Starting phenix.real_space_refine on Mon May 12 18:38:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jej_36190/05_2025/8jej_36190.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jej_36190/05_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_36190/05_2025/8jej_36190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jej_36190/05_2025/8jej_36190.map" model { file = "/net/cci-nas-00/data/ceres_data/8jej_36190/05_2025/8jej_36190.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jej_36190/05_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 5.76, per 1000 atoms: 0.67 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: 2.50 Conformation dependent library (CDL) restraints added in 1.1 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: 0.94 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: 2.36 Time building geometry restraints manager: 2.79 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: 1.470 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.190 Find NCS groups from input model: 0.080 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:10.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.130 ------------------------------------------------------------------------------- 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 : 0.934 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: 1.2017 time to fit residues: 157.8468 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 : 0.987 ------------------------------------------------------------------------------- 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 = 0.127071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.101877 restraints weight = 8934.207| |-----------------------------------------------------------------------------| 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: 0.8578 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 71.705 12091 Z= 0.519 Chirality : 0.098 3.060 1277 Planarity : 0.006 0.135 1569 Dihedral : 12.184 134.240 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 B 94 Details of bonding type rmsd hydrogen bonds : bond 0.04636 ( 314) hydrogen bonds : angle 5.63666 ( 867) metal coordination : bond 0.02275 ( 3) metal coordination : angle 31.32070 ( 9) covalent geometry : bond 0.00503 ( 8838) covalent geometry : angle 1.38126 (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 : 0.923 Fit side-chains REVERT: A 152 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8029 (tp30) REVERT: B 154 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7859 (mtt180) REVERT: B 164 HIS cc_start: 0.7360 (OUTLIER) cc_final: 0.6218 (m-70) REVERT: C 118 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.7069 (tpt) REVERT: C 302 THR cc_start: 0.7314 (OUTLIER) cc_final: 0.7024 (t) outliers start: 27 outliers final: 12 residues processed: 124 average time/residue: 1.3564 time to fit residues: 178.5490 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 : 1.083 ------------------------------------------------------------------------------- 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: 0.9990 chunk 66 optimal weight: 0.0770 chunk 33 optimal weight: 0.0270 chunk 53 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 80 optimal weight: 8.9990 chunk 37 optimal weight: 0.0060 chunk 10 optimal weight: 2.9990 overall best weight: 0.2412 ------------------------------------------------------------------------------- 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 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 = 0.3484 r_free = 0.3484 target = 0.132197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.108171 restraints weight = 9151.933| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.35 r_work: 0.3153 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.117 8853 Z= 0.144 Angle : 1.448 80.830 12091 Z= 0.411 Chirality : 0.061 1.501 1277 Planarity : 0.005 0.101 1569 Dihedral : 10.853 88.607 1296 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.37 % Allowed : 17.49 % Favored : 80.14 % 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: 0.62 (0.26), residues: 1083 helix: 1.54 (0.27), residues: 391 sheet: 1.10 (0.62), residues: 73 loop : -0.40 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 51 HIS 0.003 0.001 HIS A 110 PHE 0.013 0.001 PHE A 270 TYR 0.017 0.001 TYR A 443 ARG 0.007 0.000 ARG B 94 Details of bonding type rmsd hydrogen bonds : bond 0.03450 ( 314) hydrogen bonds : angle 5.15410 ( 867) metal coordination : bond 0.00628 ( 3) metal coordination : angle 36.27638 ( 9) covalent geometry : bond 0.00317 ( 8838) covalent geometry : angle 1.05770 (12082) Misc. bond : bond 0.02665 ( 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 140 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.927 Fit side-chains REVERT: A 152 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7945 (tp30) REVERT: A 189 GLU cc_start: 0.7296 (pt0) cc_final: 0.7021 (tp30) REVERT: A 468 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7949 (mt-10) REVERT: B 164 HIS cc_start: 0.7158 (OUTLIER) cc_final: 0.5353 (m-70) REVERT: C 110 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.7533 (p0) REVERT: C 187 ASP cc_start: 0.7613 (OUTLIER) cc_final: 0.7335 (t0) outliers start: 21 outliers final: 9 residues processed: 129 average time/residue: 1.3297 time to fit residues: 182.2198 Evaluate side-chains 126 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 152 GLU 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 A residue 484 ILE 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: 2.9990 chunk 0 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 73 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.3430 r_free = 0.3430 target = 0.126564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.102068 restraints weight = 9154.540| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.31 r_work: 0.3089 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.160 8853 Z= 0.198 Angle : 1.457 81.426 12091 Z= 0.440 Chirality : 0.064 1.482 1277 Planarity : 0.006 0.097 1569 Dihedral : 11.171 87.787 1296 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.52 % Favored : 95.38 % Rotamer: Outliers : 3.16 % Allowed : 17.16 % Favored : 79.68 % 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: 0.46 (0.26), residues: 1083 helix: 1.38 (0.27), residues: 387 sheet: 0.49 (0.58), residues: 83 loop : -0.39 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 338 HIS 0.006 0.001 HIS A 76 PHE 0.022 0.002 PHE A 80 TYR 0.013 0.002 TYR A 443 ARG 0.007 0.000 ARG B 94 Details of bonding type rmsd hydrogen bonds : bond 0.04365 ( 314) hydrogen bonds : angle 5.36967 ( 867) metal coordination : bond 0.00585 ( 3) metal coordination : angle 34.62875 ( 9) covalent geometry : bond 0.00462 ( 8838) covalent geometry : angle 1.10919 (12082) Misc. bond : bond 0.05507 ( 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 139 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.982 Fit side-chains REVERT: A 152 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7929 (tp30) REVERT: A 276 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7174 (tp40) REVERT: A 468 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7991 (mt-10) REVERT: B 154 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7882 (mtt180) REVERT: B 164 HIS cc_start: 0.7561 (OUTLIER) cc_final: 0.6470 (m-70) REVERT: C 187 ASP cc_start: 0.7590 (OUTLIER) cc_final: 0.7340 (t0) REVERT: C 302 THR cc_start: 0.7301 (OUTLIER) cc_final: 0.7043 (t) outliers start: 28 outliers final: 15 residues processed: 126 average time/residue: 1.3337 time to fit residues: 178.3630 Evaluate side-chains 131 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 276 GLN 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 484 ILE 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 B residue 183 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 449 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 80 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 48 optimal weight: 0.3980 chunk 96 optimal weight: 0.2980 chunk 17 optimal weight: 0.4980 chunk 62 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 47 optimal weight: 0.0270 chunk 92 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 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 = 0.3492 r_free = 0.3492 target = 0.131738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.108079 restraints weight = 9188.508| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.31 r_work: 0.3169 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.135 8853 Z= 0.137 Angle : 1.401 81.906 12091 Z= 0.407 Chirality : 0.061 1.478 1277 Planarity : 0.005 0.080 1569 Dihedral : 10.355 87.221 1296 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.79 % Favored : 96.12 % Rotamer: Outliers : 2.93 % Allowed : 17.61 % Favored : 79.46 % 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: 0.63 (0.26), residues: 1083 helix: 1.49 (0.27), residues: 396 sheet: 1.09 (0.63), residues: 73 loop : -0.36 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 51 HIS 0.003 0.001 HIS A 278 PHE 0.013 0.001 PHE A 270 TYR 0.021 0.001 TYR A 79 ARG 0.007 0.000 ARG B 94 Details of bonding type rmsd hydrogen bonds : bond 0.03319 ( 314) hydrogen bonds : angle 4.98954 ( 867) metal coordination : bond 0.00308 ( 3) metal coordination : angle 33.79998 ( 9) covalent geometry : bond 0.00302 ( 8838) covalent geometry : angle 1.05556 (12082) Misc. bond : bond 0.03956 ( 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 143 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 1.002 Fit side-chains REVERT: A 152 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7912 (tp30) REVERT: A 468 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7920 (mt-10) REVERT: B 154 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7748 (mtt180) REVERT: B 164 HIS cc_start: 0.7318 (OUTLIER) cc_final: 0.5425 (m-70) REVERT: C 110 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7655 (p0) REVERT: C 187 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7380 (t0) REVERT: C 443 LYS cc_start: 0.7919 (pttt) cc_final: 0.7463 (pttp) outliers start: 26 outliers final: 11 residues processed: 130 average time/residue: 1.3266 time to fit residues: 183.3511 Evaluate side-chains 129 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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 177 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 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 315 TYR 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: 2.9990 chunk 40 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.128362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.104290 restraints weight = 9125.341| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.30 r_work: 0.3116 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.190 8853 Z= 0.170 Angle : 1.441 81.555 12091 Z= 0.426 Chirality : 0.063 1.490 1277 Planarity : 0.005 0.081 1569 Dihedral : 10.652 89.627 1294 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.34 % Favored : 95.57 % Rotamer: Outliers : 2.71 % Allowed : 18.17 % Favored : 79.12 % 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: 1.49 (0.27), residues: 390 sheet: 1.04 (0.62), residues: 73 loop : -0.38 (0.25), residues: 620 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 0.018 0.002 PHE A 80 TYR 0.027 0.002 TYR A 79 ARG 0.009 0.000 ARG B 94 Details of bonding type rmsd hydrogen bonds : bond 0.03861 ( 314) hydrogen bonds : angle 5.12928 ( 867) metal coordination : bond 0.00399 ( 3) metal coordination : angle 34.48636 ( 9) covalent geometry : bond 0.00389 ( 8838) covalent geometry : angle 1.09181 (12082) Misc. bond : bond 0.05950 ( 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 136 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 1.019 Fit side-chains REVERT: A 152 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7924 (tp30) REVERT: A 384 MET cc_start: 0.8900 (mtp) cc_final: 0.8510 (mtp) REVERT: A 468 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7945 (mt-10) REVERT: B 135 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.7191 (m-30) REVERT: B 154 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7867 (mtt180) REVERT: B 164 HIS cc_start: 0.7557 (OUTLIER) cc_final: 0.6168 (m-70) REVERT: C 110 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7619 (p0) REVERT: C 187 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7266 (t0) outliers start: 24 outliers final: 13 residues processed: 125 average time/residue: 1.4137 time to fit residues: 187.4783 Evaluate side-chains 131 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 1.023 ------------------------------------------------------------------------------- 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 177 SER 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 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 135 ASP Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 183 PHE 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 315 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 50 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3460 r_free = 0.3460 target = 0.128932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.104767 restraints weight = 9161.066| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.33 r_work: 0.3126 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.184 8853 Z= 0.161 Angle : 1.434 81.386 12091 Z= 0.421 Chirality : 0.062 1.497 1277 Planarity : 0.005 0.078 1569 Dihedral : 10.555 88.465 1294 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.06 % Favored : 95.84 % Rotamer: Outliers : 2.82 % Allowed : 17.27 % Favored : 79.91 % 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: 0.61 (0.26), residues: 1083 helix: 1.53 (0.27), residues: 390 sheet: 1.03 (0.62), residues: 73 loop : -0.38 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 338 HIS 0.004 0.001 HIS A 76 PHE 0.016 0.001 PHE A 80 TYR 0.025 0.001 TYR A 79 ARG 0.008 0.000 ARG B 94 Details of bonding type rmsd hydrogen bonds : bond 0.03708 ( 314) hydrogen bonds : angle 5.10276 ( 867) metal coordination : bond 0.00381 ( 3) metal coordination : angle 34.50440 ( 9) covalent geometry : bond 0.00366 ( 8838) covalent geometry : angle 1.08163 (12082) Misc. bond : bond 0.05656 ( 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 135 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.912 Fit side-chains REVERT: A 152 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7919 (tp30) REVERT: A 276 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7113 (tp40) REVERT: B 154 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7874 (mtt180) REVERT: B 164 HIS cc_start: 0.7564 (OUTLIER) cc_final: 0.6241 (m-70) REVERT: C 110 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7627 (p0) REVERT: C 143 LYS cc_start: 0.7195 (ttpp) cc_final: 0.6968 (tttp) REVERT: C 187 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7298 (t0) outliers start: 25 outliers final: 14 residues processed: 125 average time/residue: 1.2994 time to fit residues: 172.4785 Evaluate side-chains 128 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.888 ------------------------------------------------------------------------------- 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 152 GLU 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 440 VAL 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 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 315 TYR 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: 6.9990 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- 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 = 0.3447 r_free = 0.3447 target = 0.127810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.103456 restraints weight = 9222.180| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.33 r_work: 0.3107 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.198 8853 Z= 0.178 Angle : 1.462 81.217 12091 Z= 0.431 Chirality : 0.064 1.502 1277 Planarity : 0.005 0.079 1569 Dihedral : 10.728 89.903 1294 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.71 % Favored : 95.20 % 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 : 0.10 % 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: 0.55 (0.26), residues: 1083 helix: 1.47 (0.27), residues: 390 sheet: 1.02 (0.62), residues: 73 loop : -0.42 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 338 HIS 0.005 0.001 HIS A 76 PHE 0.020 0.002 PHE A 80 TYR 0.027 0.002 TYR A 79 ARG 0.008 0.000 ARG B 94 Details of bonding type rmsd hydrogen bonds : bond 0.03949 ( 314) hydrogen bonds : angle 5.17385 ( 867) metal coordination : bond 0.00422 ( 3) metal coordination : angle 34.83737 ( 9) covalent geometry : bond 0.00406 ( 8838) covalent geometry : angle 1.11147 (12082) Misc. bond : bond 0.07782 ( 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 135 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: A 152 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7949 (tp30) REVERT: A 276 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7194 (tp40) REVERT: A 468 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7863 (mt-10) REVERT: B 164 HIS cc_start: 0.7619 (OUTLIER) cc_final: 0.6213 (m-70) REVERT: C 110 ASP cc_start: 0.8043 (OUTLIER) cc_final: 0.7663 (p0) REVERT: C 187 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7295 (t0) REVERT: C 395 MET cc_start: 0.8817 (ttt) cc_final: 0.8286 (ttt) outliers start: 28 outliers final: 15 residues processed: 123 average time/residue: 1.3278 time to fit residues: 173.3713 Evaluate side-chains 127 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.869 ------------------------------------------------------------------------------- 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 152 GLU 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 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 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 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: 0.7980 chunk 94 optimal weight: 0.0870 chunk 50 optimal weight: 0.0020 chunk 29 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 95 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.4766 ------------------------------------------------------------------------------- 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 = 0.3493 r_free = 0.3493 target = 0.131650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.108193 restraints weight = 9163.838| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.28 r_work: 0.3165 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.162 8853 Z= 0.139 Angle : 1.412 81.953 12091 Z= 0.410 Chirality : 0.061 1.482 1277 Planarity : 0.006 0.110 1569 Dihedral : 10.273 86.628 1294 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.48 % Allowed : 18.40 % Favored : 79.12 % 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: 0.72 (0.26), residues: 1083 helix: 1.66 (0.27), residues: 390 sheet: 1.01 (0.63), residues: 73 loop : -0.33 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 51 HIS 0.004 0.001 HIS A 76 PHE 0.014 0.001 PHE C 210 TYR 0.024 0.001 TYR A 79 ARG 0.009 0.000 ARG B 94 Details of bonding type rmsd hydrogen bonds : bond 0.03277 ( 314) hydrogen bonds : angle 4.95587 ( 867) metal coordination : bond 0.00360 ( 3) metal coordination : angle 33.44571 ( 9) covalent geometry : bond 0.00304 ( 8838) covalent geometry : angle 1.07856 (12082) Misc. bond : bond 0.05216 ( 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 135 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 1.045 Fit side-chains revert: symmetry clash REVERT: A 152 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7925 (tp30) REVERT: A 276 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7129 (tp40) REVERT: A 468 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7818 (mt-10) REVERT: B 164 HIS cc_start: 0.7436 (OUTLIER) cc_final: 0.5832 (m-70) REVERT: C 110 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.7654 (p0) REVERT: C 143 LYS cc_start: 0.7126 (ttpp) cc_final: 0.6822 (tttp) REVERT: C 187 ASP cc_start: 0.7593 (OUTLIER) cc_final: 0.7320 (t0) outliers start: 22 outliers final: 13 residues processed: 124 average time/residue: 1.2983 time to fit residues: 171.0390 Evaluate side-chains 127 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 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 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 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 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: 1.9990 chunk 46 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 69 optimal weight: 0.0270 chunk 45 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN A 539 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 = 0.3480 r_free = 0.3480 target = 0.130517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.106692 restraints weight = 9125.654| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.31 r_work: 0.3149 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.195 8853 Z= 0.149 Angle : 1.426 81.992 12091 Z= 0.417 Chirality : 0.062 1.476 1277 Planarity : 0.006 0.110 1569 Dihedral : 10.401 87.842 1294 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.60 % Allowed : 18.28 % Favored : 79.12 % 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: 0.71 (0.26), residues: 1083 helix: 1.63 (0.27), residues: 390 sheet: 1.02 (0.63), residues: 73 loop : -0.33 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 51 HIS 0.004 0.001 HIS A 76 PHE 0.015 0.001 PHE A 80 TYR 0.027 0.001 TYR A 79 ARG 0.009 0.000 ARG B 94 Details of bonding type rmsd hydrogen bonds : bond 0.03458 ( 314) hydrogen bonds : angle 4.97194 ( 867) metal coordination : bond 0.00410 ( 3) metal coordination : angle 33.59862 ( 9) covalent geometry : bond 0.00331 ( 8838) covalent geometry : angle 1.09280 (12082) Misc. bond : bond 0.06292 ( 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 129 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.910 Fit side-chains revert: symmetry clash REVERT: A 152 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7957 (tp30) REVERT: A 276 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7148 (tp40) REVERT: A 468 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7863 (mt-10) REVERT: B 164 HIS cc_start: 0.7533 (OUTLIER) cc_final: 0.6030 (m-70) REVERT: C 110 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7685 (p0) REVERT: C 143 LYS cc_start: 0.7160 (ttpp) cc_final: 0.6863 (tttp) REVERT: C 187 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7352 (t0) outliers start: 23 outliers final: 13 residues processed: 119 average time/residue: 1.3710 time to fit residues: 173.2833 Evaluate side-chains 124 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 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 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 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 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: 1.9990 chunk 6 optimal weight: 0.4980 chunk 11 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3474 r_free = 0.3474 target = 0.130052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.106360 restraints weight = 9209.441| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.28 r_work: 0.3140 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.211 8853 Z= 0.154 Angle : 1.431 82.059 12091 Z= 0.419 Chirality : 0.062 1.469 1277 Planarity : 0.006 0.108 1569 Dihedral : 10.462 88.670 1294 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.26 % Allowed : 18.74 % 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: 0.69 (0.26), residues: 1083 helix: 1.61 (0.27), residues: 390 sheet: 1.04 (0.63), residues: 73 loop : -0.34 (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 0.016 0.001 PHE A 80 TYR 0.028 0.001 TYR A 79 ARG 0.008 0.000 ARG B 94 Details of bonding type rmsd hydrogen bonds : bond 0.03555 ( 314) hydrogen bonds : angle 4.99926 ( 867) metal coordination : bond 0.00443 ( 3) metal coordination : angle 33.56644 ( 9) covalent geometry : bond 0.00345 ( 8838) covalent geometry : angle 1.09976 (12082) Misc. bond : bond 0.06812 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6454.14 seconds wall clock time: 111 minutes 58.00 seconds (6718.00 seconds total)