Starting phenix.real_space_refine on Sat May 24 10:13:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v3d_42946/05_2025/8v3d_42946_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v3d_42946/05_2025/8v3d_42946.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v3d_42946/05_2025/8v3d_42946.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v3d_42946/05_2025/8v3d_42946.map" model { file = "/net/cci-nas-00/data/ceres_data/8v3d_42946/05_2025/8v3d_42946_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v3d_42946/05_2025/8v3d_42946_trim.cif" } resolution = 2.95 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= 0.078 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: 5 Type Number sf(0) Gaussians S 100 5.16 5 C 8344 2.51 5 N 2018 2.21 5 O 2174 1.98 5 H 13001 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 25637 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 6366 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 383} Chain breaks: 2 Chain: "B" Number of atoms: 6366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 6366 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 383} Chain breaks: 2 Chain: "C" Number of atoms: 6366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 6366 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 383} Chain breaks: 2 Chain: "D" Number of atoms: 6531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 6531 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 9, 'TRANS': 386} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'A1AFC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.79, per 1000 atoms: 0.46 Number of scatterers: 25637 At special positions: 0 Unit cell: (115.649, 122.015, 128.381, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 100 16.00 O 2174 8.00 N 2018 7.00 C 8344 6.00 H 13001 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.71 Conformation dependent library (CDL) restraints added in 1.9 seconds 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3018 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 0 sheets defined 82.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 12 through 23 Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 34 through 63 removed outlier: 3.606A pdb=" N MET A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 93 removed outlier: 3.563A pdb=" N LEU A 70 " --> pdb=" O ASP A 66 " (cutoff:3.500A) Proline residue: A 83 - end of helix Proline residue: A 91 - end of helix Processing helix chain 'A' and resid 93 through 102 Processing helix chain 'A' and resid 103 through 106 removed outlier: 4.538A pdb=" N ASN A 106 " --> pdb=" O ILE A 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 106' Processing helix chain 'A' and resid 113 through 153 removed outlier: 4.165A pdb=" N PHE A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 242 removed outlier: 3.720A pdb=" N VAL A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) Proline residue: A 236 - end of helix removed outlier: 4.278A pdb=" N GLU A 239 " --> pdb=" O LYS A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 370 removed outlier: 5.312A pdb=" N VAL A 349 " --> pdb=" O ASP A 345 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ALA A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE A 360 " --> pdb=" O LEU A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 416 removed outlier: 4.541A pdb=" N MET A 411 " --> pdb=" O SER A 407 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 452 through 474 Processing helix chain 'B' and resid 12 through 23 Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 34 through 63 Processing helix chain 'B' and resid 67 through 93 Proline residue: B 83 - end of helix Proline residue: B 91 - end of helix Processing helix chain 'B' and resid 93 through 102 Processing helix chain 'B' and resid 103 through 106 removed outlier: 4.557A pdb=" N ASN B 106 " --> pdb=" O ILE B 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 106' Processing helix chain 'B' and resid 113 through 153 removed outlier: 3.704A pdb=" N PHE B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 242 removed outlier: 3.749A pdb=" N VAL B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) Proline residue: B 236 - end of helix removed outlier: 4.289A pdb=" N GLU B 239 " --> pdb=" O LYS B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 370 removed outlier: 5.301A pdb=" N VAL B 349 " --> pdb=" O ASP B 345 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ALA B 350 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE B 360 " --> pdb=" O LEU B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 416 removed outlier: 4.387A pdb=" N MET B 411 " --> pdb=" O SER B 407 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 422 Processing helix chain 'B' and resid 423 through 438 Processing helix chain 'B' and resid 452 through 474 Processing helix chain 'C' and resid 12 through 22 Processing helix chain 'C' and resid 31 through 63 removed outlier: 3.530A pdb=" N LYS C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE C 36 " --> pdb=" O GLU C 32 " (cutoff:3.500A) Proline residue: C 37 - end of helix removed outlier: 3.704A pdb=" N ILE C 40 " --> pdb=" O PHE C 36 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN C 59 " --> pdb=" O MET C 55 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 93 Proline residue: C 83 - end of helix Proline residue: C 91 - end of helix Processing helix chain 'C' and resid 93 through 102 Processing helix chain 'C' and resid 103 through 106 removed outlier: 4.559A pdb=" N ASN C 106 " --> pdb=" O ILE C 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 106' Processing helix chain 'C' and resid 113 through 153 Processing helix chain 'C' and resid 187 through 242 Proline residue: C 236 - end of helix removed outlier: 4.156A pdb=" N GLU C 239 " --> pdb=" O LYS C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 370 removed outlier: 4.004A pdb=" N ILE C 360 " --> pdb=" O LEU C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 416 Processing helix chain 'C' and resid 418 through 422 Processing helix chain 'C' and resid 423 through 438 Processing helix chain 'C' and resid 452 through 474 Processing helix chain 'D' and resid 6 through 16 Processing helix chain 'D' and resid 30 through 48 Proline residue: D 44 - end of helix Processing helix chain 'D' and resid 48 through 59 Processing helix chain 'D' and resid 62 through 89 Proline residue: D 72 - end of helix removed outlier: 4.336A pdb=" N GLU D 75 " --> pdb=" O VAL D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 109 removed outlier: 3.564A pdb=" N LYS D 109 " --> pdb=" O ASP D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 146 Processing helix chain 'D' and resid 146 through 160 Processing helix chain 'D' and resid 181 through 238 Processing helix chain 'D' and resid 240 through 294 removed outlier: 5.580A pdb=" N PHE D 271 " --> pdb=" O ASP D 267 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N PHE D 272 " --> pdb=" O GLY D 268 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE D 282 " --> pdb=" O LEU D 278 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N CYS D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 338 Proline residue: D 309 - end of helix removed outlier: 3.728A pdb=" N PHE D 318 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL D 332 " --> pdb=" O GLU D 328 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N SER D 333 " --> pdb=" O ALA D 329 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ASP D 334 " --> pdb=" O ARG D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 344 Processing helix chain 'D' and resid 345 through 360 Processing helix chain 'D' and resid 374 through 397 removed outlier: 4.161A pdb=" N PHE D 378 " --> pdb=" O THR D 374 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN D 379 " --> pdb=" O LEU D 375 " (cutoff:3.500A) 1033 hydrogen bonds defined for protein. 3081 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: 8.69 Time building geometry restraints manager: 8.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12971 1.03 - 1.23: 32 1.23 - 1.42: 5391 1.42 - 1.62: 7372 1.62 - 1.81: 169 Bond restraints: 25935 Sorted by residual: bond pdb=" C03 A1AFC D 501 " pdb=" S04 A1AFC D 501 " ideal model delta sigma weight residual 1.730 1.597 0.133 2.00e-02 2.50e+03 4.42e+01 bond pdb=" C05 A1AFC D 501 " pdb=" S04 A1AFC D 501 " ideal model delta sigma weight residual 1.730 1.620 0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C05 A1AFC D 501 " pdb=" N06 A1AFC D 501 " ideal model delta sigma weight residual 1.290 1.391 -0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" C02 A1AFC D 501 " pdb=" N06 A1AFC D 501 " ideal model delta sigma weight residual 1.375 1.472 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" C02 A1AFC D 501 " pdb=" C03 A1AFC D 501 " ideal model delta sigma weight residual 1.362 1.420 -0.058 2.00e-02 2.50e+03 8.30e+00 ... (remaining 25930 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 46591 1.85 - 3.70: 268 3.70 - 5.55: 40 5.55 - 7.41: 5 7.41 - 9.26: 1 Bond angle restraints: 46905 Sorted by residual: angle pdb=" C ALA C 346 " pdb=" N TYR C 347 " pdb=" CA TYR C 347 " ideal model delta sigma weight residual 122.31 115.72 6.59 2.00e+00 2.50e-01 1.09e+01 angle pdb=" C03 A1AFC D 501 " pdb=" S04 A1AFC D 501 " pdb=" C05 A1AFC D 501 " ideal model delta sigma weight residual 90.02 99.28 -9.26 3.00e+00 1.11e-01 9.52e+00 angle pdb=" C GLY B 7 " pdb=" N LEU B 8 " pdb=" CA LEU B 8 " ideal model delta sigma weight residual 121.54 127.43 -5.89 1.91e+00 2.74e-01 9.51e+00 angle pdb=" CA ILE C 40 " pdb=" CB ILE C 40 " pdb=" CG1 ILE C 40 " ideal model delta sigma weight residual 110.40 115.37 -4.97 1.70e+00 3.46e-01 8.56e+00 angle pdb=" C GLY C 348 " pdb=" N VAL C 349 " pdb=" CA VAL C 349 " ideal model delta sigma weight residual 120.46 117.30 3.16 1.37e+00 5.33e-01 5.32e+00 ... (remaining 46900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 10729 17.70 - 35.41: 996 35.41 - 53.11: 352 53.11 - 70.82: 104 70.82 - 88.52: 11 Dihedral angle restraints: 12192 sinusoidal: 6431 harmonic: 5761 Sorted by residual: dihedral pdb=" CA ASP A 421 " pdb=" CB ASP A 421 " pdb=" CG ASP A 421 " pdb=" OD1 ASP A 421 " ideal model delta sinusoidal sigma weight residual -30.00 -88.27 58.27 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CB GLU B 115 " pdb=" CG GLU B 115 " pdb=" CD GLU B 115 " pdb=" OE1 GLU B 115 " ideal model delta sinusoidal sigma weight residual 0.00 -88.52 88.52 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU B 63 " pdb=" CG GLU B 63 " pdb=" CD GLU B 63 " pdb=" OE1 GLU B 63 " ideal model delta sinusoidal sigma weight residual 0.00 88.37 -88.37 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 12189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1524 0.032 - 0.063: 341 0.063 - 0.095: 167 0.095 - 0.127: 38 0.127 - 0.159: 6 Chirality restraints: 2076 Sorted by residual: chirality pdb=" CA TYR C 347 " pdb=" N TYR C 347 " pdb=" C TYR C 347 " pdb=" CB TYR C 347 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.28e-01 chirality pdb=" CA ILE A 170 " pdb=" N ILE A 170 " pdb=" C ILE A 170 " pdb=" CB ILE A 170 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CB ILE B 398 " pdb=" CA ILE B 398 " pdb=" CG1 ILE B 398 " pdb=" CG2 ILE B 398 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.14 2.00e-01 2.50e+01 5.25e-01 ... (remaining 2073 not shown) Planarity restraints: 3642 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR C 347 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.94e+00 pdb=" C TYR C 347 " 0.034 2.00e-02 2.50e+03 pdb=" O TYR C 347 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY C 348 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 235 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.74e+00 pdb=" N PRO A 236 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 236 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 236 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 170 " 0.031 5.00e-02 4.00e+02 4.79e-02 3.67e+00 pdb=" N PRO B 171 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 171 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 171 " 0.026 5.00e-02 4.00e+02 ... (remaining 3639 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.06: 230 2.06 - 2.69: 40428 2.69 - 3.33: 77941 3.33 - 3.96: 96598 3.96 - 4.60: 153655 Nonbonded interactions: 368852 Sorted by model distance: nonbonded pdb=" OE1 GLU C 424 " pdb=" H GLU C 424 " model vdw 1.424 2.450 nonbonded pdb=" O ASN B 28 " pdb="HD21 ASN B 28 " model vdw 1.528 2.450 nonbonded pdb="HE21 GLN C 435 " pdb=" OE1 GLN D 360 " model vdw 1.579 2.450 nonbonded pdb=" HZ2 LYS C 86 " pdb=" OD1 ASP C 213 " model vdw 1.599 2.450 nonbonded pdb=" O TYR D 18 " pdb="HH22 ARG D 90 " model vdw 1.606 2.450 ... (remaining 368847 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' selection = chain 'C' } 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: 0.920 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: 0.420 Extract box with map and model: 0.910 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 51.960 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.133 12934 Z= 0.170 Angle : 0.506 9.257 17544 Z= 0.272 Chirality : 0.035 0.159 2076 Planarity : 0.004 0.048 2113 Dihedral : 17.455 88.525 4581 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.59 % Allowed : 26.91 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.21), residues: 1558 helix: 2.19 (0.14), residues: 1259 sheet: -0.27 (1.06), residues: 24 loop : -1.81 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 419 HIS 0.003 0.001 HIS B 24 PHE 0.013 0.001 PHE A 399 TYR 0.017 0.001 TYR C 347 ARG 0.001 0.000 ARG B 178 Details of bonding type rmsd hydrogen bonds : bond 0.11703 ( 1033) hydrogen bonds : angle 5.17006 ( 3081) covalent geometry : bond 0.00329 (12934) covalent geometry : angle 0.50599 (17544) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 201 time to evaluate : 1.905 Fit side-chains revert: symmetry clash REVERT: A 66 ASP cc_start: 0.7362 (OUTLIER) cc_final: 0.6974 (m-30) REVERT: B 51 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7904 (tt) REVERT: D 171 TYR cc_start: 0.7434 (OUTLIER) cc_final: 0.5622 (p90) outliers start: 36 outliers final: 29 residues processed: 229 average time/residue: 2.0377 time to fit residues: 522.1039 Evaluate side-chains 226 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 HIS Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain C residue 5 HIS Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 270 SER Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 336 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 141 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3823 r_free = 0.3823 target = 0.152462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.130064 restraints weight = 39976.716| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.30 r_work: 0.3445 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.0464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12934 Z= 0.154 Angle : 0.504 6.994 17544 Z= 0.276 Chirality : 0.036 0.173 2076 Planarity : 0.004 0.048 2113 Dihedral : 6.558 58.485 1750 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.31 % Allowed : 25.11 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.21), residues: 1558 helix: 2.63 (0.14), residues: 1264 sheet: -0.14 (1.10), residues: 24 loop : -1.79 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 104 HIS 0.003 0.001 HIS A 229 PHE 0.015 0.001 PHE A 399 TYR 0.018 0.001 TYR C 347 ARG 0.002 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.06607 ( 1033) hydrogen bonds : angle 3.98135 ( 3081) covalent geometry : bond 0.00315 (12934) covalent geometry : angle 0.50395 (17544) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 204 time to evaluate : 1.770 Fit side-chains revert: symmetry clash REVERT: B 51 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7835 (tt) REVERT: B 86 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7807 (mttm) REVERT: B 234 MET cc_start: 0.7449 (OUTLIER) cc_final: 0.7124 (ttt) REVERT: D 171 TYR cc_start: 0.7449 (OUTLIER) cc_final: 0.5643 (p90) outliers start: 46 outliers final: 20 residues processed: 243 average time/residue: 2.1863 time to fit residues: 596.8297 Evaluate side-chains 218 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 194 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 336 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 12 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.147480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.125295 restraints weight = 41364.727| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.21 r_work: 0.3378 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 12934 Z= 0.245 Angle : 0.581 8.126 17544 Z= 0.318 Chirality : 0.039 0.202 2076 Planarity : 0.004 0.054 2113 Dihedral : 5.834 59.970 1726 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.46 % Allowed : 23.60 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.21), residues: 1558 helix: 2.35 (0.14), residues: 1264 sheet: -0.08 (1.13), residues: 24 loop : -1.82 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP C 104 HIS 0.006 0.001 HIS C 229 PHE 0.020 0.002 PHE C 399 TYR 0.025 0.002 TYR C 347 ARG 0.003 0.000 ARG B 17 Details of bonding type rmsd hydrogen bonds : bond 0.07632 ( 1033) hydrogen bonds : angle 4.04688 ( 3081) covalent geometry : bond 0.00577 (12934) covalent geometry : angle 0.58063 (17544) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 203 time to evaluate : 1.829 Fit side-chains revert: symmetry clash REVERT: A 66 ASP cc_start: 0.7406 (OUTLIER) cc_final: 0.6970 (m-30) REVERT: A 438 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.7183 (mp10) REVERT: B 51 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7881 (tt) REVERT: B 86 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7892 (mttm) REVERT: B 178 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7624 (mmt90) REVERT: D 80 ASN cc_start: 0.8496 (OUTLIER) cc_final: 0.8046 (m-40) REVERT: D 171 TYR cc_start: 0.7656 (OUTLIER) cc_final: 0.5117 (p90) outliers start: 62 outliers final: 35 residues processed: 249 average time/residue: 2.0798 time to fit residues: 579.5643 Evaluate side-chains 237 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 195 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 30 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain C residue 30 TYR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 270 SER Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 336 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 118 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.148598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.126298 restraints weight = 41630.116| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.23 r_work: 0.3393 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12934 Z= 0.201 Angle : 0.540 7.849 17544 Z= 0.296 Chirality : 0.037 0.184 2076 Planarity : 0.004 0.053 2113 Dihedral : 5.886 60.698 1726 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.10 % Allowed : 24.10 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.21), residues: 1558 helix: 2.38 (0.14), residues: 1263 sheet: -0.03 (1.15), residues: 24 loop : -1.81 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 419 HIS 0.004 0.001 HIS A 229 PHE 0.016 0.002 PHE D 137 TYR 0.020 0.001 TYR C 347 ARG 0.002 0.000 ARG C 338 Details of bonding type rmsd hydrogen bonds : bond 0.07197 ( 1033) hydrogen bonds : angle 3.96583 ( 3081) covalent geometry : bond 0.00454 (12934) covalent geometry : angle 0.54046 (17544) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 200 time to evaluate : 1.799 Fit side-chains REVERT: A 66 ASP cc_start: 0.7356 (OUTLIER) cc_final: 0.6924 (m-30) REVERT: A 438 GLN cc_start: 0.9040 (OUTLIER) cc_final: 0.7096 (mp10) REVERT: A 439 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7777 (mttp) REVERT: B 51 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7886 (tt) REVERT: B 86 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7826 (mttm) REVERT: B 158 ARG cc_start: 0.7859 (mmt90) cc_final: 0.7562 (mmt90) REVERT: B 178 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7628 (mmt90) REVERT: C 19 MET cc_start: 0.8410 (mtp) cc_final: 0.8207 (mtp) REVERT: D 80 ASN cc_start: 0.8486 (OUTLIER) cc_final: 0.8059 (m-40) outliers start: 57 outliers final: 34 residues processed: 244 average time/residue: 2.0862 time to fit residues: 569.4804 Evaluate side-chains 239 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 198 time to evaluate : 1.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 30 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain C residue 5 HIS Chi-restraints excluded: chain C residue 30 TYR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 336 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3764 r_free = 0.3764 target = 0.148243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.126028 restraints weight = 41416.266| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.22 r_work: 0.3373 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12934 Z= 0.204 Angle : 0.544 7.719 17544 Z= 0.298 Chirality : 0.038 0.189 2076 Planarity : 0.004 0.054 2113 Dihedral : 5.931 61.514 1726 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.46 % Allowed : 23.81 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.21), residues: 1558 helix: 2.35 (0.14), residues: 1263 sheet: -0.09 (1.16), residues: 24 loop : -1.81 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 104 HIS 0.004 0.001 HIS A 229 PHE 0.017 0.002 PHE C 399 TYR 0.021 0.001 TYR C 347 ARG 0.002 0.000 ARG A 178 Details of bonding type rmsd hydrogen bonds : bond 0.07231 ( 1033) hydrogen bonds : angle 3.96840 ( 3081) covalent geometry : bond 0.00463 (12934) covalent geometry : angle 0.54397 (17544) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 203 time to evaluate : 2.124 Fit side-chains REVERT: A 438 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.7086 (mp10) REVERT: A 439 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7724 (mttp) REVERT: B 51 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7888 (tt) REVERT: B 86 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7843 (mttm) REVERT: B 158 ARG cc_start: 0.7879 (mmt90) cc_final: 0.7573 (mmt90) REVERT: B 178 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7634 (mmt90) REVERT: D 80 ASN cc_start: 0.8489 (OUTLIER) cc_final: 0.8059 (m-40) outliers start: 62 outliers final: 39 residues processed: 254 average time/residue: 2.0897 time to fit residues: 592.0847 Evaluate side-chains 238 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 193 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 30 TYR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain C residue 5 HIS Chi-restraints excluded: chain C residue 30 TYR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 336 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 107 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.3766 r_free = 0.3766 target = 0.148463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.126304 restraints weight = 41323.218| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.21 r_work: 0.3392 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12934 Z= 0.192 Angle : 0.541 7.629 17544 Z= 0.296 Chirality : 0.037 0.186 2076 Planarity : 0.004 0.053 2113 Dihedral : 5.945 62.219 1726 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.96 % Allowed : 23.96 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.21), residues: 1558 helix: 2.39 (0.14), residues: 1263 sheet: -0.11 (1.16), residues: 24 loop : -1.79 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 419 HIS 0.003 0.001 HIS A 229 PHE 0.017 0.002 PHE B 36 TYR 0.020 0.001 TYR C 347 ARG 0.001 0.000 ARG C 129 Details of bonding type rmsd hydrogen bonds : bond 0.07098 ( 1033) hydrogen bonds : angle 3.93029 ( 3081) covalent geometry : bond 0.00431 (12934) covalent geometry : angle 0.54060 (17544) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 196 time to evaluate : 1.900 Fit side-chains REVERT: A 66 ASP cc_start: 0.7346 (OUTLIER) cc_final: 0.6896 (m-30) REVERT: A 438 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.7114 (mp10) REVERT: A 439 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7732 (mttp) REVERT: B 51 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7883 (tt) REVERT: B 158 ARG cc_start: 0.7843 (mmt90) cc_final: 0.7546 (mmt90) REVERT: B 178 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7629 (mmt90) REVERT: C 176 MET cc_start: 0.8317 (mtp) cc_final: 0.8071 (mtp) REVERT: D 80 ASN cc_start: 0.8526 (OUTLIER) cc_final: 0.8098 (m-40) outliers start: 55 outliers final: 39 residues processed: 243 average time/residue: 2.0202 time to fit residues: 552.4837 Evaluate side-chains 237 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 192 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 30 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain C residue 5 HIS Chi-restraints excluded: chain C residue 30 TYR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 270 SER Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 336 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 129 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 61 optimal weight: 0.4980 chunk 41 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.148442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.126239 restraints weight = 41537.464| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.22 r_work: 0.3390 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12934 Z= 0.198 Angle : 0.547 7.650 17544 Z= 0.298 Chirality : 0.037 0.188 2076 Planarity : 0.004 0.053 2113 Dihedral : 5.981 62.796 1726 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.46 % Allowed : 23.67 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.21), residues: 1558 helix: 2.37 (0.14), residues: 1263 sheet: -0.07 (1.17), residues: 24 loop : -1.79 (0.38), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 341 HIS 0.004 0.001 HIS A 229 PHE 0.016 0.002 PHE C 399 TYR 0.021 0.001 TYR C 347 ARG 0.002 0.000 ARG D 90 Details of bonding type rmsd hydrogen bonds : bond 0.07133 ( 1033) hydrogen bonds : angle 3.94253 ( 3081) covalent geometry : bond 0.00448 (12934) covalent geometry : angle 0.54688 (17544) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 200 time to evaluate : 2.237 Fit side-chains REVERT: A 66 ASP cc_start: 0.7409 (OUTLIER) cc_final: 0.6984 (m-30) REVERT: A 402 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7718 (ttt180) REVERT: A 438 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.7086 (mp10) REVERT: A 439 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7770 (mttp) REVERT: B 51 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7888 (tt) REVERT: B 158 ARG cc_start: 0.7848 (mmt90) cc_final: 0.7546 (mmt90) REVERT: B 178 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7629 (mmt90) REVERT: C 119 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7516 (ttt90) REVERT: C 176 MET cc_start: 0.8293 (mtp) cc_final: 0.8064 (mtp) REVERT: D 80 ASN cc_start: 0.8490 (OUTLIER) cc_final: 0.8066 (m-40) outliers start: 62 outliers final: 44 residues processed: 251 average time/residue: 2.0829 time to fit residues: 583.3002 Evaluate side-chains 247 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 195 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 30 TYR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain C residue 5 HIS Chi-restraints excluded: chain C residue 30 TYR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 270 SER Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 336 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 111 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.3766 r_free = 0.3766 target = 0.148298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.126150 restraints weight = 41281.426| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.21 r_work: 0.3388 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12934 Z= 0.204 Angle : 0.556 7.742 17544 Z= 0.303 Chirality : 0.038 0.189 2076 Planarity : 0.004 0.053 2113 Dihedral : 6.024 63.370 1726 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.46 % Allowed : 23.60 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.21), residues: 1558 helix: 2.32 (0.14), residues: 1263 sheet: 0.00 (1.19), residues: 24 loop : -1.77 (0.38), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 104 HIS 0.004 0.001 HIS A 229 PHE 0.020 0.002 PHE D 185 TYR 0.022 0.002 TYR C 347 ARG 0.002 0.000 ARG D 90 Details of bonding type rmsd hydrogen bonds : bond 0.07196 ( 1033) hydrogen bonds : angle 3.95296 ( 3081) covalent geometry : bond 0.00464 (12934) covalent geometry : angle 0.55650 (17544) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 195 time to evaluate : 1.995 Fit side-chains REVERT: A 66 ASP cc_start: 0.7451 (OUTLIER) cc_final: 0.7020 (m-30) REVERT: A 402 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7752 (ttt180) REVERT: A 438 GLN cc_start: 0.9040 (OUTLIER) cc_final: 0.7081 (mp10) REVERT: A 439 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7720 (mttp) REVERT: B 51 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7894 (tt) REVERT: B 158 ARG cc_start: 0.7884 (mmt90) cc_final: 0.7572 (mmt90) REVERT: B 176 MET cc_start: 0.8152 (mtp) cc_final: 0.7950 (mtp) REVERT: B 178 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7626 (mmt90) REVERT: C 119 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7500 (ttt90) REVERT: C 150 THR cc_start: 0.8055 (OUTLIER) cc_final: 0.7838 (p) REVERT: D 80 ASN cc_start: 0.8496 (OUTLIER) cc_final: 0.8067 (m-40) outliers start: 62 outliers final: 44 residues processed: 247 average time/residue: 2.1137 time to fit residues: 582.8982 Evaluate side-chains 245 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 192 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 30 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain C residue 5 HIS Chi-restraints excluded: chain C residue 30 TYR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 270 SER Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 336 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 65 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 88 optimal weight: 0.2980 chunk 87 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.3785 r_free = 0.3785 target = 0.150016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.127908 restraints weight = 41342.331| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.22 r_work: 0.3415 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12934 Z= 0.160 Angle : 0.525 7.252 17544 Z= 0.284 Chirality : 0.036 0.175 2076 Planarity : 0.004 0.051 2113 Dihedral : 5.954 63.404 1726 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.38 % Allowed : 25.18 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.21), residues: 1558 helix: 2.48 (0.14), residues: 1269 sheet: -0.03 (1.18), residues: 24 loop : -1.72 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 419 HIS 0.003 0.001 HIS C 24 PHE 0.017 0.002 PHE D 185 TYR 0.019 0.001 TYR C 347 ARG 0.001 0.000 ARG C 129 Details of bonding type rmsd hydrogen bonds : bond 0.06690 ( 1033) hydrogen bonds : angle 3.87231 ( 3081) covalent geometry : bond 0.00337 (12934) covalent geometry : angle 0.52487 (17544) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 195 time to evaluate : 1.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.7427 (OUTLIER) cc_final: 0.6988 (m-30) REVERT: A 402 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7674 (ttt180) REVERT: A 438 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.7048 (mp10) REVERT: A 439 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7730 (mttp) REVERT: B 51 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7829 (tt) REVERT: B 158 ARG cc_start: 0.7892 (mmt90) cc_final: 0.7589 (mmt90) REVERT: B 176 MET cc_start: 0.8109 (mtp) cc_final: 0.7894 (mtp) REVERT: B 178 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7598 (mmt90) REVERT: D 80 ASN cc_start: 0.8498 (OUTLIER) cc_final: 0.8073 (m-40) REVERT: D 171 TYR cc_start: 0.7568 (OUTLIER) cc_final: 0.4913 (p90) outliers start: 47 outliers final: 35 residues processed: 233 average time/residue: 2.0532 time to fit residues: 534.8464 Evaluate side-chains 235 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 192 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain C residue 5 HIS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 270 SER Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 336 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 89 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.3775 r_free = 0.3775 target = 0.149253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.127124 restraints weight = 41275.533| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.22 r_work: 0.3404 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12934 Z= 0.180 Angle : 0.542 7.375 17544 Z= 0.294 Chirality : 0.037 0.185 2076 Planarity : 0.004 0.052 2113 Dihedral : 5.961 63.602 1726 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.38 % Allowed : 25.11 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.21), residues: 1558 helix: 2.44 (0.14), residues: 1272 sheet: 0.01 (1.18), residues: 24 loop : -1.76 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 419 HIS 0.004 0.001 HIS C 24 PHE 0.018 0.002 PHE D 185 TYR 0.021 0.001 TYR C 347 ARG 0.002 0.000 ARG D 90 Details of bonding type rmsd hydrogen bonds : bond 0.06862 ( 1033) hydrogen bonds : angle 3.89736 ( 3081) covalent geometry : bond 0.00397 (12934) covalent geometry : angle 0.54185 (17544) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 189 time to evaluate : 1.835 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.7436 (OUTLIER) cc_final: 0.7000 (m-30) REVERT: A 402 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7708 (ttt180) REVERT: A 438 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.7057 (mp10) REVERT: A 439 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7720 (mttp) REVERT: B 51 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7833 (tt) REVERT: B 158 ARG cc_start: 0.7890 (mmt90) cc_final: 0.7588 (mmt90) REVERT: B 176 MET cc_start: 0.8112 (mtp) cc_final: 0.7897 (mtp) REVERT: B 178 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7614 (mmt90) REVERT: C 176 MET cc_start: 0.8299 (mtp) cc_final: 0.8098 (mtp) REVERT: D 80 ASN cc_start: 0.8515 (OUTLIER) cc_final: 0.8082 (m-40) REVERT: D 171 TYR cc_start: 0.7589 (OUTLIER) cc_final: 0.4938 (p90) outliers start: 47 outliers final: 36 residues processed: 226 average time/residue: 2.0479 time to fit residues: 517.3116 Evaluate side-chains 233 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 189 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain C residue 5 HIS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 270 SER Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 336 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 6 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 153 optimal weight: 0.5980 chunk 147 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3794 r_free = 0.3794 target = 0.150959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.128869 restraints weight = 41232.529| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.22 r_work: 0.3425 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12934 Z= 0.144 Angle : 0.512 7.210 17544 Z= 0.276 Chirality : 0.036 0.168 2076 Planarity : 0.004 0.050 2113 Dihedral : 5.863 62.948 1726 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.81 % Allowed : 25.68 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.21), residues: 1558 helix: 2.61 (0.14), residues: 1263 sheet: -0.06 (1.15), residues: 24 loop : -1.72 (0.38), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 419 HIS 0.004 0.001 HIS C 24 PHE 0.020 0.001 PHE D 185 TYR 0.017 0.001 TYR C 347 ARG 0.001 0.000 ARG C 129 Details of bonding type rmsd hydrogen bonds : bond 0.06392 ( 1033) hydrogen bonds : angle 3.81879 ( 3081) covalent geometry : bond 0.00293 (12934) covalent geometry : angle 0.51210 (17544) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 15282.57 seconds wall clock time: 261 minutes 29.16 seconds (15689.16 seconds total)