7033 (mm-30) REVERT: C 21 TYR cc_start: 0.6026 (OUTLIER) cc_final: 0.5191 (t80) outliers start: 36 outliers final: 25 residues processed: 139 average time/residue: 0.1474 time to fit residues: 29.3290 Evaluate side-chains 138 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 201 ILE 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 422 LEU 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 763 LEU 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 812 GLU Chi-restraints excluded: chain B residue 813 ASN 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 208 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 0.0770 chunk 48 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 chunk 84 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 52 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6988 Z= 0.246 Angle : 0.570 8.309 9507 Z= 0.295 Chirality : 0.043 0.237 1096 Planarity : 0.004 0.043 1227 Dihedral : 4.359 20.647 990 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 6.69 % Allowed : 29.51 % Favored : 63.81 % 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: -0.46 (0.30), residues: 882 helix: 2.21 (0.27), residues: 368 sheet: -2.15 (0.42), residues: 152 loop : -2.22 (0.33), residues: 362 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 0.032 0.002 PHE B 836 TYR 0.019 0.001 TYR C 216 ARG 0.002 0.000 ARG A 339 *********************** 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 157 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 111 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 356 MET cc_start: 0.7923 (ttp) cc_final: 0.7595 (ttp) REVERT: A 456 MET cc_start: 0.8457 (mmm) cc_final: 0.8129 (mmm) REVERT: B 749 ASP cc_start: 0.8977 (t0) cc_final: 0.8741 (t0) REVERT: B 786 ASN cc_start: 0.7431 (OUTLIER) cc_final: 0.6804 (p0) REVERT: C 21 TYR cc_start: 0.6095 (OUTLIER) cc_final: 0.5231 (t80) outliers start: 46 outliers final: 36 residues processed: 142 average time/residue: 0.1521 time to fit residues: 30.5475 Evaluate side-chains 143 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 105 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 153 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 201 ILE 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 367 VAL 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 763 LEU Chi-restraints excluded: chain B residue 786 ASN Chi-restraints excluded: chain B residue 807 LEU 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 Chi-restraints excluded: chain C residue 211 SER 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 50 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 57 optimal weight: 0.0870 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 0.0670 chunk 66 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 81 optimal weight: 0.0770 chunk 74 optimal weight: 10.0000 overall best weight: 0.3856 ------------------------------------------------------------------------------- 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** B 792 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6988 Z= 0.183 Angle : 0.564 10.976 9507 Z= 0.286 Chirality : 0.042 0.267 1096 Planarity : 0.004 0.049 1227 Dihedral : 4.294 20.538 990 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 5.67 % Allowed : 30.52 % Favored : 63.81 % 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: -0.40 (0.30), residues: 882 helix: 2.25 (0.27), residues: 369 sheet: -2.10 (0.42), residues: 152 loop : -2.20 (0.33), residues: 361 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 0.025 0.001 PHE B 836 TYR 0.018 0.001 TYR C 216 ARG 0.004 0.000 ARG C 115 *********************** 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 149 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 110 time to evaluate : 0.709 Fit side-chains revert: symmetry clash REVERT: A 356 MET cc_start: 0.7861 (ttp) cc_final: 0.7566 (ttp) REVERT: A 456 MET cc_start: 0.8398 (mmm) cc_final: 0.8073 (mmm) REVERT: B 731 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7572 (tt0) REVERT: B 749 ASP cc_start: 0.8988 (t0) cc_final: 0.8752 (t0) REVERT: B 786 ASN cc_start: 0.7411 (OUTLIER) cc_final: 0.6764 (p0) REVERT: B 812 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.7013 (mm-30) REVERT: C 21 TYR cc_start: 0.6217 (OUTLIER) cc_final: 0.5294 (t80) outliers start: 39 outliers final: 27 residues processed: 137 average time/residue: 0.1566 time to fit residues: 30.4540 Evaluate side-chains 137 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 106 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 153 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 201 ILE 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 422 LEU 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 731 GLU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.0010 chunk 81 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 78 optimal weight: 0.0270 chunk 51 optimal weight: 0.0270 chunk 83 optimal weight: 7.9990 overall best weight: 0.5704 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6988 Z= 0.224 Angle : 0.598 14.534 9507 Z= 0.300 Chirality : 0.043 0.280 1096 Planarity : 0.004 0.051 1227 Dihedral : 4.296 20.571 990 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 5.38 % Allowed : 30.67 % 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: -0.43 (0.30), residues: 882 helix: 2.23 (0.27), residues: 368 sheet: -2.10 (0.42), residues: 152 loop : -2.21 (0.33), 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 0.024 0.002 PHE A 228 TYR 0.019 0.001 TYR C 216 ARG 0.004 0.000 ARG A 339 *********************** 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 140 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 103 time to evaluate : 0.779 Fit side-chains REVERT: A 356 MET cc_start: 0.7944 (ttp) cc_final: 0.7629 (ttp) REVERT: A 456 MET cc_start: 0.8484 (mmm) cc_final: 0.8158 (mmm) REVERT: B 731 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7613 (tt0) REVERT: B 749 ASP cc_start: 0.9005 (t0) cc_final: 0.8771 (t0) REVERT: B 786 ASN cc_start: 0.7431 (OUTLIER) cc_final: 0.7033 (p0) REVERT: B 812 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.7025 (mm-30) REVERT: C 21 TYR cc_start: 0.6243 (OUTLIER) cc_final: 0.5329 (t80) REVERT: C 115 ARG cc_start: 0.7512 (ttm170) cc_final: 0.7176 (ttm170) REVERT: C 201 ARG cc_start: 0.8676 (mtm-85) cc_final: 0.8136 (mtm110) outliers start: 37 outliers final: 30 residues processed: 130 average time/residue: 0.1548 time to fit residues: 29.1357 Evaluate side-chains 137 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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 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 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 763 LEU 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 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 51 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 7 optimal weight: 0.0050 chunk 53 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 55 optimal weight: 0.0970 chunk 74 optimal weight: 8.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6988 Z= 0.219 Angle : 0.602 14.047 9507 Z= 0.300 Chirality : 0.043 0.304 1096 Planarity : 0.004 0.048 1227 Dihedral : 4.303 20.647 990 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 5.23 % Allowed : 31.54 % Favored : 63.23 % 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: -0.44 (0.30), residues: 882 helix: 2.22 (0.27), residues: 368 sheet: -2.11 (0.42), residues: 152 loop : -2.22 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 778 HIS 0.006 0.001 HIS B 844 PHE 0.024 0.002 PHE B 836 TYR 0.019 0.001 TYR C 216 ARG 0.003 0.000 ARG C 115 ********************** 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 139 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 103 time to evaluate : 0.742 Fit side-chains REVERT: A 356 MET cc_start: 0.7973 (ttp) cc_final: 0.7659 (ttp) REVERT: A 456 MET cc_start: 0.8487 (mmm) cc_final: 0.8159 (mmm) REVERT: B 731 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7607 (tt0) REVERT: B 749 ASP cc_start: 0.9022 (t0) cc_final: 0.8791 (t0) REVERT: B 786 ASN cc_start: 0.7433 (OUTLIER) cc_final: 0.6771 (p0) REVERT: B 812 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.7027 (mm-30) REVERT: C 21 TYR cc_start: 0.6233 (OUTLIER) cc_final: 0.5338 (t80) REVERT: C 115 ARG cc_start: 0.7440 (ttm170) cc_final: 0.6625 (tpp80) REVERT: C 201 ARG cc_start: 0.8662 (mtm-85) cc_final: 0.8127 (mtm110) outliers start: 36 outliers final: 29 residues processed: 130 average time/residue: 0.1462 time to fit residues: 27.6226 Evaluate side-chains 136 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 103 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 352 VAL Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 367 VAL 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 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 763 LEU 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 21 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 69 optimal weight: 0.0670 chunk 29 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 61 optimal weight: 0.8980 chunk 3 optimal weight: 0.4980 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 C 152 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.145855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.104976 restraints weight = 10493.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.108324 restraints weight = 5939.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.110510 restraints weight = 4181.846| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6988 Z= 0.230 Angle : 0.607 13.846 9507 Z= 0.302 Chirality : 0.043 0.300 1096 Planarity : 0.004 0.050 1227 Dihedral : 4.306 20.733 990 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 5.38 % Allowed : 31.25 % Favored : 63.37 % 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: -0.45 (0.30), residues: 882 helix: 2.21 (0.27), residues: 368 sheet: -2.14 (0.42), residues: 152 loop : -2.22 (0.33), 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 0.024 0.002 PHE B 836 TYR 0.019 0.001 TYR C 216 ARG 0.003 0.000 ARG A 339 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1875.19 seconds wall clock time: 37 minutes 7.98 seconds (2227.98 seconds total)