Starting phenix.real_space_refine on Tue May 7 13:34:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wo7_37681/05_2024/8wo7_37681.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wo7_37681/05_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_37681/05_2024/8wo7_37681.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wo7_37681/05_2024/8wo7_37681.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wo7_37681/05_2024/8wo7_37681.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wo7_37681/05_2024/8wo7_37681.pdb" } 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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: 4.89, per 1000 atoms: 0.60 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: 3.36 Conformation dependent library (CDL) restraints added in 1.5 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: 0.74 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: 2.29 Time building geometry restraints manager: 3.60 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 2.440 nonbonded pdb=" O VAL A 539 " pdb=" OH TYR B 309 " model vdw 2.131 2.440 nonbonded pdb=" OD1 ASP B 390 " pdb=" OH TYR B 440 " model vdw 2.155 2.440 nonbonded pdb=" OH TYR A 309 " pdb=" O VAL B 539 " model vdw 2.163 2.440 nonbonded pdb=" OE2 GLU A 49 " pdb=" OG1 THR A 455 " model vdw 2.210 2.440 ... (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 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: 0.010 Normalize map: mean=0, sd=1: 0.930 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: 3.410 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 25.490 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.700 ------------------------------------------------------------------------------- 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 : 0.941 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: 1.1153 time to fit residues: 164.4306 Evaluate side-chains 98 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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: 0.8980 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 B 350 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8306 Z= 0.203 Angle : 0.567 9.686 11306 Z= 0.293 Chirality : 0.041 0.176 1354 Planarity : 0.005 0.073 1398 Dihedral : 7.406 92.158 1232 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.86 % Allowed : 8.51 % Favored : 89.63 % 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: 1.94 (0.20), residues: 646 sheet: -4.42 (0.76), residues: 20 loop : -0.23 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 482 HIS 0.002 0.001 HIS B 364 PHE 0.019 0.001 PHE B 195 TYR 0.015 0.001 TYR B 418 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 130 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 0.933 Fit side-chains REVERT: A 23 ARG cc_start: 0.7354 (mtp-110) cc_final: 0.6443 (tmt170) REVERT: A 451 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7885 (mm-30) REVERT: B 23 ARG cc_start: 0.7780 (mtp85) cc_final: 0.6963 (tmt170) REVERT: B 543 TRP cc_start: 0.8469 (t-100) cc_final: 0.8225 (t-100) REVERT: B 548 GLU cc_start: 0.7786 (tp30) cc_final: 0.7483 (mm-30) outliers start: 16 outliers final: 6 residues processed: 121 average time/residue: 1.0888 time to fit residues: 141.2041 Evaluate side-chains 104 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 98 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 48 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 276 LEU 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: 2.9990 chunk 81 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 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 0.038 8306 Z= 0.229 Angle : 0.557 10.660 11306 Z= 0.284 Chirality : 0.041 0.212 1354 Planarity : 0.005 0.072 1398 Dihedral : 6.775 80.626 1232 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.86 % Allowed : 12.00 % Favored : 86.13 % 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: 642 sheet: -4.44 (0.76), residues: 20 loop : -0.13 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 482 HIS 0.002 0.001 HIS B 364 PHE 0.017 0.001 PHE B 166 TYR 0.009 0.001 TYR B 399 ARG 0.004 0.000 ARG A 103 *********************** 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 121 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 105 time to evaluate : 1.016 Fit side-chains REVERT: A 23 ARG cc_start: 0.7347 (mtp-110) cc_final: 0.6452 (tmt170) REVERT: B 23 ARG cc_start: 0.7670 (mtp85) cc_final: 0.6963 (tmt170) REVERT: B 319 MET cc_start: 0.8511 (mmt) cc_final: 0.8306 (mmm) REVERT: B 451 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7879 (mp0) outliers start: 16 outliers final: 4 residues processed: 114 average time/residue: 1.1683 time to fit residues: 142.0838 Evaluate side-chains 95 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 B residue 139 SER 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: 3.9990 chunk 73 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 104 optimal weight: 0.0970 chunk 51 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 163 ASN A 236 GLN A 350 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 8306 Z= 0.182 Angle : 0.542 11.308 11306 Z= 0.275 Chirality : 0.040 0.183 1354 Planarity : 0.005 0.074 1398 Dihedral : 6.191 66.554 1232 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.21 % Allowed : 13.29 % Favored : 84.50 % 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: 1.56 (0.26), residues: 1076 helix: 2.01 (0.20), residues: 658 sheet: -4.41 (0.77), residues: 20 loop : -0.30 (0.32), residues: 398 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 0.016 0.001 PHE B 166 TYR 0.008 0.001 TYR A 440 ARG 0.004 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 123 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 0.905 Fit side-chains REVERT: A 23 ARG cc_start: 0.7347 (mtp-110) cc_final: 0.6485 (tmt170) REVERT: A 321 TYR cc_start: 0.8260 (m-10) cc_final: 0.7497 (m-10) REVERT: B 23 ARG cc_start: 0.7601 (mtp85) cc_final: 0.6983 (tmt170) REVERT: B 319 MET cc_start: 0.8311 (mmt) cc_final: 0.7960 (mmm) outliers start: 19 outliers final: 8 residues processed: 115 average time/residue: 1.0245 time to fit residues: 126.8898 Evaluate side-chains 99 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 91 time to evaluate : 0.834 ------------------------------------------------------------------------------- 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 451 GLU Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain B residue 139 SER 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: 0.0040 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 77 optimal weight: 0.4980 chunk 43 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 overall best weight: 1.0796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8306 Z= 0.218 Angle : 0.557 10.643 11306 Z= 0.280 Chirality : 0.041 0.199 1354 Planarity : 0.005 0.074 1398 Dihedral : 5.456 44.570 1232 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.15 % Allowed : 14.34 % Favored : 82.52 % 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: 1.84 (0.26), residues: 1076 helix: 2.23 (0.20), residues: 642 sheet: -4.42 (0.76), residues: 20 loop : -0.04 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 482 HIS 0.002 0.001 HIS A 364 PHE 0.017 0.001 PHE B 166 TYR 0.011 0.001 TYR A 440 ARG 0.004 0.000 ARG B 103 *********************** 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 121 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 94 time to evaluate : 0.922 Fit side-chains REVERT: A 23 ARG cc_start: 0.7326 (mtp-110) cc_final: 0.6520 (tmt170) REVERT: B 23 ARG cc_start: 0.7569 (mtp85) cc_final: 0.6942 (tmt170) REVERT: B 319 MET cc_start: 0.8466 (mmt) cc_final: 0.8156 (mmm) outliers start: 27 outliers final: 14 residues processed: 110 average time/residue: 1.0223 time to fit residues: 121.1051 Evaluate side-chains 106 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 92 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 374 ILE 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: 0.7980 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 0.0970 chunk 25 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 86 optimal weight: 0.0670 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 20.0000 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 overall best weight: 0.7918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 ASN ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8306 Z= 0.187 Angle : 0.527 8.462 11306 Z= 0.269 Chirality : 0.040 0.169 1354 Planarity : 0.005 0.075 1398 Dihedral : 4.983 34.494 1232 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.91 % Allowed : 14.92 % Favored : 82.17 % 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: 1.76 (0.26), residues: 1076 helix: 2.16 (0.20), residues: 656 sheet: -4.42 (0.76), residues: 20 loop : -0.18 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 482 HIS 0.001 0.000 HIS A 364 PHE 0.015 0.001 PHE A 166 TYR 0.011 0.001 TYR A 440 ARG 0.003 0.000 ARG B 103 *********************** 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 121 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 96 time to evaluate : 0.867 Fit side-chains REVERT: A 23 ARG cc_start: 0.7306 (mtp-110) cc_final: 0.6511 (tmt170) REVERT: B 23 ARG cc_start: 0.7513 (mtp85) cc_final: 0.6896 (tmt170) REVERT: B 319 MET cc_start: 0.8453 (mmt) cc_final: 0.8125 (mmm) outliers start: 25 outliers final: 16 residues processed: 112 average time/residue: 1.1206 time to fit residues: 135.6878 Evaluate side-chains 113 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 97 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 451 GLU 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 59 THR Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 76 optimal weight: 0.0030 chunk 87 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 104 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 63 optimal weight: 0.3980 chunk 48 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8306 Z= 0.146 Angle : 0.498 8.784 11306 Z= 0.258 Chirality : 0.040 0.158 1354 Planarity : 0.005 0.077 1398 Dihedral : 4.673 33.997 1232 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.10 % Allowed : 16.55 % Favored : 81.35 % 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: 1.93 (0.26), residues: 1076 helix: 2.29 (0.20), residues: 658 sheet: -4.39 (0.76), residues: 20 loop : -0.10 (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 0.013 0.001 PHE B 166 TYR 0.011 0.001 TYR B 524 ARG 0.003 0.000 ARG B 103 *********************** 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 127 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 109 time to evaluate : 0.878 Fit side-chains REVERT: A 23 ARG cc_start: 0.7299 (mtp-110) cc_final: 0.6479 (tmt170) REVERT: A 293 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7880 (mt-10) REVERT: A 321 TYR cc_start: 0.8110 (m-10) cc_final: 0.7418 (m-10) REVERT: B 23 ARG cc_start: 0.7459 (mtp85) cc_final: 0.6799 (tmt170) REVERT: B 319 MET cc_start: 0.8391 (mmt) cc_final: 0.8190 (mmm) outliers start: 18 outliers final: 8 residues processed: 116 average time/residue: 1.0052 time to fit residues: 126.0136 Evaluate side-chains 102 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 470 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 81 optimal weight: 0.1980 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 0.1980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 8306 Z= 0.253 Angle : 0.553 8.615 11306 Z= 0.286 Chirality : 0.042 0.210 1354 Planarity : 0.005 0.075 1398 Dihedral : 4.730 35.768 1232 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.91 % Allowed : 16.43 % Favored : 80.65 % 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: 1.94 (0.26), residues: 1076 helix: 2.32 (0.20), residues: 644 sheet: -4.45 (0.78), residues: 20 loop : -0.04 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 482 HIS 0.002 0.000 HIS B 541 PHE 0.018 0.001 PHE B 166 TYR 0.013 0.001 TYR A 440 ARG 0.003 0.000 ARG B 103 *********************** 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 113 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 88 time to evaluate : 0.838 Fit side-chains REVERT: A 23 ARG cc_start: 0.7290 (mtp-110) cc_final: 0.6477 (tmt170) REVERT: A 356 ILE cc_start: 0.9039 (mm) cc_final: 0.8804 (mt) REVERT: B 23 ARG cc_start: 0.7521 (mtp85) cc_final: 0.6850 (tmt170) REVERT: B 319 MET cc_start: 0.8489 (mmt) cc_final: 0.8164 (mmm) REVERT: B 468 LEU cc_start: 0.8479 (mm) cc_final: 0.8208 (mt) outliers start: 25 outliers final: 12 residues processed: 101 average time/residue: 1.0685 time to fit residues: 116.1356 Evaluate side-chains 98 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 86 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 470 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8306 Z= 0.195 Angle : 0.527 8.438 11306 Z= 0.272 Chirality : 0.041 0.170 1354 Planarity : 0.005 0.076 1398 Dihedral : 4.669 34.450 1232 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.10 % Allowed : 17.83 % Favored : 80.07 % 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: 1.97 (0.26), residues: 1076 helix: 2.34 (0.20), residues: 644 sheet: -4.43 (0.77), residues: 20 loop : -0.03 (0.32), 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 541 PHE 0.017 0.001 PHE B 166 TYR 0.012 0.001 TYR A 440 ARG 0.003 0.000 ARG B 103 *********************** 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 108 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 90 time to evaluate : 0.967 Fit side-chains REVERT: A 23 ARG cc_start: 0.7298 (mtp-110) cc_final: 0.6477 (tmt170) REVERT: B 23 ARG cc_start: 0.7492 (mtp85) cc_final: 0.6831 (tmt170) REVERT: B 319 MET cc_start: 0.8462 (mmt) cc_final: 0.8150 (mmm) outliers start: 18 outliers final: 12 residues processed: 97 average time/residue: 1.0867 time to fit residues: 113.3476 Evaluate side-chains 101 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 89 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain B residue 501 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 85 optimal weight: 4.9990 chunk 8 optimal weight: 0.0770 chunk 66 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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: 0.8264 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8306 Z= 0.170 Angle : 0.522 8.299 11306 Z= 0.269 Chirality : 0.041 0.178 1354 Planarity : 0.005 0.075 1398 Dihedral : 4.570 34.409 1232 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.10 % Allowed : 17.72 % 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: 2.04 (0.26), residues: 1076 helix: 2.39 (0.20), residues: 646 sheet: -4.40 (0.78), residues: 20 loop : 0.01 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 482 HIS 0.001 0.000 HIS A 350 PHE 0.016 0.001 PHE B 166 TYR 0.012 0.001 TYR B 524 ARG 0.002 0.000 ARG B 103 ********************** 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 111 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 93 time to evaluate : 0.922 Fit side-chains REVERT: A 23 ARG cc_start: 0.7254 (mtp-110) cc_final: 0.6445 (tmt170) REVERT: A 286 MET cc_start: 0.8714 (tpt) cc_final: 0.8486 (tpt) REVERT: A 293 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7957 (mt-10) REVERT: B 23 ARG cc_start: 0.7451 (mtp85) cc_final: 0.6786 (tmt170) REVERT: B 286 MET cc_start: 0.8721 (tpt) cc_final: 0.8471 (tpt) REVERT: B 293 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7982 (mt-10) outliers start: 18 outliers final: 9 residues processed: 100 average time/residue: 1.0671 time to fit residues: 114.9700 Evaluate side-chains 97 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 88 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain B residue 59 THR 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: 0.7980 chunk 26 optimal weight: 0.1980 chunk 79 optimal weight: 20.0000 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.148340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.119681 restraints weight = 9885.278| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.17 r_work: 0.3322 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2219 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= 0.181 Angle : 0.523 8.248 11306 Z= 0.270 Chirality : 0.041 0.171 1354 Planarity : 0.005 0.075 1398 Dihedral : 4.524 34.407 1232 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.63 % Allowed : 18.65 % 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: 2.04 (0.26), residues: 1076 helix: 2.39 (0.20), residues: 646 sheet: -4.40 (0.77), residues: 20 loop : 0.02 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 482 HIS 0.001 0.000 HIS B 541 PHE 0.016 0.001 PHE B 166 TYR 0.012 0.001 TYR B 524 ARG 0.002 0.000 ARG B 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2868.84 seconds wall clock time: 52 minutes 22.00 seconds (3142.00 seconds total)