Starting phenix.real_space_refine on Fri Aug 22 23:38:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k6j_36920/08_2025/8k6j_36920.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k6j_36920/08_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_36920/08_2025/8k6j_36920.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k6j_36920/08_2025/8k6j_36920.map" model { file = "/net/cci-nas-00/data/ceres_data/8k6j_36920/08_2025/8k6j_36920.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k6j_36920/08_2025/8k6j_36920.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.66, per 1000 atoms: 0.19 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: 0.71 Conformation dependent library (CDL) restraints added in 195.9 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.29 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: 1.28 Time building geometry restraints manager: 0.86 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: 1.760 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.570 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:8.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.770 ------------------------------------------------------------------------------- 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 : 8.08 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.014 0.000 ARG A 264 TYR 0.014 0.001 TYR A 210 PHE 0.029 0.001 PHE C 156 TRP 0.007 0.001 TRP B 128 HIS 0.003 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.02958 ( 8813) covalent geometry : angle 1.25952 (12049) hydrogen bonds : bond 0.16717 ( 327) hydrogen bonds : angle 7.00869 ( 909) metal coordination : bond 0.03281 ( 3) metal coordination : angle 38.68817 ( 9) 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 : 0.262 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: 0.5257 time to fit residues: 60.4420 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 : 0.330 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.0030 chunk 33 optimal weight: 0.0980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.079397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.062932 restraints weight = 16768.182| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 2.68 r_work: 0.2660 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.232 8828 Z= 0.170 Angle : 1.608 100.933 12058 Z= 0.405 Chirality : 0.069 1.914 1275 Planarity : 0.005 0.058 1564 Dihedral : 9.779 89.107 1310 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.51 % Allowed : 20.16 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.26), residues: 1081 helix: 1.90 (0.28), residues: 381 sheet: -0.20 (0.61), residues: 83 loop : -0.19 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 264 TYR 0.008 0.001 TYR A 232 PHE 0.014 0.001 PHE C 156 TRP 0.006 0.001 TRP A 51 HIS 0.003 0.001 HIS A 409 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 8813) covalent geometry : angle 1.02437 (12049) hydrogen bonds : bond 0.03414 ( 327) hydrogen bonds : angle 5.32298 ( 909) metal coordination : bond 0.02893 ( 3) metal coordination : angle 45.37602 ( 9) Misc. bond : bond 0.09997 ( 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 133 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 THR cc_start: 0.9111 (OUTLIER) cc_final: 0.8890 (p) REVERT: B 68 ASP cc_start: 0.7977 (t0) cc_final: 0.7664 (t0) REVERT: B 112 MET cc_start: 0.8025 (ttp) cc_final: 0.7816 (ttp) REVERT: B 136 GLU cc_start: 0.8198 (mp0) cc_final: 0.7908 (mp0) REVERT: B 145 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8301 (tm-30) REVERT: C 267 MET cc_start: 0.9064 (tpt) cc_final: 0.8075 (tpt) outliers start: 31 outliers final: 15 residues processed: 124 average time/residue: 0.5700 time to fit residues: 75.3824 Evaluate side-chains 105 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 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 75 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 67 optimal weight: 0.0170 chunk 22 optimal weight: 2.9990 chunk 97 optimal weight: 0.0030 chunk 0 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 overall best weight: 1.5632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN C 326 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.077159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.060753 restraints weight = 16885.880| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 2.71 r_work: 0.2615 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2492 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.291 8828 Z= 0.210 Angle : 1.552 84.496 12058 Z= 0.415 Chirality : 0.062 1.517 1275 Planarity : 0.005 0.050 1564 Dihedral : 9.520 89.351 1295 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.40 % Allowed : 20.95 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.26), residues: 1081 helix: 1.85 (0.28), residues: 389 sheet: -0.44 (0.60), residues: 83 loop : -0.21 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 264 TYR 0.012 0.001 TYR A 210 PHE 0.019 0.001 PHE A 80 TRP 0.009 0.001 TRP B 128 HIS 0.003 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00492 ( 8813) covalent geometry : angle 1.05880 (12049) hydrogen bonds : bond 0.03442 ( 327) hydrogen bonds : angle 5.11965 ( 909) metal coordination : bond 0.00895 ( 3) metal coordination : angle 41.55609 ( 9) Misc. bond : bond 0.12163 ( 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 119 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 89 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 THR cc_start: 0.9242 (OUTLIER) cc_final: 0.9028 (p) REVERT: A 175 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8237 (mtt) REVERT: A 211 ASP cc_start: 0.8810 (t0) cc_final: 0.7940 (t0) REVERT: A 303 ASN cc_start: 0.8175 (OUTLIER) cc_final: 0.7720 (m-40) REVERT: B 112 MET cc_start: 0.8197 (ttp) cc_final: 0.7978 (ttp) REVERT: B 136 GLU cc_start: 0.8238 (mp0) cc_final: 0.8000 (mp0) REVERT: B 145 GLU cc_start: 0.8746 (tm-30) cc_final: 0.8529 (tm-30) REVERT: C 267 MET cc_start: 0.9290 (tpt) cc_final: 0.7749 (tpt) outliers start: 30 outliers final: 18 residues processed: 110 average time/residue: 0.5164 time to fit residues: 60.7320 Evaluate side-chains 107 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 303 ASN 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 109 ASP Chi-restraints excluded: chain B residue 123 GLN 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 89 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.076785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.060443 restraints weight = 17043.963| |-----------------------------------------------------------------------------| r_work (start): 0.2695 rms_B_bonded: 2.68 r_work: 0.2577 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2455 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.299 8828 Z= 0.205 Angle : 1.584 84.770 12058 Z= 0.411 Chirality : 0.061 1.499 1275 Planarity : 0.005 0.052 1564 Dihedral : 9.392 89.271 1294 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.08 % Allowed : 20.39 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.26), residues: 1081 helix: 1.85 (0.28), residues: 388 sheet: -0.58 (0.59), residues: 83 loop : -0.25 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 264 TYR 0.011 0.001 TYR A 210 PHE 0.017 0.001 PHE A 80 TRP 0.009 0.001 TRP B 128 HIS 0.003 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00481 ( 8813) covalent geometry : angle 1.05098 (12049) hydrogen bonds : bond 0.03267 ( 327) hydrogen bonds : angle 4.98528 ( 909) metal coordination : bond 0.00452 ( 3) metal coordination : angle 43.38601 ( 9) Misc. bond : bond 0.12602 ( 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 124 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 88 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8235 (mtt) REVERT: A 211 ASP cc_start: 0.8830 (t0) cc_final: 0.8259 (t0) REVERT: A 231 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8791 (ptm) REVERT: A 303 ASN cc_start: 0.8129 (OUTLIER) cc_final: 0.7647 (m-40) REVERT: B 91 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8732 (mppt) REVERT: B 112 MET cc_start: 0.8216 (ttp) cc_final: 0.7949 (ttp) REVERT: B 136 GLU cc_start: 0.8243 (mp0) cc_final: 0.7961 (mp0) REVERT: B 145 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8570 (tm-30) REVERT: C 139 MET cc_start: 0.9046 (mmp) cc_final: 0.8721 (mmp) REVERT: C 267 MET cc_start: 0.9270 (tpt) cc_final: 0.7758 (tpt) REVERT: C 395 MET cc_start: 0.9164 (OUTLIER) cc_final: 0.8189 (tpt) outliers start: 36 outliers final: 16 residues processed: 111 average time/residue: 0.6091 time to fit residues: 72.1696 Evaluate side-chains 108 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 231 MET Chi-restraints excluded: chain A residue 303 ASN 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 88 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 123 GLN 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 92 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.077054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.060702 restraints weight = 16969.252| |-----------------------------------------------------------------------------| r_work (start): 0.2710 rms_B_bonded: 2.73 r_work: 0.2593 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2470 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.290 8828 Z= 0.188 Angle : 1.602 84.820 12058 Z= 0.412 Chirality : 0.061 1.498 1275 Planarity : 0.005 0.053 1564 Dihedral : 9.279 89.298 1294 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.17 % Allowed : 21.97 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.26), residues: 1081 helix: 1.85 (0.28), residues: 387 sheet: -0.63 (0.58), residues: 83 loop : -0.28 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 264 TYR 0.012 0.001 TYR A 79 PHE 0.016 0.001 PHE A 80 TRP 0.008 0.001 TRP B 128 HIS 0.003 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 8813) covalent geometry : angle 1.04837 (12049) hydrogen bonds : bond 0.03141 ( 327) hydrogen bonds : angle 4.90397 ( 909) metal coordination : bond 0.00402 ( 3) metal coordination : angle 44.35314 ( 9) Misc. bond : bond 0.11851 ( 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 119 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 0.373 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: 0.8776 (OUTLIER) cc_final: 0.8271 (mtt) REVERT: A 211 ASP cc_start: 0.8857 (t0) cc_final: 0.8230 (t0) REVERT: A 231 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8656 (ptm) REVERT: A 303 ASN cc_start: 0.8161 (OUTLIER) cc_final: 0.7706 (m-40) REVERT: B 91 LYS cc_start: 0.9208 (mppt) cc_final: 0.8669 (mppt) REVERT: B 112 MET cc_start: 0.8218 (ttp) cc_final: 0.7921 (ttp) REVERT: B 136 GLU cc_start: 0.8270 (mp0) cc_final: 0.7947 (mp0) REVERT: B 145 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8554 (tm-30) REVERT: C 139 MET cc_start: 0.9057 (mmp) cc_final: 0.8679 (mmp) REVERT: C 395 MET cc_start: 0.9155 (OUTLIER) cc_final: 0.8173 (tpt) outliers start: 28 outliers final: 13 residues processed: 108 average time/residue: 0.5938 time to fit residues: 68.3482 Evaluate side-chains 106 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 231 MET Chi-restraints excluded: chain A residue 303 ASN 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 123 GLN 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 103 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 15 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 106 optimal weight: 0.9980 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN C 185 ASN 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 = 0.078555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.062231 restraints weight = 16881.443| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 2.75 r_work: 0.2660 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2540 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.244 8828 Z= 0.152 Angle : 1.577 83.089 12058 Z= 0.403 Chirality : 0.060 1.487 1275 Planarity : 0.004 0.051 1564 Dihedral : 9.071 89.510 1293 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.74 % Allowed : 21.63 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.26), residues: 1081 helix: 2.03 (0.28), residues: 382 sheet: -0.38 (0.60), residues: 81 loop : -0.25 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 264 TYR 0.014 0.001 TYR A 79 PHE 0.012 0.001 PHE A 270 TRP 0.006 0.001 TRP A 51 HIS 0.002 0.000 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 8813) covalent geometry : angle 1.03154 (12049) hydrogen bonds : bond 0.02853 ( 327) hydrogen bonds : angle 4.77602 ( 909) metal coordination : bond 0.00269 ( 3) metal coordination : angle 43.65188 ( 9) Misc. bond : bond 0.10463 ( 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 133 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8226 (mtt) REVERT: A 192 SER cc_start: 0.8783 (p) cc_final: 0.8566 (p) REVERT: A 211 ASP cc_start: 0.8865 (t0) cc_final: 0.8214 (t0) REVERT: A 303 ASN cc_start: 0.8158 (OUTLIER) cc_final: 0.7655 (m-40) REVERT: A 419 LEU cc_start: 0.9220 (tp) cc_final: 0.8959 (tm) REVERT: A 505 ASN cc_start: 0.9033 (t0) cc_final: 0.8761 (t160) REVERT: B 91 LYS cc_start: 0.9216 (OUTLIER) cc_final: 0.8731 (mppt) REVERT: B 94 ARG cc_start: 0.8745 (mtm180) cc_final: 0.8187 (mtm-85) REVERT: B 112 MET cc_start: 0.8188 (ttp) cc_final: 0.7837 (ttp) REVERT: B 136 GLU cc_start: 0.8348 (mp0) cc_final: 0.8008 (mp0) REVERT: C 139 MET cc_start: 0.9080 (mmp) cc_final: 0.8707 (mmp) REVERT: C 267 MET cc_start: 0.9275 (tpt) cc_final: 0.7704 (tpt) REVERT: C 395 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8127 (tpt) REVERT: C 443 LYS cc_start: 0.8661 (mmpt) cc_final: 0.7811 (mttp) outliers start: 33 outliers final: 15 residues processed: 120 average time/residue: 0.5544 time to fit residues: 71.1464 Evaluate side-chains 113 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 303 ASN 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 123 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 HIS 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 Chi-restraints excluded: chain C residue 447 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 2 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 53 optimal weight: 0.4980 chunk 24 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN C 185 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.077365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.061098 restraints weight = 17011.254| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 2.69 r_work: 0.2625 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2501 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 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 : 0.006 0.295 8828 Z= 0.198 Angle : 1.619 85.280 12058 Z= 0.416 Chirality : 0.061 1.507 1275 Planarity : 0.005 0.054 1564 Dihedral : 9.153 89.425 1293 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.28 % Allowed : 22.08 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.26), residues: 1081 helix: 1.89 (0.28), residues: 389 sheet: -0.42 (0.60), residues: 81 loop : -0.30 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 264 TYR 0.019 0.001 TYR A 79 PHE 0.022 0.001 PHE A 80 TRP 0.009 0.001 TRP B 128 HIS 0.004 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 8813) covalent geometry : angle 1.05644 (12049) hydrogen bonds : bond 0.03086 ( 327) hydrogen bonds : angle 4.82711 ( 909) metal coordination : bond 0.00349 ( 3) metal coordination : angle 44.90694 ( 9) Misc. bond : bond 0.11909 ( 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 123 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.8988 (OUTLIER) cc_final: 0.8584 (mtt) REVERT: A 211 ASP cc_start: 0.8947 (t0) cc_final: 0.8343 (t0) REVERT: A 276 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.7747 (mp10) REVERT: A 303 ASN cc_start: 0.8329 (OUTLIER) cc_final: 0.7835 (m-40) REVERT: A 419 LEU cc_start: 0.9327 (tp) cc_final: 0.9064 (tm) REVERT: B 91 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.8770 (mppt) REVERT: B 112 MET cc_start: 0.8286 (ttp) cc_final: 0.7995 (ttp) REVERT: B 136 GLU cc_start: 0.8454 (mp0) cc_final: 0.8049 (mp0) REVERT: C 139 MET cc_start: 0.9210 (mmp) cc_final: 0.8837 (mmp) REVERT: C 267 MET cc_start: 0.9381 (tpt) cc_final: 0.7745 (tpt) REVERT: C 395 MET cc_start: 0.9249 (OUTLIER) cc_final: 0.8221 (tpt) REVERT: C 443 LYS cc_start: 0.8666 (mmpt) cc_final: 0.7848 (mttp) outliers start: 29 outliers final: 15 residues processed: 111 average time/residue: 0.6193 time to fit residues: 73.2593 Evaluate side-chains 111 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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 276 GLN Chi-restraints excluded: chain A residue 303 ASN 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 88 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 HIS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 100 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 76 optimal weight: 20.0000 chunk 55 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.075708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.059431 restraints weight = 16920.734| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 2.67 r_work: 0.2598 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2474 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.354 8828 Z= 0.245 Angle : 1.657 86.554 12058 Z= 0.429 Chirality : 0.062 1.513 1275 Planarity : 0.005 0.060 1564 Dihedral : 9.297 88.917 1293 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.72 % Allowed : 22.99 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.26), residues: 1081 helix: 1.79 (0.28), residues: 389 sheet: -0.55 (0.59), residues: 81 loop : -0.39 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 264 TYR 0.020 0.001 TYR A 79 PHE 0.023 0.002 PHE A 80 TRP 0.013 0.001 TRP B 128 HIS 0.004 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00582 ( 8813) covalent geometry : angle 1.07958 (12049) hydrogen bonds : bond 0.03341 ( 327) hydrogen bonds : angle 4.93575 ( 909) metal coordination : bond 0.00360 ( 3) metal coordination : angle 46.01661 ( 9) Misc. bond : bond 0.14144 ( 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 114 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 THR cc_start: 0.7651 (OUTLIER) cc_final: 0.7073 (t) REVERT: A 175 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8580 (mtt) REVERT: A 211 ASP cc_start: 0.9003 (t0) cc_final: 0.8432 (t0) REVERT: A 276 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7850 (mp10) REVERT: A 419 LEU cc_start: 0.9343 (tp) cc_final: 0.9069 (tm) REVERT: B 55 MET cc_start: 0.8919 (tpp) cc_final: 0.8699 (mmp) REVERT: B 91 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.8748 (mppt) REVERT: B 112 MET cc_start: 0.8335 (ttp) cc_final: 0.8082 (ttp) REVERT: B 136 GLU cc_start: 0.8448 (mp0) cc_final: 0.8099 (mp0) REVERT: C 139 MET cc_start: 0.9237 (mmp) cc_final: 0.8861 (mmp) REVERT: C 267 MET cc_start: 0.9362 (tpt) cc_final: 0.7860 (tpt) REVERT: C 395 MET cc_start: 0.9271 (OUTLIER) cc_final: 0.8153 (ttt) REVERT: C 443 LYS cc_start: 0.8702 (mmpt) cc_final: 0.7913 (mttp) outliers start: 24 outliers final: 13 residues processed: 106 average time/residue: 0.5742 time to fit residues: 65.0576 Evaluate side-chains 105 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 276 GLN 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 123 GLN 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 22 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 79 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN B 164 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.078072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.061853 restraints weight = 16913.451| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 2.68 r_work: 0.2642 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2517 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.283 8828 Z= 0.160 Angle : 1.594 83.967 12058 Z= 0.411 Chirality : 0.060 1.487 1275 Planarity : 0.005 0.059 1564 Dihedral : 9.008 89.318 1291 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.27 % Allowed : 23.44 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.26), residues: 1081 helix: 1.89 (0.28), residues: 388 sheet: -0.52 (0.59), residues: 81 loop : -0.37 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 264 TYR 0.018 0.001 TYR A 79 PHE 0.021 0.001 PHE C 210 TRP 0.007 0.001 TRP A 51 HIS 0.003 0.001 HIS B 164 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 8813) covalent geometry : angle 1.04148 (12049) hydrogen bonds : bond 0.02941 ( 327) hydrogen bonds : angle 4.81463 ( 909) metal coordination : bond 0.00189 ( 3) metal coordination : angle 44.18742 ( 9) Misc. bond : bond 0.12546 ( 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: 20 poor density : 92 time to evaluate : 0.346 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: 0.8877 (OUTLIER) cc_final: 0.8388 (mtt) REVERT: A 211 ASP cc_start: 0.8958 (t0) cc_final: 0.8351 (t0) REVERT: A 276 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7846 (mp10) REVERT: B 55 MET cc_start: 0.8885 (tpp) cc_final: 0.8681 (mmp) REVERT: B 91 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.8774 (mppt) REVERT: B 94 ARG cc_start: 0.8755 (mtm180) cc_final: 0.8188 (mtm-85) REVERT: B 112 MET cc_start: 0.8266 (ttp) cc_final: 0.8031 (ttp) REVERT: B 136 GLU cc_start: 0.8463 (mp0) cc_final: 0.8114 (mp0) REVERT: C 395 MET cc_start: 0.9178 (OUTLIER) cc_final: 0.8123 (ttt) REVERT: C 443 LYS cc_start: 0.8650 (mmpt) cc_final: 0.7857 (mttp) outliers start: 20 outliers final: 12 residues processed: 103 average time/residue: 0.6061 time to fit residues: 66.6991 Evaluate side-chains 102 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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 276 GLN Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 123 GLN 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 21 optimal weight: 0.7980 chunk 65 optimal weight: 0.0470 chunk 30 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 5 optimal weight: 0.0770 chunk 38 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.079707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.063567 restraints weight = 16778.374| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 2.68 r_work: 0.2679 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2556 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.238 8828 Z= 0.143 Angle : 1.552 83.053 12058 Z= 0.408 Chirality : 0.060 1.483 1275 Planarity : 0.005 0.061 1564 Dihedral : 8.819 88.852 1291 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.59 % Allowed : 24.46 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.26), residues: 1081 helix: 2.08 (0.28), residues: 382 sheet: -0.55 (0.58), residues: 83 loop : -0.30 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 264 TYR 0.014 0.001 TYR A 79 PHE 0.024 0.001 PHE C 210 TRP 0.008 0.001 TRP A 51 HIS 0.002 0.000 HIS B 164 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 8813) covalent geometry : angle 1.04493 (12049) hydrogen bonds : bond 0.02718 ( 327) hydrogen bonds : angle 4.70731 ( 909) metal coordination : bond 0.00084 ( 3) metal coordination : angle 42.00050 ( 9) Misc. bond : bond 0.11486 ( 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 107 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.367 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: 0.8908 (OUTLIER) cc_final: 0.8408 (mtt) REVERT: A 192 SER cc_start: 0.8847 (p) cc_final: 0.8628 (p) REVERT: A 211 ASP cc_start: 0.8965 (t0) cc_final: 0.8132 (t0) REVERT: B 91 LYS cc_start: 0.9270 (OUTLIER) cc_final: 0.8776 (mppt) REVERT: B 94 ARG cc_start: 0.8772 (mtm180) cc_final: 0.8345 (mtm180) REVERT: B 112 MET cc_start: 0.8249 (ttp) cc_final: 0.8010 (ttp) REVERT: B 136 GLU cc_start: 0.8491 (mp0) cc_final: 0.8079 (mp0) REVERT: C 139 MET cc_start: 0.9229 (mmp) cc_final: 0.8863 (mmp) REVERT: C 395 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.8096 (ttt) REVERT: C 443 LYS cc_start: 0.8572 (mmpt) cc_final: 0.7775 (mttp) outliers start: 14 outliers final: 9 residues processed: 99 average time/residue: 0.6548 time to fit residues: 69.0749 Evaluate side-chains 100 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 91 LYS Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 158 VAL 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 62 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 82 optimal weight: 0.0030 chunk 33 optimal weight: 0.9980 chunk 12 optimal weight: 0.0870 overall best weight: 0.5568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 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 = 0.3098 r_free = 0.3098 target = 0.080149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.063928 restraints weight = 16822.932| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 2.69 r_work: 0.2689 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2564 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.250 8828 Z= 0.143 Angle : 1.555 82.987 12058 Z= 0.408 Chirality : 0.060 1.493 1275 Planarity : 0.005 0.063 1564 Dihedral : 8.671 87.926 1289 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.70 % Allowed : 24.46 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.26), residues: 1081 helix: 2.09 (0.28), residues: 382 sheet: -0.54 (0.58), residues: 83 loop : -0.29 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 264 TYR 0.009 0.001 TYR A 443 PHE 0.026 0.001 PHE C 210 TRP 0.007 0.001 TRP A 51 HIS 0.002 0.000 HIS C 200 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 8813) covalent geometry : angle 1.04766 (12049) hydrogen bonds : bond 0.02691 ( 327) hydrogen bonds : angle 4.67301 ( 909) metal coordination : bond 0.00037 ( 3) metal coordination : angle 42.08296 ( 9) Misc. bond : bond 0.11161 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2853.42 seconds wall clock time: 49 minutes 26.56 seconds (2966.56 seconds total)