Starting phenix.real_space_refine on Wed Apr 30 05:44:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jej_36190/04_2025/8jej_36190.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jej_36190/04_2025/8jej_36190.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jej_36190/04_2025/8jej_36190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jej_36190/04_2025/8jej_36190.map" model { file = "/net/cci-nas-00/data/ceres_data/8jej_36190/04_2025/8jej_36190.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jej_36190/04_2025/8jej_36190.cif" } resolution = 2.5 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= 0.002 sd= 0.047 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 5421 2.51 5 N 1490 2.21 5 O 1639 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8604 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4167 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 503} Chain: "B" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1080 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "C" Number of atoms: 3130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3130 Classifications: {'peptide': 413} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 387} 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 1767 SG CYS A 226 52.668 65.790 36.133 1.00 17.16 S ATOM 1738 SG CYS A 222 53.574 70.572 32.001 1.00 21.97 S ATOM 1698 SG CYS A 216 52.124 65.227 29.426 1.00 25.68 S Time building chain proxies: 4.93, per 1000 atoms: 0.57 Number of scatterers: 8604 At special positions: 0 Unit cell: (103.53, 109.62, 76.56, 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 1639 8.00 N 1490 7.00 C 5421 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: 2.69 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S A 602 " pdb="FE1 F3S A 602 " - pdb=" SG CYS A 226 " pdb="FE4 F3S A 602 " - pdb=" SG CYS A 216 " pdb="FE3 F3S A 602 " - pdb=" SG CYS A 222 " Number of angles added : 9 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2012 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 8 sheets defined 41.1% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 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: 3.609A pdb=" N LYS A 97 " --> pdb=" O THR A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 111 removed outlier: 3.744A pdb=" N TRP A 111 " --> pdb=" O THR A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 123 Processing helix chain 'A' and resid 124 through 130 Processing helix chain 'A' and resid 138 through 154 Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 181 through 194 Processing helix chain 'A' and resid 234 through 244 Processing helix chain 'A' and resid 292 through 301 Processing helix chain 'A' and resid 355 through 360 removed outlier: 3.614A pdb=" N SER A 359 " --> pdb=" O ASP A 356 " (cutoff:3.500A) 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: 4.243A pdb=" N VAL A 444 " --> pdb=" O VAL A 440 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE A 450 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 514 Processing helix chain 'A' and resid 522 through 542 Processing helix chain 'B' and resid 49 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 168 through 172 Processing helix chain 'C' and resid 41 through 50 Processing helix chain 'C' and resid 52 through 57 removed outlier: 3.883A pdb=" N HIS C 56 " --> pdb=" O CYS C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 106 removed outlier: 3.532A pdb=" N GLY C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 127 through 142 removed outlier: 4.015A pdb=" N VAL C 142 " --> pdb=" O ILE C 138 " (cutoff:3.500A) 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: 3.870A 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 removed outlier: 3.508A pdb=" N LEU C 278 " --> pdb=" O LEU C 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 275 through 278' Processing helix chain 'C' and resid 279 through 291 Processing helix chain 'C' and resid 317 through 324 removed outlier: 3.915A 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 373 through 383 Processing helix chain 'C' and resid 408 through 423 Processing helix chain 'C' and resid 431 through 440 Processing helix chain 'C' and resid 445 through 451 Processing sheet with id=AA1, first strand: chain 'A' and resid 247 through 249 removed outlier: 6.825A pdb=" N LEU A 34 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL A 10 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N LEU A 36 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE A 12 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ASP A 9 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N VAL A 286 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL A 11 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA A 282 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N THR A 266 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE A 265 " --> pdb=" O THR A 259 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THR A 259 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA A 267 " --> pdb=" O MET A 257 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N MET A 257 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N SER A 269 " --> pdb=" O TYR A 255 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 247 through 249 removed outlier: 6.825A pdb=" N LEU A 34 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL A 10 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N LEU A 36 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE A 12 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ASP A 9 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N VAL A 286 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL A 11 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N PHE A 507 " --> pdb=" O LYS A 283 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N PHE A 285 " --> pdb=" O PHE A 507 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.404A pdb=" N ILE A 87 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N HIS A 433 " --> pdb=" O SER A 422 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 156 through 157 Processing sheet with id=AA5, first strand: chain 'A' and resid 198 through 200 removed outlier: 5.479A pdb=" N SER A 347 " --> pdb=" O TYR A 368 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TYR A 368 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 366 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY A 328 " --> pdb=" O MET A 469 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N MET A 469 " --> pdb=" O GLY A 328 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N SER A 330 " --> pdb=" O ILE A 467 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE A 467 " --> pdb=" O SER A 330 " (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 384 through 388 317 hydrogen bonds defined for protein. 867 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: 2.38 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.76: 8745 1.76 - 2.30: 90 2.30 - 2.85: 0 2.85 - 3.39: 0 3.39 - 3.93: 3 Bond restraints: 8838 Sorted by residual: bond pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " ideal model delta sigma weight residual 2.300 3.928 -1.628 2.00e-02 2.50e+03 6.63e+03 bond pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " ideal model delta sigma weight residual 2.258 3.816 -1.558 2.00e-02 2.50e+03 6.06e+03 bond pdb=" S4 F3S A 602 " pdb="FE1 F3S A 602 " ideal model delta sigma weight residual 2.233 3.786 -1.553 2.00e-02 2.50e+03 6.03e+03 bond pdb=" C2D HEC C 502 " pdb=" C3D HEC C 502 " ideal model delta sigma weight residual 1.544 1.331 0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C2D HEC C 503 " pdb=" C3D HEC C 503 " ideal model delta sigma weight residual 1.544 1.332 0.212 2.00e-02 2.50e+03 1.12e+02 ... (remaining 8833 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.50: 12061 9.50 - 19.00: 10 19.00 - 28.50: 1 28.50 - 38.00: 8 38.00 - 47.50: 2 Bond angle restraints: 12082 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 67.25 47.50 3.00e+00 1.11e-01 2.51e+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 67.92 44.67 3.00e+00 1.11e-01 2.22e+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 68.73 34.53 3.00e+00 1.11e-01 1.32e+02 angle pdb=" S1 F3S A 602 " pdb="FE3 F3S A 602 " pdb=" S2 F3S A 602 " ideal model delta sigma weight residual 103.25 69.61 33.64 3.00e+00 1.11e-01 1.26e+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 39.35 32.74 3.00e+00 1.11e-01 1.19e+02 ... (remaining 12077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 4991 35.83 - 71.65: 215 71.65 - 107.47: 18 107.47 - 143.30: 1 143.30 - 179.12: 1 Dihedral angle restraints: 5226 sinusoidal: 2074 harmonic: 3152 Sorted by residual: dihedral pdb=" CA PHE A 80 " pdb=" C PHE A 80 " pdb=" N PRO A 81 " pdb=" CA PRO A 81 " ideal model delta harmonic sigma weight residual -180.00 -105.59 -74.41 0 5.00e+00 4.00e-02 2.21e+02 dihedral pdb=" C27 U10 C 504 " pdb=" C28 U10 C 504 " pdb=" C29 U10 C 504 " pdb=" C31 U10 C 504 " ideal model delta sinusoidal sigma weight residual 181.72 2.59 179.12 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C2C HEC C 501 " pdb=" C3C HEC C 501 " pdb=" CAC HEC C 501 " pdb=" CBC HEC C 501 " ideal model delta sinusoidal sigma weight residual 60.00 -11.17 71.17 2 1.00e+01 1.00e-02 4.30e+01 ... (remaining 5223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.460: 1276 3.460 - 6.920: 0 6.920 - 10.380: 0 10.380 - 13.840: 0 13.840 - 17.300: 1 Chirality restraints: 1277 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 -6.53 17.30 2.00e-01 2.50e+01 7.48e+03 chirality pdb=" CB ILE C 393 " pdb=" CA ILE C 393 " pdb=" CG1 ILE C 393 " pdb=" CG2 ILE C 393 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.44e+00 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 2.51 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 1274 not shown) Planarity restraints: 1569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 U10 C 504 " 0.013 2.00e-02 2.50e+03 1.00e-01 1.75e+02 pdb=" C1M U10 C 504 " -0.117 2.00e-02 2.50e+03 pdb=" C2 U10 C 504 " 0.092 2.00e-02 2.50e+03 pdb=" C3 U10 C 504 " 0.053 2.00e-02 2.50e+03 pdb=" C4 U10 C 504 " -0.184 2.00e-02 2.50e+03 pdb=" C5 U10 C 504 " 0.046 2.00e-02 2.50e+03 pdb=" C6 U10 C 504 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 80 " 0.125 5.00e-02 4.00e+02 1.92e-01 5.92e+01 pdb=" N PRO A 81 " -0.333 5.00e-02 4.00e+02 pdb=" CA PRO A 81 " 0.115 5.00e-02 4.00e+02 pdb=" CD PRO A 81 " 0.093 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CBD HEC C 501 " -0.032 2.00e-02 2.50e+03 6.75e-02 4.56e+01 pdb=" CGD HEC C 501 " 0.117 2.00e-02 2.50e+03 pdb=" O1D HEC C 501 " -0.042 2.00e-02 2.50e+03 pdb=" O2D HEC C 501 " -0.043 2.00e-02 2.50e+03 ... (remaining 1566 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 307 2.71 - 3.26: 8611 3.26 - 3.81: 15309 3.81 - 4.35: 20471 4.35 - 4.90: 32177 Nonbonded interactions: 76875 Sorted by model distance: nonbonded pdb=" N GLU C 129 " pdb=" OE1 GLU C 129 " model vdw 2.165 3.120 nonbonded pdb=" OH TYR A 139 " pdb=" O PRO A 168 " model vdw 2.243 3.040 nonbonded pdb=" S4 F3S A 602 " pdb="FE4 F3S A 602 " model vdw 2.259 2.688 nonbonded pdb=" S3 F3S A 602 " pdb="FE3 F3S A 602 " model vdw 2.261 2.688 nonbonded pdb=" S1 F3S A 602 " pdb="FE1 F3S A 602 " model vdw 2.262 2.688 ... (remaining 76870 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: 1.680 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: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.220 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 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 1.628 8853 Z= 1.508 Angle : 1.356 47.497 12091 Z= 0.502 Chirality : 0.486 17.300 1277 Planarity : 0.008 0.192 1569 Dihedral : 18.651 179.124 3214 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.60 % Allowed : 16.70 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % 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: 0.11 (0.25), residues: 1083 helix: 1.15 (0.27), residues: 379 sheet: 0.08 (0.54), residues: 92 loop : -0.60 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 338 HIS 0.005 0.001 HIS A 76 PHE 0.019 0.001 PHE A 270 TYR 0.023 0.001 TYR A 443 ARG 0.002 0.000 ARG B 94 Details of bonding type rmsd hydrogen bonds : bond 0.13801 ( 314) hydrogen bonds : angle 6.84134 ( 867) metal coordination : bond 0.00068 ( 3) metal coordination : angle 8.70977 ( 9) covalent geometry : bond 0.03034 ( 8838) covalent geometry : angle 1.33580 (12082) Misc. bond : bond 0.06444 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 1.483 Fit side-chains revert: symmetry clash REVERT: B 164 HIS cc_start: 0.7121 (OUTLIER) cc_final: 0.6242 (m-70) REVERT: C 187 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.6888 (m-30) outliers start: 23 outliers final: 21 residues processed: 123 average time/residue: 1.4633 time to fit residues: 191.8909 Evaluate side-chains 127 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 449 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 98 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN A 501 HIS B 138 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.127072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.101871 restraints weight = 8934.334| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.35 r_work: 0.3077 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.0609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.186 8853 Z= 0.227 Angle : 1.624 71.701 12091 Z= 0.519 Chirality : 0.098 3.060 1277 Planarity : 0.006 0.135 1569 Dihedral : 12.184 134.234 1322 Min Nonbonded Distance : 1.474 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.16 % Favored : 95.75 % Rotamer: Outliers : 3.05 % Allowed : 16.03 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % 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: 0.38 (0.26), residues: 1083 helix: 1.32 (0.27), residues: 385 sheet: 0.65 (0.58), residues: 82 loop : -0.47 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 338 HIS 0.005 0.001 HIS A 76 PHE 0.017 0.002 PHE A 80 TYR 0.017 0.002 TYR A 443 ARG 0.001 0.000 ARG A 499 Details of bonding type rmsd hydrogen bonds : bond 0.04636 ( 314) hydrogen bonds : angle 5.63664 ( 867) metal coordination : bond 0.02275 ( 3) metal coordination : angle 31.32207 ( 9) covalent geometry : bond 0.00503 ( 8838) covalent geometry : angle 1.38125 (12082) Misc. bond : bond 0.03751 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.882 Fit side-chains REVERT: A 152 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8028 (tp30) REVERT: B 154 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7860 (mtt180) REVERT: B 164 HIS cc_start: 0.7361 (OUTLIER) cc_final: 0.6221 (m-70) REVERT: C 118 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.7055 (tpt) REVERT: C 302 THR cc_start: 0.7308 (OUTLIER) cc_final: 0.7018 (t) outliers start: 27 outliers final: 12 residues processed: 124 average time/residue: 1.3589 time to fit residues: 178.7227 Evaluate side-chains 124 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 4 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 33 optimal weight: 0.0770 chunk 53 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 10 optimal weight: 2.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 ASN A 351 ASN A 501 HIS B 138 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.130191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.105820 restraints weight = 9086.088| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.35 r_work: 0.3122 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 8853 Z= 0.150 Angle : 1.440 80.707 12091 Z= 0.417 Chirality : 0.061 1.484 1277 Planarity : 0.005 0.103 1569 Dihedral : 11.077 90.685 1296 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.60 % Favored : 96.31 % Rotamer: Outliers : 2.82 % Allowed : 17.16 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % 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: 0.53 (0.26), residues: 1083 helix: 1.47 (0.27), residues: 391 sheet: 1.05 (0.62), residues: 73 loop : -0.45 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 51 HIS 0.004 0.001 HIS A 76 PHE 0.015 0.001 PHE A 270 TYR 0.016 0.001 TYR A 443 ARG 0.005 0.000 ARG B 94 Details of bonding type rmsd hydrogen bonds : bond 0.03717 ( 314) hydrogen bonds : angle 5.25549 ( 867) metal coordination : bond 0.00412 ( 3) metal coordination : angle 35.50303 ( 9) covalent geometry : bond 0.00337 ( 8838) covalent geometry : angle 1.06562 (12082) Misc. bond : bond 0.02942 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.947 Fit side-chains REVERT: A 152 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7980 (tp30) REVERT: A 189 GLU cc_start: 0.7346 (pt0) cc_final: 0.7040 (tp30) REVERT: A 468 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7977 (mt-10) REVERT: B 154 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7829 (mtt180) REVERT: B 164 HIS cc_start: 0.7333 (OUTLIER) cc_final: 0.5846 (m-70) REVERT: C 110 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7505 (p0) REVERT: C 187 ASP cc_start: 0.7582 (OUTLIER) cc_final: 0.7257 (t0) outliers start: 25 outliers final: 12 residues processed: 132 average time/residue: 1.4975 time to fit residues: 209.9883 Evaluate side-chains 130 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 315 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 104 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 73 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN A 476 ASN A 501 HIS B 138 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.122766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.097549 restraints weight = 9134.678| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.36 r_work: 0.3017 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.186 8853 Z= 0.310 Angle : 1.542 79.458 12091 Z= 0.489 Chirality : 0.069 1.519 1277 Planarity : 0.007 0.112 1569 Dihedral : 11.980 84.470 1296 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.99 % Favored : 94.92 % Rotamer: Outliers : 3.27 % Allowed : 16.82 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % 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: 0.08 (0.25), residues: 1083 helix: 0.99 (0.26), residues: 385 sheet: -0.04 (0.53), residues: 94 loop : -0.51 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 338 HIS 0.008 0.002 HIS A 76 PHE 0.028 0.002 PHE A 80 TYR 0.013 0.002 TYR A 232 ARG 0.007 0.001 ARG B 94 Details of bonding type rmsd hydrogen bonds : bond 0.05416 ( 314) hydrogen bonds : angle 5.72434 ( 867) metal coordination : bond 0.00643 ( 3) metal coordination : angle 36.25739 ( 9) covalent geometry : bond 0.00743 ( 8838) covalent geometry : angle 1.18276 (12082) Misc. bond : bond 0.07773 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.850 Fit side-chains REVERT: A 276 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7121 (tp40) REVERT: B 135 ASP cc_start: 0.7559 (OUTLIER) cc_final: 0.7293 (m-30) REVERT: C 64 PHE cc_start: 0.6725 (OUTLIER) cc_final: 0.5482 (p90) REVERT: C 187 ASP cc_start: 0.7565 (OUTLIER) cc_final: 0.7272 (t0) REVERT: C 302 THR cc_start: 0.7213 (OUTLIER) cc_final: 0.6914 (t) outliers start: 29 outliers final: 18 residues processed: 122 average time/residue: 1.4022 time to fit residues: 181.1269 Evaluate side-chains 121 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 64 PHE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 80 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN A 501 HIS B 138 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.127038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.102228 restraints weight = 9096.622| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.36 r_work: 0.3069 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.168 8853 Z= 0.164 Angle : 1.459 80.841 12091 Z= 0.429 Chirality : 0.063 1.530 1277 Planarity : 0.006 0.089 1569 Dihedral : 11.089 89.054 1296 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.88 % Favored : 96.03 % Rotamer: Outliers : 3.16 % Allowed : 17.38 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % 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: 0.42 (0.26), residues: 1083 helix: 1.29 (0.27), residues: 388 sheet: 1.15 (0.63), residues: 70 loop : -0.45 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 51 HIS 0.005 0.001 HIS A 110 PHE 0.015 0.001 PHE A 80 TYR 0.014 0.001 TYR A 443 ARG 0.008 0.000 ARG B 94 Details of bonding type rmsd hydrogen bonds : bond 0.03970 ( 314) hydrogen bonds : angle 5.31191 ( 867) metal coordination : bond 0.00328 ( 3) metal coordination : angle 35.43143 ( 9) covalent geometry : bond 0.00370 ( 8838) covalent geometry : angle 1.09260 (12082) Misc. bond : bond 0.07262 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.871 Fit side-chains REVERT: A 468 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7871 (mt-10) REVERT: B 164 HIS cc_start: 0.7711 (OUTLIER) cc_final: 0.6300 (m-70) REVERT: C 110 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7620 (p0) REVERT: C 187 ASP cc_start: 0.7582 (OUTLIER) cc_final: 0.7281 (t0) REVERT: C 302 THR cc_start: 0.7307 (OUTLIER) cc_final: 0.7022 (t) REVERT: C 395 MET cc_start: 0.8901 (ttt) cc_final: 0.8604 (ttt) outliers start: 28 outliers final: 14 residues processed: 123 average time/residue: 1.3152 time to fit residues: 171.8837 Evaluate side-chains 121 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 449 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 81 optimal weight: 4.9990 chunk 46 optimal weight: 0.0270 chunk 40 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN A 501 HIS B 138 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.129081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.105077 restraints weight = 9124.461| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.31 r_work: 0.3103 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.175 8853 Z= 0.149 Angle : 1.434 81.297 12091 Z= 0.417 Chirality : 0.062 1.505 1277 Planarity : 0.005 0.080 1569 Dihedral : 10.568 87.180 1296 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.97 % Favored : 95.94 % Rotamer: Outliers : 3.05 % Allowed : 17.95 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % 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: 0.53 (0.26), residues: 1083 helix: 1.45 (0.27), residues: 390 sheet: 1.05 (0.62), residues: 73 loop : -0.44 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 51 HIS 0.004 0.001 HIS A 76 PHE 0.015 0.001 PHE A 270 TYR 0.014 0.001 TYR A 443 ARG 0.007 0.000 ARG B 94 Details of bonding type rmsd hydrogen bonds : bond 0.03577 ( 314) hydrogen bonds : angle 5.10062 ( 867) metal coordination : bond 0.00352 ( 3) metal coordination : angle 34.72326 ( 9) covalent geometry : bond 0.00332 ( 8838) covalent geometry : angle 1.07745 (12082) Misc. bond : bond 0.05793 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: A 247 LYS cc_start: 0.8618 (tttp) cc_final: 0.8337 (tttm) REVERT: A 276 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7103 (tp40) REVERT: A 468 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7882 (mt-10) REVERT: B 154 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7832 (mtt180) REVERT: B 164 HIS cc_start: 0.7536 (OUTLIER) cc_final: 0.6119 (m-70) REVERT: C 110 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7689 (p0) REVERT: C 143 LYS cc_start: 0.7161 (ttpp) cc_final: 0.6937 (tttp) REVERT: C 187 ASP cc_start: 0.7616 (OUTLIER) cc_final: 0.7297 (t0) REVERT: C 302 THR cc_start: 0.7360 (OUTLIER) cc_final: 0.7099 (t) outliers start: 27 outliers final: 12 residues processed: 126 average time/residue: 1.3458 time to fit residues: 180.5144 Evaluate side-chains 125 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 50 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN A 476 ASN A 501 HIS B 138 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.124101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.098992 restraints weight = 9150.853| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.36 r_work: 0.3034 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.222 8853 Z= 0.262 Angle : 1.528 80.028 12091 Z= 0.468 Chirality : 0.068 1.524 1277 Planarity : 0.006 0.095 1569 Dihedral : 11.361 85.156 1296 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.89 % Favored : 95.01 % Rotamer: Outliers : 3.84 % Allowed : 17.04 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % 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: 0.19 (0.25), residues: 1083 helix: 1.14 (0.27), residues: 387 sheet: 0.12 (0.54), residues: 90 loop : -0.51 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 338 HIS 0.007 0.001 HIS A 76 PHE 0.030 0.002 PHE A 80 TYR 0.017 0.002 TYR A 96 ARG 0.008 0.001 ARG B 94 Details of bonding type rmsd hydrogen bonds : bond 0.04900 ( 314) hydrogen bonds : angle 5.49716 ( 867) metal coordination : bond 0.00480 ( 3) metal coordination : angle 36.62717 ( 9) covalent geometry : bond 0.00622 ( 8838) covalent geometry : angle 1.15647 (12082) Misc. bond : bond 0.08595 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 104 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: A 276 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7103 (tp40) REVERT: A 468 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7864 (mt-10) REVERT: C 64 PHE cc_start: 0.6707 (OUTLIER) cc_final: 0.5287 (p90) REVERT: C 110 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7640 (p0) REVERT: C 187 ASP cc_start: 0.7581 (OUTLIER) cc_final: 0.7259 (t0) REVERT: C 302 THR cc_start: 0.7247 (OUTLIER) cc_final: 0.6951 (t) REVERT: C 329 LEU cc_start: 0.6425 (OUTLIER) cc_final: 0.6077 (pp) outliers start: 34 outliers final: 18 residues processed: 127 average time/residue: 1.3530 time to fit residues: 182.4462 Evaluate side-chains 128 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 64 PHE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 449 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 70 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 85 optimal weight: 0.0970 chunk 106 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN A 501 HIS B 138 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.127989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.103289 restraints weight = 9182.692| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.37 r_work: 0.3091 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.201 8853 Z= 0.157 Angle : 1.463 80.925 12091 Z= 0.425 Chirality : 0.063 1.530 1277 Planarity : 0.005 0.080 1569 Dihedral : 10.684 89.301 1296 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.88 % Favored : 96.03 % Rotamer: Outliers : 3.61 % Allowed : 17.49 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % 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: 0.48 (0.26), residues: 1083 helix: 1.41 (0.27), residues: 388 sheet: 0.96 (0.62), residues: 73 loop : -0.45 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 51 HIS 0.005 0.001 HIS A 76 PHE 0.017 0.002 PHE A 80 TYR 0.023 0.001 TYR A 79 ARG 0.009 0.000 ARG B 94 Details of bonding type rmsd hydrogen bonds : bond 0.03765 ( 314) hydrogen bonds : angle 5.19832 ( 867) metal coordination : bond 0.00319 ( 3) metal coordination : angle 36.06052 ( 9) covalent geometry : bond 0.00352 ( 8838) covalent geometry : angle 1.08377 (12082) Misc. bond : bond 0.06871 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 276 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7116 (tp40) REVERT: A 468 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7852 (mt-10) REVERT: B 154 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7824 (mtt180) REVERT: B 164 HIS cc_start: 0.7757 (OUTLIER) cc_final: 0.6157 (m-70) REVERT: C 110 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7646 (p0) REVERT: C 129 GLU cc_start: 0.7807 (mp0) cc_final: 0.7493 (mp0) REVERT: C 182 HIS cc_start: 0.7772 (m-70) cc_final: 0.7549 (m-70) REVERT: C 187 ASP cc_start: 0.7602 (OUTLIER) cc_final: 0.7302 (t0) REVERT: C 302 THR cc_start: 0.7325 (OUTLIER) cc_final: 0.7052 (t) outliers start: 32 outliers final: 17 residues processed: 125 average time/residue: 1.5066 time to fit residues: 199.9648 Evaluate side-chains 128 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 449 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 57 optimal weight: 0.3980 chunk 94 optimal weight: 2.9990 chunk 50 optimal weight: 0.0670 chunk 29 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 95 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.6522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN A 476 ASN B 138 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.129728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.105527 restraints weight = 9206.365| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.36 r_work: 0.3116 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.174 8853 Z= 0.149 Angle : 1.450 80.830 12091 Z= 0.417 Chirality : 0.063 1.544 1277 Planarity : 0.005 0.076 1569 Dihedral : 10.332 86.739 1295 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.34 % Favored : 95.57 % Rotamer: Outliers : 2.82 % Allowed : 18.28 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % 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: 0.58 (0.26), residues: 1083 helix: 1.53 (0.27), residues: 390 sheet: 0.98 (0.62), residues: 73 loop : -0.42 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 51 HIS 0.004 0.001 HIS A 76 PHE 0.015 0.001 PHE A 270 TYR 0.025 0.001 TYR A 79 ARG 0.009 0.000 ARG B 94 Details of bonding type rmsd hydrogen bonds : bond 0.03497 ( 314) hydrogen bonds : angle 5.05707 ( 867) metal coordination : bond 0.00310 ( 3) metal coordination : angle 35.74718 ( 9) covalent geometry : bond 0.00332 ( 8838) covalent geometry : angle 1.07358 (12082) Misc. bond : bond 0.05270 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 276 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7092 (tp40) REVERT: A 468 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7869 (mt-10) REVERT: B 154 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7818 (mtt180) REVERT: B 164 HIS cc_start: 0.7623 (OUTLIER) cc_final: 0.6065 (m-70) REVERT: C 110 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7643 (p0) REVERT: C 129 GLU cc_start: 0.7814 (mp0) cc_final: 0.7490 (mp0) REVERT: C 143 LYS cc_start: 0.7133 (ttpp) cc_final: 0.6902 (tttp) REVERT: C 187 ASP cc_start: 0.7585 (OUTLIER) cc_final: 0.7254 (t0) REVERT: C 302 THR cc_start: 0.7277 (OUTLIER) cc_final: 0.7010 (t) outliers start: 25 outliers final: 17 residues processed: 129 average time/residue: 1.6280 time to fit residues: 225.5735 Evaluate side-chains 133 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 449 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 87 optimal weight: 9.9990 chunk 46 optimal weight: 0.3980 chunk 52 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN B 138 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.129454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.105132 restraints weight = 9126.276| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.33 r_work: 0.3097 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.192 8853 Z= 0.154 Angle : 1.455 80.637 12091 Z= 0.420 Chirality : 0.063 1.546 1277 Planarity : 0.005 0.077 1569 Dihedral : 10.418 87.347 1294 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.16 % Favored : 95.75 % Rotamer: Outliers : 2.82 % Allowed : 18.28 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % 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: 0.60 (0.26), residues: 1083 helix: 1.53 (0.27), residues: 390 sheet: 0.97 (0.62), residues: 73 loop : -0.39 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 51 HIS 0.004 0.001 HIS A 76 PHE 0.015 0.001 PHE C 210 TYR 0.027 0.001 TYR A 79 ARG 0.009 0.000 ARG B 94 Details of bonding type rmsd hydrogen bonds : bond 0.03587 ( 314) hydrogen bonds : angle 5.06309 ( 867) metal coordination : bond 0.00372 ( 3) metal coordination : angle 35.76759 ( 9) covalent geometry : bond 0.00346 ( 8838) covalent geometry : angle 1.07999 (12082) Misc. bond : bond 0.05956 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 276 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7108 (tp40) REVERT: A 468 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7838 (mt-10) REVERT: B 154 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7829 (mtt180) REVERT: B 164 HIS cc_start: 0.7707 (OUTLIER) cc_final: 0.6099 (m-70) REVERT: C 110 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7665 (p0) REVERT: C 129 GLU cc_start: 0.7835 (mp0) cc_final: 0.7523 (mp0) REVERT: C 187 ASP cc_start: 0.7532 (OUTLIER) cc_final: 0.7214 (t0) REVERT: C 302 THR cc_start: 0.7263 (OUTLIER) cc_final: 0.7002 (t) outliers start: 25 outliers final: 17 residues processed: 126 average time/residue: 1.4461 time to fit residues: 193.1363 Evaluate side-chains 134 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 449 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 63 optimal weight: 3.9990 chunk 6 optimal weight: 0.1980 chunk 11 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.128530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.104351 restraints weight = 9267.264| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.32 r_work: 0.3082 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.193 8853 Z= 0.165 Angle : 1.460 80.243 12091 Z= 0.425 Chirality : 0.064 1.562 1277 Planarity : 0.006 0.078 1569 Dihedral : 10.505 88.681 1294 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.43 % Favored : 95.48 % Rotamer: Outliers : 2.82 % Allowed : 18.17 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % 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: 0.56 (0.26), residues: 1083 helix: 1.51 (0.27), residues: 390 sheet: 0.90 (0.62), residues: 73 loop : -0.42 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 338 HIS 0.005 0.001 HIS A 76 PHE 0.017 0.002 PHE A 80 TYR 0.028 0.002 TYR A 79 ARG 0.008 0.000 ARG B 94 Details of bonding type rmsd hydrogen bonds : bond 0.03721 ( 314) hydrogen bonds : angle 5.09846 ( 867) metal coordination : bond 0.00425 ( 3) metal coordination : angle 35.74310 ( 9) covalent geometry : bond 0.00373 ( 8838) covalent geometry : angle 1.08673 (12082) Misc. bond : bond 0.05977 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7122.50 seconds wall clock time: 125 minutes 17.00 seconds (7517.00 seconds total)