Starting phenix.real_space_refine on Thu Feb 13 18:08:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jej_36190/02_2025/8jej_36190.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jej_36190/02_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_36190/02_2025/8jej_36190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jej_36190/02_2025/8jej_36190.map" model { file = "/net/cci-nas-00/data/ceres_data/8jej_36190/02_2025/8jej_36190.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jej_36190/02_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-5592/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: 5.71, per 1000 atoms: 0.66 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: 2.88 Conformation dependent library (CDL) restraints added in 1.0 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: 1.02 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: 2.51 Time building geometry restraints manager: 2.90 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: 1.590 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 25.250 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:11.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.180 ------------------------------------------------------------------------------- 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 8838 Z= 1.898 Angle : 1.336 47.497 12082 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 *********************** 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 : 0.974 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: 1.3048 time to fit residues: 171.4336 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 : 0.945 ------------------------------------------------------------------------------- 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 8838 Z= 0.330 Angle : 1.381 71.705 12082 Z= 0.514 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 *********************** 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 : 0.974 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: 1.3958 time to fit residues: 183.7279 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 8838 Z= 0.199 Angle : 1.058 80.830 12082 Z= 0.403 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 *********************** 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 : 1.030 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: 1.3907 time to fit residues: 190.8073 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 : 0.916 ------------------------------------------------------------------------------- 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: 0.8980 chunk 73 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3461 r_free = 0.3461 target = 0.129172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.105134 restraints weight = 9173.103| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.27 r_work: 0.3124 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 8838 Z= 0.234 Angle : 1.084 82.558 12082 Z= 0.415 Chirality : 0.061 1.439 1277 Planarity : 0.005 0.090 1569 Dihedral : 10.765 88.638 1296 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.34 % Favored : 95.57 % Rotamer: Outliers : 3.16 % Allowed : 17.27 % Favored : 79.57 % 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: 1.43 (0.27), residues: 395 sheet: 1.02 (0.62), residues: 73 loop : -0.40 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 338 HIS 0.005 0.001 HIS A 76 PHE 0.017 0.001 PHE A 80 TYR 0.014 0.001 TYR A 443 ARG 0.008 0.000 ARG B 94 *********************** 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 142 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.956 Fit side-chains REVERT: A 152 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7937 (tp30) REVERT: A 247 LYS cc_start: 0.8635 (tttp) cc_final: 0.8328 (tttm) REVERT: A 276 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7123 (tp40) REVERT: B 154 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7863 (mtt180) REVERT: B 164 HIS cc_start: 0.7423 (OUTLIER) cc_final: 0.5926 (m-70) REVERT: C 110 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7543 (p0) REVERT: C 143 LYS cc_start: 0.7151 (ttpp) cc_final: 0.6939 (tttp) REVERT: C 182 HIS cc_start: 0.7768 (m-70) cc_final: 0.7548 (m-70) REVERT: C 187 ASP cc_start: 0.7602 (OUTLIER) cc_final: 0.7276 (t0) REVERT: C 302 THR cc_start: 0.7323 (OUTLIER) cc_final: 0.7075 (t) outliers start: 28 outliers final: 15 residues processed: 129 average time/residue: 1.3653 time to fit residues: 187.3772 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 : 0.865 ------------------------------------------------------------------------------- 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 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 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: 6.9990 chunk 35 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 96 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3444 r_free = 0.3444 target = 0.127679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.103282 restraints weight = 9144.660| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.31 r_work: 0.3106 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 8838 Z= 0.270 Angle : 1.094 81.305 12082 Z= 0.423 Chirality : 0.063 1.493 1277 Planarity : 0.006 0.087 1569 Dihedral : 10.872 89.984 1296 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.25 % Favored : 95.66 % 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: 0.47 (0.26), residues: 1083 helix: 1.35 (0.27), residues: 396 sheet: 1.02 (0.62), residues: 73 loop : -0.45 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 338 HIS 0.005 0.001 HIS A 76 PHE 0.020 0.002 PHE A 80 TYR 0.013 0.002 TYR A 443 ARG 0.008 0.000 ARG B 94 *********************** 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: 28 poor density : 115 time to evaluate : 0.906 Fit side-chains REVERT: A 468 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7985 (mt-10) REVERT: B 154 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7881 (mtt180) REVERT: B 164 HIS cc_start: 0.7577 (OUTLIER) cc_final: 0.6276 (m-70) REVERT: C 110 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.7577 (p0) REVERT: C 143 LYS cc_start: 0.7155 (ttpp) cc_final: 0.6943 (tttp) REVERT: C 182 HIS cc_start: 0.7796 (m-70) cc_final: 0.7487 (m-70) REVERT: C 187 ASP cc_start: 0.7584 (OUTLIER) cc_final: 0.7302 (t0) REVERT: C 272 GLU cc_start: 0.8692 (pt0) cc_final: 0.8484 (pt0) REVERT: C 302 THR cc_start: 0.7341 (OUTLIER) cc_final: 0.7090 (t) outliers start: 28 outliers final: 15 residues processed: 130 average time/residue: 1.4175 time to fit residues: 195.6882 Evaluate side-chains 133 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 81 optimal weight: 0.0060 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.6996 ------------------------------------------------------------------------------- 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 = 0.3465 r_free = 0.3465 target = 0.129497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.105625 restraints weight = 9113.773| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.27 r_work: 0.3133 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.112 8838 Z= 0.214 Angle : 1.085 81.597 12082 Z= 0.409 Chirality : 0.062 1.488 1277 Planarity : 0.006 0.105 1569 Dihedral : 10.540 87.281 1296 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.82 % Allowed : 17.95 % Favored : 79.23 % 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: 0.57 (0.26), residues: 1083 helix: 1.45 (0.27), residues: 396 sheet: 1.00 (0.62), residues: 73 loop : -0.40 (0.25), residues: 614 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 80 TYR 0.023 0.001 TYR A 79 ARG 0.007 0.000 ARG B 94 *********************** 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 135 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 1.067 Fit side-chains REVERT: A 152 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7914 (tp30) REVERT: A 276 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7132 (tp40) REVERT: A 468 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7955 (mt-10) REVERT: B 154 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7831 (mtt180) REVERT: B 164 HIS cc_start: 0.7510 (OUTLIER) cc_final: 0.6062 (m-70) REVERT: C 110 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7620 (p0) REVERT: C 182 HIS cc_start: 0.7812 (m-70) cc_final: 0.7608 (m-70) REVERT: C 187 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7290 (t0) REVERT: C 395 MET cc_start: 0.8710 (ttt) cc_final: 0.8337 (ttt) outliers start: 25 outliers final: 11 residues processed: 123 average time/residue: 1.4713 time to fit residues: 191.3496 Evaluate side-chains 123 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 50 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3446 r_free = 0.3446 target = 0.127816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.103497 restraints weight = 9161.727| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.31 r_work: 0.3111 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 8838 Z= 0.257 Angle : 1.102 81.292 12082 Z= 0.422 Chirality : 0.063 1.497 1277 Planarity : 0.006 0.100 1569 Dihedral : 10.701 89.551 1294 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.43 % Favored : 95.48 % Rotamer: Outliers : 3.05 % Allowed : 17.83 % 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: 0.53 (0.26), residues: 1083 helix: 1.46 (0.27), residues: 390 sheet: 0.92 (0.62), residues: 73 loop : -0.42 (0.24), 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 *********************** 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 131 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: A 152 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7952 (tp30) REVERT: A 276 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7126 (tp40) REVERT: A 468 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7975 (mt-10) REVERT: B 154 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7901 (mtt180) REVERT: B 164 HIS cc_start: 0.7633 (OUTLIER) cc_final: 0.6438 (m-70) REVERT: C 110 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7640 (p0) REVERT: C 187 ASP cc_start: 0.7607 (OUTLIER) cc_final: 0.7256 (t0) REVERT: C 302 THR cc_start: 0.7341 (OUTLIER) cc_final: 0.7089 (t) REVERT: C 395 MET cc_start: 0.8804 (ttt) cc_final: 0.8591 (ttt) outliers start: 27 outliers final: 14 residues processed: 119 average time/residue: 1.4609 time to fit residues: 184.1393 Evaluate side-chains 127 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 469 MET 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 70 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 90 optimal weight: 0.0980 chunk 91 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 85 optimal weight: 0.0010 chunk 106 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 34 optimal weight: 0.9980 overall best weight: 0.4186 ------------------------------------------------------------------------------- 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 = 0.3494 r_free = 0.3494 target = 0.131772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.108300 restraints weight = 9249.758| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.28 r_work: 0.3166 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 8838 Z= 0.191 Angle : 1.069 81.984 12082 Z= 0.401 Chirality : 0.061 1.484 1277 Planarity : 0.005 0.090 1569 Dihedral : 10.232 86.944 1294 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.60 % Allowed : 18.06 % Favored : 79.35 % 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: 0.73 (0.26), residues: 1083 helix: 1.65 (0.27), residues: 390 sheet: 1.03 (0.62), residues: 73 loop : -0.32 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 51 HIS 0.003 0.001 HIS A 76 PHE 0.013 0.001 PHE C 210 TYR 0.024 0.001 TYR A 79 ARG 0.009 0.000 ARG B 94 *********************** 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 136 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: A 152 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7897 (tp30) REVERT: A 247 LYS cc_start: 0.8578 (tttp) cc_final: 0.8371 (tttm) REVERT: A 468 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7901 (mt-10) REVERT: B 154 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7732 (mtt180) REVERT: B 164 HIS cc_start: 0.7378 (OUTLIER) cc_final: 0.5702 (m-70) REVERT: C 110 ASP cc_start: 0.7959 (OUTLIER) cc_final: 0.7694 (p0) REVERT: C 187 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.7351 (t0) outliers start: 23 outliers final: 11 residues processed: 125 average time/residue: 1.3448 time to fit residues: 178.5830 Evaluate side-chains 126 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 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 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 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: 0.9980 chunk 94 optimal weight: 0.0070 chunk 50 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 23 optimal weight: 0.1980 chunk 9 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 overall best weight: 1.4402 ------------------------------------------------------------------------------- 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 = 0.3441 r_free = 0.3441 target = 0.127285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.102835 restraints weight = 9160.308| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.33 r_work: 0.3101 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 8838 Z= 0.290 Angle : 1.111 80.955 12082 Z= 0.430 Chirality : 0.065 1.507 1277 Planarity : 0.006 0.095 1569 Dihedral : 10.833 87.776 1294 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.43 % Favored : 95.48 % Rotamer: Outliers : 2.60 % Allowed : 18.62 % Favored : 78.78 % 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: 1.48 (0.27), residues: 390 sheet: 1.01 (0.62), residues: 73 loop : -0.41 (0.24), residues: 620 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 0.029 0.002 TYR A 79 ARG 0.008 0.000 ARG B 94 *********************** 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 130 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.916 Fit side-chains revert: symmetry clash REVERT: A 152 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7928 (tp30) REVERT: A 276 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7208 (tp40) REVERT: A 468 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7958 (mt-10) REVERT: B 164 HIS cc_start: 0.7696 (OUTLIER) cc_final: 0.6200 (m-70) REVERT: C 110 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7635 (p0) REVERT: C 187 ASP cc_start: 0.7584 (OUTLIER) cc_final: 0.7281 (t0) outliers start: 23 outliers final: 13 residues processed: 119 average time/residue: 1.5062 time to fit residues: 190.5491 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 : 1.040 ------------------------------------------------------------------------------- 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 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 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: 4.9990 chunk 46 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 69 optimal weight: 0.1980 chunk 45 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 = 0.3473 r_free = 0.3473 target = 0.129926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.105954 restraints weight = 9128.944| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.32 r_work: 0.3142 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 8838 Z= 0.215 Angle : 1.080 81.621 12082 Z= 0.410 Chirality : 0.062 1.491 1277 Planarity : 0.005 0.089 1569 Dihedral : 10.473 87.623 1294 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.88 % Favored : 96.03 % Rotamer: Outliers : 2.26 % Allowed : 18.96 % Favored : 78.78 % 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: 0.65 (0.26), residues: 1083 helix: 1.58 (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 0.009 0.001 TRP A 51 HIS 0.004 0.001 HIS A 76 PHE 0.015 0.001 PHE A 270 TYR 0.026 0.001 TYR A 79 ARG 0.009 0.000 ARG B 94 ********************** 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: 20 poor density : 109 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: A 152 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7926 (tp30) REVERT: A 247 LYS cc_start: 0.8628 (tttp) cc_final: 0.8419 (tttm) REVERT: A 276 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7151 (tp40) REVERT: A 468 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7882 (mt-10) REVERT: B 164 HIS cc_start: 0.7572 (OUTLIER) cc_final: 0.6193 (m-70) REVERT: C 110 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7637 (p0) REVERT: C 143 LYS cc_start: 0.7140 (ttpp) cc_final: 0.6925 (tttp) REVERT: C 187 ASP cc_start: 0.7585 (OUTLIER) cc_final: 0.7274 (t0) outliers start: 20 outliers final: 12 residues processed: 118 average time/residue: 1.4303 time to fit residues: 178.8129 Evaluate side-chains 125 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 152 GLU Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 276 GLN 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 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: 0.9980 chunk 6 optimal weight: 0.0970 chunk 11 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 59 optimal weight: 8.9990 chunk 97 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.3482 r_free = 0.3482 target = 0.130613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.106707 restraints weight = 9237.560| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.33 r_work: 0.3151 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 8838 Z= 0.207 Angle : 1.078 81.971 12082 Z= 0.408 Chirality : 0.061 1.476 1277 Planarity : 0.005 0.088 1569 Dihedral : 10.389 87.238 1294 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.34 % Favored : 95.57 % Rotamer: Outliers : 2.26 % Allowed : 19.07 % Favored : 78.67 % 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: 0.70 (0.26), residues: 1083 helix: 1.64 (0.27), residues: 390 sheet: 1.03 (0.62), residues: 73 loop : -0.35 (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 0.014 0.001 PHE A 270 TYR 0.026 0.001 TYR A 79 ARG 0.009 0.000 ARG B 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6527.83 seconds wall clock time: 116 minutes 1.93 seconds (6961.93 seconds total)