Starting phenix.real_space_refine on Sat Aug 3 12:09:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wo7_37681/08_2024/8wo7_37681.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wo7_37681/08_2024/8wo7_37681.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wo7_37681/08_2024/8wo7_37681.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wo7_37681/08_2024/8wo7_37681.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wo7_37681/08_2024/8wo7_37681.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wo7_37681/08_2024/8wo7_37681.cif" } resolution = 2.9 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 5290 2.51 5 N 1306 2.21 5 O 1470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 49": "OE1" <-> "OE2" Residue "A ASP 73": "OD1" <-> "OD2" Residue "A TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A ASP 351": "OD1" <-> "OD2" Residue "A ASP 358": "OD1" <-> "OD2" Residue "A PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 390": "OD1" <-> "OD2" Residue "A GLU 444": "OE1" <-> "OE2" Residue "A TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 505": "OE1" <-> "OE2" Residue "A GLU 509": "OE1" <-> "OE2" Residue "A PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 548": "OE1" <-> "OE2" Residue "B TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 358": "OD1" <-> "OD2" Residue "B PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 381": "OE1" <-> "OE2" Residue "B ASP 393": "OD1" <-> "OD2" Residue "B PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 505": "OE1" <-> "OE2" Residue "B PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 548": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8118 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4031 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 516} Chain: "B" Number of atoms: 4031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4031 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 516} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.61, per 1000 atoms: 0.57 Number of scatterers: 8118 At special positions: 0 Unit cell: (92.759, 105.524, 100.418, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1470 8.00 N 1306 7.00 C 5290 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 123 " distance=2.03 Simple disulfide: pdb=" SG CYS A 83 " - pdb=" SG CYS A 111 " distance=2.04 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 254 " - pdb=" SG CYS A 287 " distance=2.03 Simple disulfide: pdb=" SG CYS B 78 " - pdb=" SG CYS B 123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 83 " - pdb=" SG CYS B 111 " distance=2.04 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 254 " - pdb=" SG CYS B 287 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG C 1 " - " ASN A 270 " " NAG D 1 " - " ASN B 270 " Time building additional restraints: 2.91 Conformation dependent library (CDL) restraints added in 1.4 seconds 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1940 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 7 sheets defined 67.6% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 19 through 30 Processing helix chain 'A' and resid 31 through 38 Processing helix chain 'A' and resid 39 through 43 Processing helix chain 'A' and resid 45 through 61 Processing helix chain 'A' and resid 62 through 74 removed outlier: 4.459A pdb=" N ALA A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 93 through 97 Processing helix chain 'A' and resid 108 through 112 Processing helix chain 'A' and resid 117 through 149 Processing helix chain 'A' and resid 159 through 169 Processing helix chain 'A' and resid 180 through 201 Processing helix chain 'A' and resid 203 through 208 Processing helix chain 'A' and resid 212 through 232 removed outlier: 4.315A pdb=" N SER A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 294 through 313 Processing helix chain 'A' and resid 317 through 331 Processing helix chain 'A' and resid 343 through 355 removed outlier: 3.895A pdb=" N LYS A 355 " --> pdb=" O ASP A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 405 removed outlier: 3.594A pdb=" N TRP A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 435 Processing helix chain 'A' and resid 444 through 451 removed outlier: 4.058A pdb=" N GLY A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 470 Processing helix chain 'A' and resid 472 through 477 Processing helix chain 'A' and resid 480 through 496 Proline residue: A 486 - end of helix removed outlier: 3.520A pdb=" N ILE A 489 " --> pdb=" O GLY A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 502 removed outlier: 3.540A pdb=" N THR A 500 " --> pdb=" O LYS A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 523 Proline residue: A 512 - end of helix Proline residue: A 521 - end of helix Processing helix chain 'A' and resid 525 through 554 removed outlier: 4.508A pdb=" N TRP A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ASP A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 30 Processing helix chain 'B' and resid 31 through 38 Processing helix chain 'B' and resid 39 through 43 Processing helix chain 'B' and resid 45 through 61 Processing helix chain 'B' and resid 62 through 74 removed outlier: 4.704A pdb=" N ALA B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER B 74 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 93 through 97 Processing helix chain 'B' and resid 108 through 112 Processing helix chain 'B' and resid 117 through 149 removed outlier: 3.570A pdb=" N CYS B 123 " --> pdb=" O GLY B 119 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 124 " --> pdb=" O TYR B 120 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 169 Processing helix chain 'B' and resid 180 through 201 removed outlier: 3.558A pdb=" N PHE B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 210 Processing helix chain 'B' and resid 212 through 232 removed outlier: 4.151A pdb=" N SER B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 294 through 313 Processing helix chain 'B' and resid 317 through 331 Processing helix chain 'B' and resid 343 through 355 removed outlier: 3.886A pdb=" N LYS B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 405 removed outlier: 3.710A pdb=" N TRP B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 435 Processing helix chain 'B' and resid 444 through 452 removed outlier: 4.282A pdb=" N GLY B 448 " --> pdb=" O GLU B 444 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE B 449 " --> pdb=" O SER B 445 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU B 451 " --> pdb=" O THR B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 470 Processing helix chain 'B' and resid 472 through 477 Processing helix chain 'B' and resid 480 through 496 Proline residue: B 486 - end of helix Processing helix chain 'B' and resid 497 through 502 removed outlier: 3.524A pdb=" N THR B 500 " --> pdb=" O LYS B 497 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU B 501 " --> pdb=" O SER B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 523 Proline residue: B 512 - end of helix removed outlier: 3.806A pdb=" N MET B 520 " --> pdb=" O THR B 516 " (cutoff:3.500A) Proline residue: B 521 - end of helix Processing helix chain 'B' and resid 525 through 541 Processing helix chain 'B' and resid 541 through 554 Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA2, first strand: chain 'A' and resid 156 through 158 Processing sheet with id=AA3, first strand: chain 'A' and resid 242 through 244 Processing sheet with id=AA4, first strand: chain 'A' and resid 286 through 287 removed outlier: 3.610A pdb=" N SER A 261 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER B 261 " --> pdb=" O VAL A 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AA6, first strand: chain 'B' and resid 156 through 158 Processing sheet with id=AA7, first strand: chain 'B' and resid 241 through 242 507 hydrogen bonds defined for protein. 1434 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: 2.31 Time building geometry restraints manager: 3.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1258 1.31 - 1.44: 2240 1.44 - 1.57: 4723 1.57 - 1.69: 1 1.69 - 1.82: 84 Bond restraints: 8306 Sorted by residual: bond pdb=" C5 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.413 1.540 -0.127 2.00e-02 2.50e+03 4.06e+01 bond pdb=" C5 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.413 1.533 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" C5 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.413 1.528 -0.115 2.00e-02 2.50e+03 3.33e+01 bond pdb=" C5 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.413 1.526 -0.113 2.00e-02 2.50e+03 3.18e+01 bond pdb=" C7 NAG C 2 " pdb=" N2 NAG C 2 " ideal model delta sigma weight residual 1.346 1.453 -0.107 2.00e-02 2.50e+03 2.84e+01 ... (remaining 8301 not shown) Histogram of bond angle deviations from ideal: 98.49 - 105.59: 182 105.59 - 112.69: 4517 112.69 - 119.79: 2577 119.79 - 126.89: 3938 126.89 - 134.00: 92 Bond angle restraints: 11306 Sorted by residual: angle pdb=" N LEU B 275 " pdb=" CA LEU B 275 " pdb=" C LEU B 275 " ideal model delta sigma weight residual 110.91 116.11 -5.20 1.17e+00 7.31e-01 1.97e+01 angle pdb=" N LEU A 275 " pdb=" CA LEU A 275 " pdb=" C LEU A 275 " ideal model delta sigma weight residual 110.91 115.84 -4.93 1.17e+00 7.31e-01 1.78e+01 angle pdb=" N SER A 274 " pdb=" CA SER A 274 " pdb=" C SER A 274 " ideal model delta sigma weight residual 109.94 116.25 -6.31 1.57e+00 4.06e-01 1.61e+01 angle pdb=" N SER B 274 " pdb=" CA SER B 274 " pdb=" C SER B 274 " ideal model delta sigma weight residual 109.94 116.15 -6.21 1.57e+00 4.06e-01 1.57e+01 angle pdb=" C THR A 247 " pdb=" N LEU A 248 " pdb=" CA LEU A 248 " ideal model delta sigma weight residual 121.54 128.40 -6.86 1.91e+00 2.74e-01 1.29e+01 ... (remaining 11301 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.82: 4651 22.82 - 45.64: 222 45.64 - 68.47: 22 68.47 - 91.29: 2 91.29 - 114.11: 3 Dihedral angle restraints: 4900 sinusoidal: 1846 harmonic: 3054 Sorted by residual: dihedral pdb=" CA VAL B 484 " pdb=" C VAL B 484 " pdb=" N GLY B 485 " pdb=" CA GLY B 485 " ideal model delta harmonic sigma weight residual 180.00 142.36 37.64 0 5.00e+00 4.00e-02 5.67e+01 dihedral pdb=" CB CYS A 254 " pdb=" SG CYS A 254 " pdb=" SG CYS A 287 " pdb=" CB CYS A 287 " ideal model delta sinusoidal sigma weight residual 93.00 157.27 -64.27 1 1.00e+01 1.00e-02 5.43e+01 dihedral pdb=" CB CYS B 254 " pdb=" SG CYS B 254 " pdb=" SG CYS B 287 " pdb=" CB CYS B 287 " ideal model delta sinusoidal sigma weight residual 93.00 157.00 -64.00 1 1.00e+01 1.00e-02 5.39e+01 ... (remaining 4897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1075 0.052 - 0.105: 239 0.105 - 0.157: 32 0.157 - 0.210: 5 0.210 - 0.262: 3 Chirality restraints: 1354 Sorted by residual: chirality pdb=" C5 NAG C 1 " pdb=" C4 NAG C 1 " pdb=" C6 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.41 -2.67 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB THR B 250 " pdb=" CA THR B 250 " pdb=" OG1 THR B 250 " pdb=" CG2 THR B 250 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" C5 NAG C 2 " pdb=" C4 NAG C 2 " pdb=" C6 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.41 -2.63 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 1351 not shown) Planarity restraints: 1400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 248 " 0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C LEU A 248 " -0.062 2.00e-02 2.50e+03 pdb=" O LEU A 248 " 0.023 2.00e-02 2.50e+03 pdb=" N VAL A 249 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 486 " -0.049 5.00e-02 4.00e+02 7.38e-02 8.71e+00 pdb=" N PRO A 487 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 487 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 487 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 486 " -0.043 5.00e-02 4.00e+02 6.39e-02 6.54e+00 pdb=" N PRO B 487 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 487 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 487 " -0.036 5.00e-02 4.00e+02 ... (remaining 1397 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 118 2.67 - 3.22: 8314 3.22 - 3.78: 13371 3.78 - 4.34: 18337 4.34 - 4.90: 30079 Nonbonded interactions: 70219 Sorted by model distance: nonbonded pdb=" OG1 THR A 162 " pdb=" OH TYR A 440 " model vdw 2.107 3.040 nonbonded pdb=" O VAL A 539 " pdb=" OH TYR B 309 " model vdw 2.131 3.040 nonbonded pdb=" OD1 ASP B 390 " pdb=" OH TYR B 440 " model vdw 2.155 3.040 nonbonded pdb=" OH TYR A 309 " pdb=" O VAL B 539 " model vdw 2.163 3.040 nonbonded pdb=" OE2 GLU A 49 " pdb=" OG1 THR A 455 " model vdw 2.210 3.040 ... (remaining 70214 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.500 Find NCS groups from input model: 0.180 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:10.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 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 : 0.007 0.127 8306 Z= 0.467 Angle : 0.691 8.581 11306 Z= 0.365 Chirality : 0.045 0.262 1354 Planarity : 0.005 0.074 1398 Dihedral : 13.009 114.111 2936 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.26), residues: 1076 helix: 1.66 (0.20), residues: 640 sheet: -4.54 (0.75), residues: 20 loop : -0.14 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 380 HIS 0.003 0.001 HIS B 364 PHE 0.026 0.002 PHE B 442 TYR 0.018 0.001 TYR A 524 ARG 0.002 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.166 Fit side-chains REVERT: A 23 ARG cc_start: 0.7331 (mtp-110) cc_final: 0.6392 (tmt170) REVERT: A 356 ILE cc_start: 0.9056 (mm) cc_final: 0.8814 (mt) REVERT: A 451 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7906 (mp0) REVERT: B 23 ARG cc_start: 0.7950 (mtp85) cc_final: 0.7135 (tmt170) REVERT: B 139 SER cc_start: 0.8692 (m) cc_final: 0.8457 (m) REVERT: B 356 ILE cc_start: 0.9089 (mm) cc_final: 0.8852 (mt) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 1.0245 time to fit residues: 151.4146 Evaluate side-chains 98 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 84 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 63 optimal weight: 0.3980 chunk 98 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 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8306 Z= 0.204 Angle : 0.589 9.348 11306 Z= 0.306 Chirality : 0.041 0.169 1354 Planarity : 0.005 0.073 1398 Dihedral : 7.546 93.675 1232 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.52 % Allowed : 8.74 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.26), residues: 1076 helix: 1.96 (0.20), residues: 646 sheet: -4.51 (0.74), residues: 20 loop : -0.25 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 482 HIS 0.002 0.000 HIS B 364 PHE 0.018 0.001 PHE B 195 TYR 0.022 0.002 TYR A 440 ARG 0.003 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 121 time to evaluate : 1.020 Fit side-chains REVERT: A 23 ARG cc_start: 0.7341 (mtp-110) cc_final: 0.6422 (tmt170) REVERT: A 451 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7976 (mp0) REVERT: B 23 ARG cc_start: 0.7784 (mtp85) cc_final: 0.6956 (tmt170) REVERT: B 548 GLU cc_start: 0.7835 (tp30) cc_final: 0.7521 (mm-30) outliers start: 13 outliers final: 6 residues processed: 126 average time/residue: 1.0250 time to fit residues: 138.6621 Evaluate side-chains 101 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 95 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 81 optimal weight: 0.0970 chunk 66 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN B 236 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8306 Z= 0.225 Angle : 0.573 10.607 11306 Z= 0.292 Chirality : 0.041 0.210 1354 Planarity : 0.005 0.073 1398 Dihedral : 6.862 81.041 1232 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.86 % Allowed : 12.35 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.26), residues: 1076 helix: 2.06 (0.20), residues: 644 sheet: -4.50 (0.74), residues: 20 loop : -0.26 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 482 HIS 0.002 0.000 HIS B 364 PHE 0.017 0.001 PHE B 166 TYR 0.022 0.001 TYR A 440 ARG 0.003 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 0.931 Fit side-chains REVERT: A 23 ARG cc_start: 0.7362 (mtp-110) cc_final: 0.6463 (tmt170) REVERT: A 321 TYR cc_start: 0.8313 (m-10) cc_final: 0.7460 (m-10) REVERT: B 23 ARG cc_start: 0.7696 (mtp85) cc_final: 0.6969 (tmt170) REVERT: B 451 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7869 (mp0) outliers start: 16 outliers final: 7 residues processed: 118 average time/residue: 1.0230 time to fit residues: 129.7097 Evaluate side-chains 102 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 451 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 46 optimal weight: 0.1980 chunk 65 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8306 Z= 0.195 Angle : 0.559 11.324 11306 Z= 0.284 Chirality : 0.041 0.210 1354 Planarity : 0.005 0.074 1398 Dihedral : 6.185 64.923 1232 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.33 % Allowed : 13.87 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.26), residues: 1076 helix: 2.17 (0.20), residues: 644 sheet: -4.45 (0.76), residues: 20 loop : -0.20 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 482 HIS 0.001 0.000 HIS B 364 PHE 0.016 0.001 PHE B 166 TYR 0.019 0.001 TYR A 440 ARG 0.002 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 113 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: A 23 ARG cc_start: 0.7347 (mtp-110) cc_final: 0.6463 (tmt170) REVERT: A 321 TYR cc_start: 0.8285 (m-10) cc_final: 0.7449 (m-10) REVERT: B 23 ARG cc_start: 0.7646 (mtp85) cc_final: 0.6938 (tmt170) REVERT: B 319 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.8043 (mmm) outliers start: 20 outliers final: 8 residues processed: 122 average time/residue: 0.9248 time to fit residues: 122.2019 Evaluate side-chains 101 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 422 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN A 350 HIS B 67 ASN ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN B 350 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.074 8306 Z= 0.575 Angle : 0.718 11.037 11306 Z= 0.365 Chirality : 0.048 0.271 1354 Planarity : 0.005 0.066 1398 Dihedral : 5.865 41.067 1232 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.91 % Allowed : 15.38 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.26), residues: 1076 helix: 1.78 (0.20), residues: 642 sheet: -4.35 (0.80), residues: 20 loop : -0.26 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 482 HIS 0.005 0.001 HIS A 364 PHE 0.024 0.002 PHE A 166 TYR 0.024 0.002 TYR A 440 ARG 0.003 0.001 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 90 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: A 23 ARG cc_start: 0.7412 (mtp-110) cc_final: 0.6493 (tmt170) REVERT: A 518 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8592 (tt) REVERT: B 23 ARG cc_start: 0.7765 (mtp85) cc_final: 0.7025 (tmt170) REVERT: B 319 MET cc_start: 0.8614 (mmt) cc_final: 0.8342 (mmm) REVERT: B 548 GLU cc_start: 0.7810 (tp30) cc_final: 0.7504 (mm-30) outliers start: 25 outliers final: 14 residues processed: 108 average time/residue: 0.9761 time to fit residues: 113.7179 Evaluate side-chains 98 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 83 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 432 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 61 optimal weight: 8.9990 chunk 25 optimal weight: 20.0000 chunk 104 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8306 Z= 0.264 Angle : 0.579 9.604 11306 Z= 0.298 Chirality : 0.042 0.213 1354 Planarity : 0.005 0.068 1398 Dihedral : 5.380 42.406 1232 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.62 % Favored : 96.28 % Rotamer: Outliers : 2.80 % Allowed : 17.48 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.26), residues: 1076 helix: 1.96 (0.20), residues: 644 sheet: -4.47 (0.78), residues: 20 loop : -0.25 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 482 HIS 0.002 0.001 HIS A 364 PHE 0.017 0.001 PHE B 166 TYR 0.021 0.001 TYR A 440 ARG 0.001 0.000 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 95 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: A 23 ARG cc_start: 0.7400 (mtp-110) cc_final: 0.6469 (tmt170) REVERT: A 275 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7818 (mm) REVERT: A 518 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8589 (tt) REVERT: B 23 ARG cc_start: 0.7656 (mtp85) cc_final: 0.6930 (tmt170) REVERT: B 103 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7396 (ptm160) REVERT: B 319 MET cc_start: 0.8522 (mmt) cc_final: 0.8233 (mmm) outliers start: 24 outliers final: 12 residues processed: 113 average time/residue: 0.9695 time to fit residues: 118.2143 Evaluate side-chains 102 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 87 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 440 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 76 optimal weight: 0.3980 chunk 87 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8306 Z= 0.180 Angle : 0.532 9.232 11306 Z= 0.275 Chirality : 0.041 0.169 1354 Planarity : 0.005 0.072 1398 Dihedral : 5.166 47.968 1232 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.16 % Favored : 96.65 % Rotamer: Outliers : 3.38 % Allowed : 16.67 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.26), residues: 1076 helix: 2.04 (0.20), residues: 658 sheet: -4.39 (0.75), residues: 20 loop : -0.23 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 482 HIS 0.001 0.000 HIS A 364 PHE 0.014 0.001 PHE B 166 TYR 0.017 0.001 TYR A 440 ARG 0.001 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 96 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: A 23 ARG cc_start: 0.7367 (mtp-110) cc_final: 0.6469 (tmt170) REVERT: A 321 TYR cc_start: 0.8187 (m-10) cc_final: 0.7466 (m-10) REVERT: A 518 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8567 (tt) REVERT: B 23 ARG cc_start: 0.7572 (mtp85) cc_final: 0.6950 (tmt170) REVERT: B 319 MET cc_start: 0.8496 (mmt) cc_final: 0.8271 (mmm) outliers start: 29 outliers final: 11 residues processed: 117 average time/residue: 0.9825 time to fit residues: 123.8013 Evaluate side-chains 103 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 440 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 70 optimal weight: 0.4980 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8306 Z= 0.215 Angle : 0.545 8.411 11306 Z= 0.282 Chirality : 0.042 0.184 1354 Planarity : 0.005 0.072 1398 Dihedral : 5.160 47.737 1232 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.70 % Favored : 97.12 % Rotamer: Outliers : 2.33 % Allowed : 17.13 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.26), residues: 1076 helix: 2.23 (0.20), residues: 644 sheet: -4.52 (0.73), residues: 20 loop : -0.13 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 482 HIS 0.001 0.000 HIS B 350 PHE 0.016 0.001 PHE A 166 TYR 0.018 0.001 TYR A 440 ARG 0.002 0.000 ARG B 204 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 97 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.7369 (mtp-110) cc_final: 0.6469 (tmt170) REVERT: A 235 ASN cc_start: 0.8440 (p0) cc_final: 0.8197 (p0) REVERT: A 518 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8549 (tt) REVERT: B 23 ARG cc_start: 0.7571 (mtp85) cc_final: 0.6956 (tmt170) REVERT: B 319 MET cc_start: 0.8522 (mmt) cc_final: 0.8283 (mmm) outliers start: 20 outliers final: 15 residues processed: 110 average time/residue: 0.8992 time to fit residues: 107.2867 Evaluate side-chains 105 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 89 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 440 TYR Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 76 optimal weight: 0.0000 chunk 29 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8306 Z= 0.178 Angle : 0.524 7.921 11306 Z= 0.271 Chirality : 0.041 0.172 1354 Planarity : 0.005 0.074 1398 Dihedral : 5.076 46.771 1232 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.25 % Favored : 96.56 % Rotamer: Outliers : 2.56 % Allowed : 17.13 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.26), residues: 1076 helix: 2.27 (0.20), residues: 646 sheet: -4.40 (0.75), residues: 20 loop : -0.06 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 482 HIS 0.001 0.000 HIS B 350 PHE 0.014 0.001 PHE B 166 TYR 0.016 0.001 TYR A 440 ARG 0.002 0.000 ARG B 204 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 101 time to evaluate : 0.813 Fit side-chains revert: symmetry clash REVERT: A 23 ARG cc_start: 0.7323 (mtp-110) cc_final: 0.6419 (tmt170) REVERT: A 235 ASN cc_start: 0.8336 (p0) cc_final: 0.8134 (p0) REVERT: B 23 ARG cc_start: 0.7501 (mtp85) cc_final: 0.6920 (tmt170) REVERT: B 35 LYS cc_start: 0.8489 (mttp) cc_final: 0.8166 (mmtp) REVERT: B 319 MET cc_start: 0.8502 (mmt) cc_final: 0.8266 (mmm) outliers start: 22 outliers final: 15 residues processed: 113 average time/residue: 0.9091 time to fit residues: 111.3786 Evaluate side-chains 108 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 93 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 440 TYR Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 chunk 71 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 99 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 66 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8306 Z= 0.293 Angle : 0.573 9.029 11306 Z= 0.297 Chirality : 0.043 0.239 1354 Planarity : 0.005 0.072 1398 Dihedral : 5.190 47.483 1232 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.62 % Favored : 96.19 % Rotamer: Outliers : 1.98 % Allowed : 17.48 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.26), residues: 1076 helix: 2.19 (0.20), residues: 644 sheet: -4.47 (0.77), residues: 20 loop : -0.12 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 482 HIS 0.004 0.001 HIS A 364 PHE 0.018 0.001 PHE B 166 TYR 0.017 0.001 TYR A 440 ARG 0.001 0.000 ARG A 450 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 0.883 Fit side-chains revert: symmetry clash REVERT: A 23 ARG cc_start: 0.7382 (mtp-110) cc_final: 0.6479 (tmt170) REVERT: A 235 ASN cc_start: 0.8437 (p0) cc_final: 0.8203 (p0) REVERT: A 518 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8592 (tt) REVERT: B 23 ARG cc_start: 0.7563 (mtp85) cc_final: 0.6953 (tmt170) REVERT: B 319 MET cc_start: 0.8523 (mmt) cc_final: 0.8286 (mmm) outliers start: 17 outliers final: 14 residues processed: 97 average time/residue: 0.9809 time to fit residues: 102.6444 Evaluate side-chains 100 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 440 TYR Chi-restraints excluded: chain B residue 470 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 12 optimal weight: 0.3980 chunk 23 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 0.4980 chunk 75 optimal weight: 0.5980 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 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 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 = 0.3751 r_free = 0.3751 target = 0.146324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.118347 restraints weight = 10031.854| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.15 r_work: 0.3301 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8306 Z= 0.183 Angle : 0.530 8.025 11306 Z= 0.276 Chirality : 0.041 0.172 1354 Planarity : 0.005 0.073 1398 Dihedral : 5.080 46.593 1232 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.35 % Favored : 96.47 % Rotamer: Outliers : 1.86 % Allowed : 17.95 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.26), residues: 1076 helix: 2.24 (0.20), residues: 646 sheet: -4.39 (0.76), residues: 20 loop : -0.06 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 482 HIS 0.002 0.000 HIS A 364 PHE 0.015 0.001 PHE B 166 TYR 0.015 0.001 TYR A 440 ARG 0.001 0.000 ARG A 36 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2792.67 seconds wall clock time: 49 minutes 46.34 seconds (2986.34 seconds total)