Starting phenix.real_space_refine on Sat Jul 26 12:55:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k6j_36920/07_2025/8k6j_36920.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k6j_36920/07_2025/8k6j_36920.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k6j_36920/07_2025/8k6j_36920.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k6j_36920/07_2025/8k6j_36920.map" model { file = "/net/cci-nas-00/data/ceres_data/8k6j_36920/07_2025/8k6j_36920.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k6j_36920/07_2025/8k6j_36920.cif" } resolution = 2.77 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= 0.001 sd= 0.014 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: 6 Type Number sf(0) Gaussians Fe 6 7.16 5 P 2 5.49 5 S 46 5.16 5 C 5408 2.51 5 N 1482 2.21 5 O 1636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 8580 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4154 Classifications: {'peptide': 539} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 502} Chain: "B" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1069 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain: "C" Number of atoms: 3130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3130 Classifications: {'peptide': 413} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 388} Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'F3S': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 167 Unusual residues: {'HEC': 3, 'U10': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 20 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1690 SG CYS A 216 51.847 62.208 31.752 1.00139.41 S ATOM 1759 SG CYS A 226 52.396 63.171 35.919 1.00104.53 S ATOM 1730 SG CYS A 222 53.627 67.396 32.557 1.00124.35 S ATOM 1690 SG CYS A 216 51.847 62.208 31.752 1.00139.41 S Time building chain proxies: 5.87, per 1000 atoms: 0.68 Number of scatterers: 8580 At special positions: 0 Unit cell: (103.2, 105.78, 78.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 6 26.01 S 46 16.00 P 2 15.00 O 1636 8.00 N 1482 7.00 C 5408 6.00 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.73 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S A 602 " pdb="FE1 F3S A 602 " - pdb=" SG CYS A 216 " pdb="FE3 F3S A 602 " - pdb=" SG CYS A 222 " pdb="FE1 F3S A 602 " - pdb=" SG CYS A 226 " Number of angles added : 9 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2008 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 9 sheets defined 42.9% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 16 through 28 Processing helix chain 'A' and resid 43 through 53 Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 92 through 97 removed outlier: 3.756A pdb=" N LYS A 97 " --> pdb=" O THR A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 110 removed outlier: 3.849A pdb=" N THR A 108 " --> pdb=" O GLY A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'A' and resid 124 through 130 Processing helix chain 'A' and resid 138 through 154 removed outlier: 3.563A pdb=" N LEU A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 181 through 195 Processing helix chain 'A' and resid 233 through 244 removed outlier: 4.056A pdb=" N ALA A 237 " --> pdb=" O ASN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 301 Processing helix chain 'A' and resid 355 through 360 Processing helix chain 'A' and resid 373 through 384 Processing helix chain 'A' and resid 388 through 401 Processing helix chain 'A' and resid 440 through 462 removed outlier: 4.315A pdb=" N VAL A 444 " --> pdb=" O VAL A 440 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE A 450 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLN A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 removed outlier: 3.724A pdb=" N SER A 492 " --> pdb=" O PRO A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 514 removed outlier: 3.668A pdb=" N THR A 513 " --> pdb=" O THR A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 542 Processing helix chain 'B' and resid 50 through 63 Processing helix chain 'B' and resid 68 through 83 Processing helix chain 'B' and resid 85 through 101 Processing helix chain 'B' and resid 104 through 111 Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 150 through 154 Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'C' and resid 41 through 51 Processing helix chain 'C' and resid 51 through 56 removed outlier: 3.996A pdb=" N CYS C 55 " --> pdb=" O ASP C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 105 Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 127 through 141 Processing helix chain 'C' and resid 163 through 172 Processing helix chain 'C' and resid 185 through 197 Processing helix chain 'C' and resid 201 through 206 Processing helix chain 'C' and resid 215 through 219 removed outlier: 3.688A pdb=" N TYR C 219 " --> pdb=" O GLN C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 256 Processing helix chain 'C' and resid 265 through 274 Processing helix chain 'C' and resid 275 through 278 Processing helix chain 'C' and resid 279 through 292 removed outlier: 3.589A pdb=" N SER C 292 " --> pdb=" O THR C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 324 removed outlier: 3.840A pdb=" N SER C 322 " --> pdb=" O ASN C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 373 through 383 Processing helix chain 'C' and resid 408 through 423 Processing helix chain 'C' and resid 431 through 441 Processing helix chain 'C' and resid 445 through 450 removed outlier: 3.794A pdb=" N LEU C 450 " --> pdb=" O PRO C 446 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 247 through 249 removed outlier: 6.823A pdb=" N LEU A 34 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL A 10 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N LEU A 36 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE A 12 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N SER A 7 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ALA A 282 " --> pdb=" O SER A 7 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ASP A 9 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA A 282 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N THR A 266 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 267 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N TYR A 271 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N VAL A 254 " --> pdb=" O TYR A 271 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 247 through 249 removed outlier: 6.823A pdb=" N LEU A 34 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL A 10 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N LEU A 36 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE A 12 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N SER A 7 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ALA A 282 " --> pdb=" O SER A 7 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ASP A 9 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89 removed outlier: 4.718A pdb=" N HIS A 433 " --> pdb=" O SER A 422 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 198 through 200 removed outlier: 5.308A pdb=" N SER A 347 " --> pdb=" O TYR A 368 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N TYR A 368 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A 366 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASP A 404 " --> pdb=" O ASN A 369 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N GLN A 332 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLU A 466 " --> pdb=" O GLN A 332 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 319 through 322 removed outlier: 6.199A pdb=" N ASN A 320 " --> pdb=" O GLY A 482 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY A 482 " --> pdb=" O ASN A 320 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 70 through 73 Processing sheet with id=AA7, first strand: chain 'C' and resid 223 through 224 Processing sheet with id=AA8, first strand: chain 'C' and resid 257 through 258 Processing sheet with id=AA9, first strand: chain 'C' and resid 385 through 388 removed outlier: 3.659A pdb=" N ARG C 386 " --> pdb=" O ILE C 393 " (cutoff:3.500A) 334 hydrogen bonds defined for protein. 909 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.59 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.78: 8724 1.78 - 2.33: 86 2.33 - 2.89: 0 2.89 - 3.44: 0 3.44 - 4.00: 3 Bond restraints: 8813 Sorted by residual: bond pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " ideal model delta sigma weight residual 2.300 3.999 -1.699 2.00e-02 2.50e+03 7.22e+03 bond pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " ideal model delta sigma weight residual 2.258 3.895 -1.637 2.00e-02 2.50e+03 6.70e+03 bond pdb=" S4 F3S A 602 " pdb="FE1 F3S A 602 " ideal model delta sigma weight residual 2.233 3.498 -1.265 2.00e-02 2.50e+03 4.00e+03 bond pdb=" C2D HEC C 502 " pdb=" C3D HEC C 502 " ideal model delta sigma weight residual 1.544 1.327 0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C2D HEC C 503 " pdb=" C3D HEC C 503 " ideal model delta sigma weight residual 1.544 1.331 0.213 2.00e-02 2.50e+03 1.14e+02 ... (remaining 8808 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.31: 12037 10.31 - 20.63: 2 20.63 - 30.94: 3 30.94 - 41.26: 5 41.26 - 51.57: 2 Bond angle restraints: 12049 Sorted by residual: angle pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " pdb=" S3 F3S A 602 " ideal model delta sigma weight residual 114.75 63.18 51.57 3.00e+00 1.11e-01 2.96e+02 angle pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " pdb=" S4 F3S A 602 " ideal model delta sigma weight residual 103.26 61.43 41.83 3.00e+00 1.11e-01 1.94e+02 angle pdb=" S3 F3S A 602 " pdb="FE1 F3S A 602 " pdb=" S4 F3S A 602 " ideal model delta sigma weight residual 112.59 72.86 39.73 3.00e+00 1.11e-01 1.75e+02 angle pdb="FE1 F3S A 602 " pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " ideal model delta sigma weight residual 72.09 36.85 35.24 3.00e+00 1.11e-01 1.38e+02 angle pdb="FE3 F3S A 602 " pdb=" S2 F3S A 602 " pdb="FE4 F3S A 602 " ideal model delta sigma weight residual 71.75 39.57 32.18 3.00e+00 1.11e-01 1.15e+02 ... (remaining 12044 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 4487 17.89 - 35.78: 512 35.78 - 53.68: 148 53.68 - 71.57: 52 71.57 - 89.46: 12 Dihedral angle restraints: 5211 sinusoidal: 2065 harmonic: 3146 Sorted by residual: dihedral pdb=" CA THR A 164 " pdb=" C THR A 164 " pdb=" N PRO A 165 " pdb=" CA PRO A 165 " ideal model delta harmonic sigma weight residual -180.00 -141.86 -38.14 0 5.00e+00 4.00e-02 5.82e+01 dihedral pdb=" CA LEU C 394 " pdb=" C LEU C 394 " pdb=" N MET C 395 " pdb=" CA MET C 395 " ideal model delta harmonic sigma weight residual 180.00 155.17 24.83 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA ILE B 159 " pdb=" C ILE B 159 " pdb=" N PRO B 160 " pdb=" CA PRO B 160 " ideal model delta harmonic sigma weight residual -180.00 -155.38 -24.62 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 5208 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.482: 1274 3.482 - 6.965: 0 6.965 - 10.447: 0 10.447 - 13.929: 0 13.929 - 17.412: 1 Chirality restraints: 1275 Sorted by residual: chirality pdb=" S2 F3S A 602 " pdb="FE1 F3S A 602 " pdb="FE3 F3S A 602 " pdb="FE4 F3S A 602 " both_signs ideal model delta sigma weight residual False 10.77 -6.64 17.41 2.00e-01 2.50e+01 7.58e+03 chirality pdb=" CA PRO A 165 " pdb=" N PRO A 165 " pdb=" C PRO A 165 " pdb=" CB PRO A 165 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.17 2.00e-01 2.50e+01 7.54e-01 chirality pdb=" CA PRO B 160 " pdb=" N PRO B 160 " pdb=" C PRO B 160 " pdb=" CB PRO B 160 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.90e-01 ... (remaining 1272 not shown) Planarity restraints: 1564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CBD HEC C 503 " 0.019 2.00e-02 2.50e+03 3.95e-02 1.56e+01 pdb=" CGD HEC C 503 " -0.068 2.00e-02 2.50e+03 pdb=" O1D HEC C 503 " 0.024 2.00e-02 2.50e+03 pdb=" O2D HEC C 503 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR C 115 " -0.051 5.00e-02 4.00e+02 7.65e-02 9.36e+00 pdb=" N PRO C 116 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO C 116 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 116 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CBA HEC C 503 " 0.014 2.00e-02 2.50e+03 2.98e-02 8.86e+00 pdb=" CGA HEC C 503 " -0.051 2.00e-02 2.50e+03 pdb=" O1A HEC C 503 " 0.019 2.00e-02 2.50e+03 pdb=" O2A HEC C 503 " 0.019 2.00e-02 2.50e+03 ... (remaining 1561 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 241 2.68 - 3.24: 8423 3.24 - 3.79: 14759 3.79 - 4.35: 19691 4.35 - 4.90: 32317 Nonbonded interactions: 75431 Sorted by model distance: nonbonded pdb=" OG1 THR A 107 " pdb=" O2A FAD A 601 " model vdw 2.130 3.040 nonbonded pdb=" O ARG A 358 " pdb=" OH TYR A 443 " model vdw 2.199 3.040 nonbonded pdb=" N GLU B 136 " pdb=" OE1 GLU B 136 " model vdw 2.204 3.120 nonbonded pdb=" N GLU C 129 " pdb=" OE1 GLU C 129 " model vdw 2.205 3.120 nonbonded pdb=" OD2 ASP A 63 " pdb=" OG1 THR A 66 " model vdw 2.222 3.040 ... (remaining 75426 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.340 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 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 : 0.030 1.699 8828 Z= 1.469 Angle : 1.644 75.920 12058 Z= 0.478 Chirality : 0.490 17.412 1275 Planarity : 0.005 0.076 1564 Dihedral : 17.758 89.459 3203 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.49 % Allowed : 23.22 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.26), residues: 1081 helix: 1.88 (0.28), residues: 368 sheet: 0.10 (0.61), residues: 81 loop : -0.09 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 128 HIS 0.003 0.001 HIS A 76 PHE 0.029 0.001 PHE C 156 TYR 0.014 0.001 TYR A 210 ARG 0.014 0.000 ARG A 264 Details of bonding type rmsd hydrogen bonds : bond 0.16717 ( 327) hydrogen bonds : angle 7.00869 ( 909) metal coordination : bond 0.03281 ( 3) metal coordination : angle 38.68817 ( 9) covalent geometry : bond 0.02958 ( 8813) covalent geometry : angle 1.25952 (12049) Misc. bond : bond 0.08604 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 ASN cc_start: 0.8242 (OUTLIER) cc_final: 0.7754 (m-40) outliers start: 22 outliers final: 18 residues processed: 108 average time/residue: 1.2325 time to fit residues: 142.7961 Evaluate side-chains 107 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 414 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 ASN A 505 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.078351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.061722 restraints weight = 16747.286| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 2.68 r_work: 0.2630 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.0784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.250 8828 Z= 0.187 Angle : 1.644 105.104 12058 Z= 0.411 Chirality : 0.067 1.806 1275 Planarity : 0.005 0.058 1564 Dihedral : 9.841 89.457 1310 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.62 % Allowed : 19.93 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.26), residues: 1081 helix: 1.85 (0.28), residues: 387 sheet: -0.23 (0.60), residues: 83 loop : -0.19 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 51 HIS 0.004 0.001 HIS A 409 PHE 0.013 0.001 PHE C 156 TYR 0.008 0.001 TYR A 232 ARG 0.006 0.000 ARG A 264 Details of bonding type rmsd hydrogen bonds : bond 0.03585 ( 327) hydrogen bonds : angle 5.36647 ( 909) metal coordination : bond 0.02510 ( 3) metal coordination : angle 46.72390 ( 9) covalent geometry : bond 0.00448 ( 8813) covalent geometry : angle 1.03694 (12049) Misc. bond : bond 0.10788 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 95 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 THR cc_start: 0.9110 (OUTLIER) cc_final: 0.8889 (p) REVERT: B 112 MET cc_start: 0.8045 (ttp) cc_final: 0.7832 (ttp) REVERT: B 136 GLU cc_start: 0.8190 (mp0) cc_final: 0.7905 (mp0) REVERT: B 145 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8316 (tm-30) REVERT: C 267 MET cc_start: 0.9071 (tpt) cc_final: 0.8031 (tpt) outliers start: 32 outliers final: 16 residues processed: 118 average time/residue: 1.2393 time to fit residues: 156.0162 Evaluate side-chains 104 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain C residue 414 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 45 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 76 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 ASN B 56 GLN C 89 HIS C 326 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.077410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.060757 restraints weight = 16882.584| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 2.77 r_work: 0.2631 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2509 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.278 8828 Z= 0.192 Angle : 1.533 84.658 12058 Z= 0.410 Chirality : 0.062 1.548 1275 Planarity : 0.005 0.051 1564 Dihedral : 9.514 89.384 1295 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.28 % Allowed : 20.84 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.26), residues: 1081 helix: 1.88 (0.28), residues: 387 sheet: -0.45 (0.59), residues: 83 loop : -0.22 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 128 HIS 0.003 0.001 HIS A 76 PHE 0.015 0.001 PHE A 80 TYR 0.011 0.001 TYR A 210 ARG 0.004 0.000 ARG A 264 Details of bonding type rmsd hydrogen bonds : bond 0.03383 ( 327) hydrogen bonds : angle 5.12225 ( 909) metal coordination : bond 0.00878 ( 3) metal coordination : angle 40.97053 ( 9) covalent geometry : bond 0.00452 ( 8813) covalent geometry : angle 1.04840 (12049) Misc. bond : bond 0.11501 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 THR cc_start: 0.9163 (OUTLIER) cc_final: 0.8952 (p) REVERT: A 175 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8017 (mtt) REVERT: A 211 ASP cc_start: 0.8724 (t0) cc_final: 0.7815 (t0) REVERT: A 514 MET cc_start: 0.9394 (mtp) cc_final: 0.9174 (mtp) REVERT: B 90 ILE cc_start: 0.8843 (mm) cc_final: 0.8589 (mp) REVERT: B 91 LYS cc_start: 0.9193 (mppt) cc_final: 0.8621 (mppt) REVERT: B 112 MET cc_start: 0.8084 (ttp) cc_final: 0.7781 (ttp) REVERT: B 136 GLU cc_start: 0.8185 (mp0) cc_final: 0.7942 (mp0) REVERT: B 145 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8506 (tm-30) REVERT: C 267 MET cc_start: 0.9225 (tpt) cc_final: 0.7765 (tpt) outliers start: 29 outliers final: 16 residues processed: 109 average time/residue: 1.1614 time to fit residues: 135.6060 Evaluate side-chains 105 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 395 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 99 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN B 56 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.078795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.062230 restraints weight = 16728.638| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 2.78 r_work: 0.2648 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.237 8828 Z= 0.152 Angle : 1.509 83.185 12058 Z= 0.399 Chirality : 0.060 1.476 1275 Planarity : 0.004 0.049 1564 Dihedral : 9.250 89.205 1294 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.51 % Allowed : 20.72 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.26), residues: 1081 helix: 2.01 (0.28), residues: 382 sheet: -0.41 (0.60), residues: 81 loop : -0.20 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 51 HIS 0.002 0.000 HIS C 200 PHE 0.012 0.001 PHE A 270 TYR 0.009 0.001 TYR A 443 ARG 0.008 0.000 ARG A 264 Details of bonding type rmsd hydrogen bonds : bond 0.03025 ( 327) hydrogen bonds : angle 4.89579 ( 909) metal coordination : bond 0.00382 ( 3) metal coordination : angle 40.42578 ( 9) covalent geometry : bond 0.00350 ( 8813) covalent geometry : angle 1.02841 (12049) Misc. bond : bond 0.10502 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 94 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 THR cc_start: 0.9120 (OUTLIER) cc_final: 0.8899 (p) REVERT: A 175 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.7948 (mtt) REVERT: A 192 SER cc_start: 0.8761 (p) cc_final: 0.8551 (p) REVERT: A 211 ASP cc_start: 0.8629 (t0) cc_final: 0.7671 (t0) REVERT: A 469 MET cc_start: 0.9016 (ttt) cc_final: 0.8781 (tpp) REVERT: B 90 ILE cc_start: 0.8774 (mm) cc_final: 0.8565 (mp) REVERT: B 91 LYS cc_start: 0.9179 (mppt) cc_final: 0.8630 (mppt) REVERT: B 112 MET cc_start: 0.8168 (ttp) cc_final: 0.7920 (ttp) REVERT: B 136 GLU cc_start: 0.8263 (mp0) cc_final: 0.7971 (mp0) REVERT: C 139 MET cc_start: 0.9017 (mmp) cc_final: 0.8658 (mmp) REVERT: C 267 MET cc_start: 0.9184 (tpt) cc_final: 0.7639 (tpt) REVERT: C 395 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8112 (tpt) outliers start: 31 outliers final: 15 residues processed: 117 average time/residue: 1.1166 time to fit residues: 140.0896 Evaluate side-chains 107 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain C residue 414 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 37 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 100 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN B 56 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.074349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.058160 restraints weight = 16980.902| |-----------------------------------------------------------------------------| r_work (start): 0.2677 rms_B_bonded: 2.67 r_work: 0.2562 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2439 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.375 8828 Z= 0.275 Angle : 1.661 87.628 12058 Z= 0.433 Chirality : 0.063 1.511 1275 Planarity : 0.005 0.059 1564 Dihedral : 9.544 89.722 1294 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.62 % Allowed : 21.29 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.26), residues: 1081 helix: 1.76 (0.28), residues: 391 sheet: -0.74 (0.57), residues: 83 loop : -0.29 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 128 HIS 0.004 0.001 HIS A 76 PHE 0.029 0.002 PHE A 80 TYR 0.012 0.001 TYR C 359 ARG 0.008 0.001 ARG A 264 Details of bonding type rmsd hydrogen bonds : bond 0.03605 ( 327) hydrogen bonds : angle 5.04580 ( 909) metal coordination : bond 0.00462 ( 3) metal coordination : angle 45.90647 ( 9) covalent geometry : bond 0.00653 ( 8813) covalent geometry : angle 1.08998 (12049) Misc. bond : bond 0.14462 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 89 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 THR cc_start: 0.7314 (OUTLIER) cc_final: 0.6778 (t) REVERT: A 175 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8161 (mtt) REVERT: B 90 ILE cc_start: 0.8826 (mm) cc_final: 0.8625 (mp) REVERT: B 91 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8661 (mppt) REVERT: B 112 MET cc_start: 0.8215 (ttp) cc_final: 0.7920 (ttp) REVERT: B 136 GLU cc_start: 0.8157 (mp0) cc_final: 0.7907 (mp0) REVERT: B 145 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8569 (tm-30) REVERT: C 139 MET cc_start: 0.9026 (mmp) cc_final: 0.8683 (mmp) REVERT: C 267 MET cc_start: 0.9159 (tpt) cc_final: 0.7655 (tpt) outliers start: 32 outliers final: 13 residues processed: 109 average time/residue: 1.1876 time to fit residues: 138.4518 Evaluate side-chains 101 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain C residue 64 PHE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain C residue 414 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 38 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 9 optimal weight: 0.0970 chunk 55 optimal weight: 2.9990 chunk 74 optimal weight: 0.0970 chunk 35 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN B 56 GLN B 164 HIS C 185 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.078332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.062365 restraints weight = 16835.592| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 2.72 r_work: 0.2650 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2529 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.237 8828 Z= 0.142 Angle : 1.563 83.054 12058 Z= 0.401 Chirality : 0.059 1.480 1275 Planarity : 0.005 0.056 1564 Dihedral : 8.999 89.362 1290 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.94 % Allowed : 22.20 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.26), residues: 1081 helix: 2.03 (0.28), residues: 382 sheet: -0.70 (0.58), residues: 83 loop : -0.23 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 51 HIS 0.002 0.000 HIS B 164 PHE 0.017 0.001 PHE C 210 TYR 0.009 0.001 TYR A 79 ARG 0.010 0.000 ARG A 264 Details of bonding type rmsd hydrogen bonds : bond 0.02872 ( 327) hydrogen bonds : angle 4.79216 ( 909) metal coordination : bond 0.00259 ( 3) metal coordination : angle 43.22981 ( 9) covalent geometry : bond 0.00318 ( 8813) covalent geometry : angle 1.02480 (12049) Misc. bond : bond 0.10754 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.7878 (mtt) REVERT: A 192 SER cc_start: 0.8734 (p) cc_final: 0.8516 (p) REVERT: A 211 ASP cc_start: 0.8796 (t0) cc_final: 0.8149 (t0) REVERT: A 469 MET cc_start: 0.8981 (ttt) cc_final: 0.8656 (tpp) REVERT: A 505 ASN cc_start: 0.8993 (t0) cc_final: 0.8723 (t160) REVERT: B 87 SER cc_start: 0.8875 (m) cc_final: 0.8117 (m) REVERT: B 90 ILE cc_start: 0.8827 (mm) cc_final: 0.8616 (mp) REVERT: B 91 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8635 (mppt) REVERT: B 94 ARG cc_start: 0.8629 (mtm180) cc_final: 0.8400 (mtm180) REVERT: B 112 MET cc_start: 0.8121 (ttp) cc_final: 0.7774 (ttp) REVERT: B 136 GLU cc_start: 0.8209 (mp0) cc_final: 0.7930 (mp0) REVERT: C 139 MET cc_start: 0.9026 (mmp) cc_final: 0.8646 (mmp) REVERT: C 267 MET cc_start: 0.9183 (tpt) cc_final: 0.7600 (tpt) REVERT: C 395 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8100 (ttt) outliers start: 26 outliers final: 11 residues processed: 110 average time/residue: 1.2065 time to fit residues: 142.1073 Evaluate side-chains 106 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain C residue 414 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 32 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 13 optimal weight: 0.2980 chunk 74 optimal weight: 0.2980 chunk 26 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN B 56 GLN C 185 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.078831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.062339 restraints weight = 16907.829| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 2.77 r_work: 0.2664 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.229 8828 Z= 0.146 Angle : 1.566 83.197 12058 Z= 0.405 Chirality : 0.059 1.479 1275 Planarity : 0.004 0.050 1564 Dihedral : 8.846 89.903 1288 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.15 % Allowed : 23.33 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.26), residues: 1081 helix: 2.06 (0.28), residues: 383 sheet: -0.66 (0.58), residues: 83 loop : -0.20 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 51 HIS 0.002 0.000 HIS A 76 PHE 0.018 0.001 PHE C 210 TYR 0.015 0.001 TYR A 79 ARG 0.014 0.000 ARG A 264 Details of bonding type rmsd hydrogen bonds : bond 0.02820 ( 327) hydrogen bonds : angle 4.71138 ( 909) metal coordination : bond 0.00214 ( 3) metal coordination : angle 43.11494 ( 9) covalent geometry : bond 0.00333 ( 8813) covalent geometry : angle 1.03304 (12049) Misc. bond : bond 0.10081 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8129 (mtt) REVERT: A 192 SER cc_start: 0.8752 (p) cc_final: 0.8535 (p) REVERT: A 211 ASP cc_start: 0.8746 (t0) cc_final: 0.8083 (t0) REVERT: A 469 MET cc_start: 0.8992 (ttt) cc_final: 0.8675 (tpp) REVERT: A 505 ASN cc_start: 0.8911 (t0) cc_final: 0.8647 (t160) REVERT: B 87 SER cc_start: 0.8885 (m) cc_final: 0.8148 (m) REVERT: B 90 ILE cc_start: 0.8791 (mm) cc_final: 0.8568 (mp) REVERT: B 91 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8656 (mppt) REVERT: B 94 ARG cc_start: 0.8615 (mtm180) cc_final: 0.8219 (mtm180) REVERT: B 112 MET cc_start: 0.8134 (ttp) cc_final: 0.7811 (ttp) REVERT: B 136 GLU cc_start: 0.8288 (mp0) cc_final: 0.7863 (mp0) REVERT: C 139 MET cc_start: 0.9051 (mmp) cc_final: 0.8672 (mmp) REVERT: C 267 MET cc_start: 0.9150 (tpt) cc_final: 0.7564 (tpt) REVERT: C 395 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.7995 (tpt) REVERT: C 443 LYS cc_start: 0.8582 (mmpt) cc_final: 0.7720 (mttp) outliers start: 19 outliers final: 8 residues processed: 105 average time/residue: 1.2450 time to fit residues: 139.6826 Evaluate side-chains 102 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 395 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 106 optimal weight: 0.0370 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 ASN B 56 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.078837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.062804 restraints weight = 16982.814| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 2.73 r_work: 0.2669 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.216 8828 Z= 0.146 Angle : 1.567 83.218 12058 Z= 0.403 Chirality : 0.059 1.481 1275 Planarity : 0.004 0.051 1564 Dihedral : 8.753 89.033 1288 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.72 % Allowed : 22.54 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.26), residues: 1081 helix: 2.09 (0.28), residues: 382 sheet: -0.45 (0.60), residues: 81 loop : -0.22 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 51 HIS 0.002 0.000 HIS B 64 PHE 0.020 0.001 PHE C 210 TYR 0.021 0.001 TYR A 79 ARG 0.012 0.000 ARG A 264 Details of bonding type rmsd hydrogen bonds : bond 0.02762 ( 327) hydrogen bonds : angle 4.67089 ( 909) metal coordination : bond 0.00181 ( 3) metal coordination : angle 43.17507 ( 9) covalent geometry : bond 0.00336 ( 8813) covalent geometry : angle 1.03227 (12049) Misc. bond : bond 0.10028 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8088 (mtt) REVERT: A 192 SER cc_start: 0.8730 (p) cc_final: 0.8515 (p) REVERT: A 211 ASP cc_start: 0.8737 (t0) cc_final: 0.7810 (t0) REVERT: A 469 MET cc_start: 0.8972 (ttt) cc_final: 0.8671 (tpp) REVERT: A 505 ASN cc_start: 0.8881 (t0) cc_final: 0.8611 (t160) REVERT: B 87 SER cc_start: 0.8901 (m) cc_final: 0.8214 (m) REVERT: B 90 ILE cc_start: 0.8787 (mm) cc_final: 0.8576 (mp) REVERT: B 91 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8663 (mppt) REVERT: B 112 MET cc_start: 0.8127 (ttp) cc_final: 0.7805 (ttp) REVERT: B 136 GLU cc_start: 0.8296 (mp0) cc_final: 0.7866 (mp0) REVERT: C 139 MET cc_start: 0.9054 (mmp) cc_final: 0.8677 (mmp) REVERT: C 267 MET cc_start: 0.9135 (tpt) cc_final: 0.7511 (tpt) REVERT: C 395 MET cc_start: 0.8942 (OUTLIER) cc_final: 0.7933 (tpt) REVERT: C 443 LYS cc_start: 0.8534 (mmpt) cc_final: 0.7658 (mttp) outliers start: 24 outliers final: 11 residues processed: 107 average time/residue: 1.2155 time to fit residues: 139.0390 Evaluate side-chains 103 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 395 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 106 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 ASN B 56 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.078145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.062091 restraints weight = 16827.977| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 2.70 r_work: 0.2654 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2532 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.220 8828 Z= 0.152 Angle : 1.579 83.208 12058 Z= 0.406 Chirality : 0.060 1.486 1275 Planarity : 0.005 0.059 1564 Dihedral : 8.746 87.944 1288 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.38 % Allowed : 23.10 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.26), residues: 1081 helix: 1.97 (0.28), residues: 389 sheet: -0.43 (0.60), residues: 81 loop : -0.26 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 128 HIS 0.002 0.000 HIS A 76 PHE 0.024 0.001 PHE C 210 TYR 0.022 0.001 TYR A 79 ARG 0.013 0.000 ARG A 264 Details of bonding type rmsd hydrogen bonds : bond 0.02790 ( 327) hydrogen bonds : angle 4.66389 ( 909) metal coordination : bond 0.00149 ( 3) metal coordination : angle 43.52849 ( 9) covalent geometry : bond 0.00350 ( 8813) covalent geometry : angle 1.03886 (12049) Misc. bond : bond 0.10188 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8076 (mtt) REVERT: A 192 SER cc_start: 0.8662 (p) cc_final: 0.8449 (p) REVERT: A 211 ASP cc_start: 0.8796 (t0) cc_final: 0.7875 (t0) REVERT: A 469 MET cc_start: 0.8973 (ttt) cc_final: 0.8657 (tpp) REVERT: A 505 ASN cc_start: 0.8978 (t0) cc_final: 0.8670 (t160) REVERT: B 87 SER cc_start: 0.8863 (m) cc_final: 0.8196 (m) REVERT: B 90 ILE cc_start: 0.8788 (mm) cc_final: 0.8577 (mp) REVERT: B 91 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8659 (mppt) REVERT: B 112 MET cc_start: 0.8014 (ttp) cc_final: 0.7655 (ttp) REVERT: B 136 GLU cc_start: 0.8284 (mp0) cc_final: 0.7871 (mp0) REVERT: C 139 MET cc_start: 0.8991 (mmp) cc_final: 0.8602 (mmp) REVERT: C 395 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.7874 (tpt) REVERT: C 443 LYS cc_start: 0.8550 (mmpt) cc_final: 0.7647 (mttm) outliers start: 21 outliers final: 11 residues processed: 102 average time/residue: 1.2170 time to fit residues: 132.7718 Evaluate side-chains 102 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 395 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 53 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 2 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 ASN B 56 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.078309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.062292 restraints weight = 16835.333| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 2.69 r_work: 0.2656 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2533 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.219 8828 Z= 0.152 Angle : 1.579 83.437 12058 Z= 0.405 Chirality : 0.060 1.487 1275 Planarity : 0.005 0.064 1564 Dihedral : 8.711 87.361 1288 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.15 % Allowed : 23.33 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.26), residues: 1081 helix: 1.96 (0.28), residues: 388 sheet: -0.40 (0.60), residues: 81 loop : -0.25 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 128 HIS 0.002 0.000 HIS A 76 PHE 0.025 0.001 PHE C 210 TYR 0.018 0.001 TYR A 79 ARG 0.015 0.000 ARG A 264 Details of bonding type rmsd hydrogen bonds : bond 0.02787 ( 327) hydrogen bonds : angle 4.66165 ( 909) metal coordination : bond 0.00120 ( 3) metal coordination : angle 43.61048 ( 9) covalent geometry : bond 0.00351 ( 8813) covalent geometry : angle 1.03723 (12049) Misc. bond : bond 0.10331 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8043 (mtt) REVERT: A 192 SER cc_start: 0.8649 (p) cc_final: 0.8437 (p) REVERT: A 211 ASP cc_start: 0.8795 (t0) cc_final: 0.8132 (t0) REVERT: A 469 MET cc_start: 0.8982 (ttt) cc_final: 0.8665 (tpp) REVERT: A 505 ASN cc_start: 0.8976 (t0) cc_final: 0.8658 (t160) REVERT: B 87 SER cc_start: 0.8850 (m) cc_final: 0.8205 (m) REVERT: B 90 ILE cc_start: 0.8767 (mm) cc_final: 0.8481 (mp) REVERT: B 91 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8656 (mppt) REVERT: B 94 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7977 (mtm-85) REVERT: B 112 MET cc_start: 0.8006 (ttp) cc_final: 0.7588 (ttp) REVERT: B 136 GLU cc_start: 0.8278 (mp0) cc_final: 0.7859 (mp0) REVERT: C 139 MET cc_start: 0.8984 (mmp) cc_final: 0.8594 (mmp) REVERT: C 395 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.7852 (tpt) REVERT: C 443 LYS cc_start: 0.8541 (mmpt) cc_final: 0.7636 (mttm) outliers start: 19 outliers final: 11 residues processed: 104 average time/residue: 1.2279 time to fit residues: 136.9257 Evaluate side-chains 105 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 94 ARG Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 395 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 67 optimal weight: 0.0040 chunk 86 optimal weight: 7.9990 chunk 100 optimal weight: 0.4980 chunk 27 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 65 optimal weight: 0.2980 chunk 53 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 0 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 33 optimal weight: 0.0870 overall best weight: 0.3170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 ASN B 56 GLN B 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.080976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.065041 restraints weight = 16825.608| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 2.74 r_work: 0.2716 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.223 8828 Z= 0.132 Angle : 1.518 83.040 12058 Z= 0.397 Chirality : 0.059 1.477 1275 Planarity : 0.004 0.047 1564 Dihedral : 8.332 86.901 1287 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.04 % Allowed : 23.56 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.26), residues: 1081 helix: 2.13 (0.28), residues: 382 sheet: -0.52 (0.59), residues: 83 loop : -0.17 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 51 HIS 0.003 0.000 HIS A 409 PHE 0.027 0.001 PHE C 210 TYR 0.007 0.001 TYR C 120 ARG 0.005 0.000 ARG A 264 Details of bonding type rmsd hydrogen bonds : bond 0.02540 ( 327) hydrogen bonds : angle 4.56535 ( 909) metal coordination : bond 0.00044 ( 3) metal coordination : angle 41.06463 ( 9) covalent geometry : bond 0.00293 ( 8813) covalent geometry : angle 1.02306 (12049) Misc. bond : bond 0.09210 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5626.53 seconds wall clock time: 97 minutes 1.50 seconds (5821.50 seconds total)