Starting phenix.real_space_refine on Thu Sep 18 11:36:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9irk_60816/09_2025/9irk_60816_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9irk_60816/09_2025/9irk_60816.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9irk_60816/09_2025/9irk_60816_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9irk_60816/09_2025/9irk_60816_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9irk_60816/09_2025/9irk_60816.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9irk_60816/09_2025/9irk_60816.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.102 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: 5 Type Number sf(0) Gaussians S 63 5.16 5 C 5247 2.51 5 N 1428 2.21 5 O 1539 1.98 5 H 8155 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16432 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 7403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 7403 Classifications: {'peptide': 477} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 456} Chain breaks: 3 Chain: "A" Number of atoms: 8261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8261 Classifications: {'peptide': 533} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 511} Chain breaks: 3 Chain: "B" Number of atoms: 682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 682 Classifications: {'peptide': 42} Link IDs: {'TRANS': 41} Chain breaks: 1 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'O6E': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'O6E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.69, per 1000 atoms: 0.16 Number of scatterers: 16432 At special positions: 0 Unit cell: (68.85, 118.15, 122.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 O 1539 8.00 N 1428 7.00 C 5247 6.00 H 8155 1.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 459.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1964 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 7 sheets defined 46.5% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'C' and resid 136 through 141 Processing helix chain 'C' and resid 162 through 167 Processing helix chain 'C' and resid 168 through 180 Processing helix chain 'C' and resid 183 through 188 removed outlier: 4.058A pdb=" N ASN C 188 " --> pdb=" O THR C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 247 removed outlier: 4.104A pdb=" N GLN C 235 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA C 238 " --> pdb=" O SER C 234 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLN C 244 " --> pdb=" O ARG C 240 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA C 247 " --> pdb=" O SER C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 269 removed outlier: 3.613A pdb=" N LEU C 256 " --> pdb=" O ASP C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 319 removed outlier: 3.786A pdb=" N LYS C 317 " --> pdb=" O ARG C 313 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN C 318 " --> pdb=" O PHE C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 366 Processing helix chain 'C' and resid 411 through 458 removed outlier: 4.000A pdb=" N GLN C 423 " --> pdb=" O GLU C 419 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA C 424 " --> pdb=" O PHE C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 465 removed outlier: 3.506A pdb=" N THR C 465 " --> pdb=" O GLY C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 511 removed outlier: 3.602A pdb=" N ALA C 511 " --> pdb=" O LEU C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 Processing helix chain 'C' and resid 556 through 561 removed outlier: 3.501A pdb=" N ILE C 561 " --> pdb=" O ALA C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 589 Processing helix chain 'C' and resid 600 through 621 Processing helix chain 'A' and resid 55 through 78 removed outlier: 4.516A pdb=" N TYR A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N THR A 62 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 90 Processing helix chain 'A' and resid 97 through 110 removed outlier: 3.688A pdb=" N ILE A 101 " --> pdb=" O PRO A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 142 Processing helix chain 'A' and resid 162 through 167 removed outlier: 3.780A pdb=" N PHE A 167 " --> pdb=" O ARG A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 180 Processing helix chain 'A' and resid 223 through 247 removed outlier: 3.517A pdb=" N SER A 227 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 269 removed outlier: 3.678A pdb=" N GLU A 262 " --> pdb=" O ASP A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 308 removed outlier: 3.781A pdb=" N ASP A 307 " --> pdb=" O PRO A 304 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE A 308 " --> pdb=" O ALA A 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 304 through 308' Processing helix chain 'A' and resid 309 through 316 removed outlier: 3.519A pdb=" N ARG A 313 " --> pdb=" O PRO A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 366 Processing helix chain 'A' and resid 411 through 457 Processing helix chain 'A' and resid 459 through 464 removed outlier: 3.856A pdb=" N ILE A 463 " --> pdb=" O PRO A 460 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL A 464 " --> pdb=" O ALA A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 511 removed outlier: 3.690A pdb=" N LYS A 500 " --> pdb=" O GLU A 496 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 533 Processing helix chain 'A' and resid 556 through 560 Processing helix chain 'A' and resid 580 through 589 Processing helix chain 'A' and resid 600 through 621 Processing helix chain 'B' and resid 45 through 54 Processing helix chain 'B' and resid 56 through 61 Processing sheet with id=AA1, first strand: chain 'C' and resid 113 through 114 removed outlier: 6.544A pdb=" N ALA C 122 " --> pdb=" O ILE C 131 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N TYR C 133 " --> pdb=" O MET C 120 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N MET C 120 " --> pdb=" O TYR C 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 302 through 303 removed outlier: 6.601A pdb=" N VAL C 275 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLU C 289 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL C 273 " --> pdb=" O GLU C 289 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TRP C 397 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL C 375 " --> pdb=" O TRP C 397 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LEU C 399 " --> pdb=" O MET C 373 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N MET C 373 " --> pdb=" O LEU C 399 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL C 401 " --> pdb=" O LEU C 371 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU C 371 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N HIS C 403 " --> pdb=" O ALA C 369 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ALA C 369 " --> pdb=" O HIS C 403 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 486 through 491 Processing sheet with id=AA4, first strand: chain 'A' and resid 113 through 114 removed outlier: 6.340A pdb=" N ALA A 122 " --> pdb=" O ILE A 131 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N TYR A 133 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N MET A 120 " --> pdb=" O TYR A 133 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 302 through 303 removed outlier: 5.625A pdb=" N VAL A 286 " --> pdb=" O LYS A 277 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LYS A 277 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA A 288 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TRP A 397 " --> pdb=" O PHE A 278 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL A 375 " --> pdb=" O TRP A 397 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LEU A 399 " --> pdb=" O MET A 373 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N MET A 373 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL A 401 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU A 371 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N HIS A 403 " --> pdb=" O ALA A 369 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA A 369 " --> pdb=" O HIS A 403 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 486 through 491 Processing sheet with id=AA7, first strand: chain 'B' and resid 19 through 23 457 hydrogen bonds defined for protein. 1251 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: 3.49 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 8102 1.04 - 1.23: 368 1.23 - 1.43: 3226 1.43 - 1.63: 4797 1.63 - 1.83: 104 Bond restraints: 16597 Sorted by residual: bond pdb=" N VAL C 190 " pdb=" H VAL C 190 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.80e+01 bond pdb=" N LEU C 187 " pdb=" H LEU C 187 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.78e+01 bond pdb=" N ASN C 188 " pdb=" H ASN C 188 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.76e+01 bond pdb=" ND2 ASN C 188 " pdb="HD21 ASN C 188 " ideal model delta sigma weight residual 0.860 1.016 -0.156 2.00e-02 2.50e+03 6.09e+01 bond pdb=" ND2 ASN C 188 " pdb="HD22 ASN C 188 " ideal model delta sigma weight residual 0.860 1.016 -0.156 2.00e-02 2.50e+03 6.06e+01 ... (remaining 16592 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 29760 2.36 - 4.73: 149 4.73 - 7.09: 12 7.09 - 9.45: 3 9.45 - 11.82: 4 Bond angle restraints: 29928 Sorted by residual: angle pdb=" N PRO C 189 " pdb=" CA PRO C 189 " pdb=" CB PRO C 189 " ideal model delta sigma weight residual 102.60 96.38 6.22 1.10e+00 8.26e-01 3.20e+01 angle pdb=" CA VAL C 190 " pdb=" C VAL C 190 " pdb=" O VAL C 190 " ideal model delta sigma weight residual 121.54 115.41 6.13 1.22e+00 6.72e-01 2.53e+01 angle pdb=" CA LEU C 187 " pdb=" C LEU C 187 " pdb=" O LEU C 187 " ideal model delta sigma weight residual 121.17 115.26 5.91 1.24e+00 6.50e-01 2.27e+01 angle pdb=" C VAL C 190 " pdb=" N TRP C 191 " pdb=" CA TRP C 191 " ideal model delta sigma weight residual 123.05 129.32 -6.27 1.40e+00 5.10e-01 2.01e+01 angle pdb=" CA ASN C 188 " pdb=" C ASN C 188 " pdb=" N PRO C 189 " ideal model delta sigma weight residual 119.06 123.61 -4.55 1.05e+00 9.07e-01 1.88e+01 ... (remaining 29923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 7174 17.89 - 35.77: 432 35.77 - 53.66: 180 53.66 - 71.54: 49 71.54 - 89.43: 11 Dihedral angle restraints: 7846 sinusoidal: 4310 harmonic: 3536 Sorted by residual: dihedral pdb=" CA ASN C 319 " pdb=" C ASN C 319 " pdb=" N ARG C 320 " pdb=" CA ARG C 320 " ideal model delta harmonic sigma weight residual -180.00 -161.49 -18.51 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA PHE A 201 " pdb=" C PHE A 201 " pdb=" N TYR A 202 " pdb=" CA TYR A 202 " ideal model delta harmonic sigma weight residual 180.00 163.76 16.24 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CG ARG C 578 " pdb=" CD ARG C 578 " pdb=" NE ARG C 578 " pdb=" CZ ARG C 578 " ideal model delta sinusoidal sigma weight residual 90.00 134.23 -44.23 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 7843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1168 0.068 - 0.137: 104 0.137 - 0.205: 3 0.205 - 0.273: 0 0.273 - 0.342: 4 Chirality restraints: 1279 Sorted by residual: chirality pdb=" CBJ O6E C1001 " pdb=" CAC O6E C1001 " pdb=" CBD O6E C1001 " pdb=" CBN O6E C1001 " both_signs ideal model delta sigma weight residual False 2.70 3.04 -0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" CBD O6E C1001 " pdb=" CAT O6E C1001 " pdb=" CAX O6E C1001 " pdb=" CBJ O6E C1001 " both_signs ideal model delta sigma weight residual False -2.69 -2.40 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CBD O6E A1001 " pdb=" CAT O6E A1001 " pdb=" CAX O6E A1001 " pdb=" CBJ O6E A1001 " both_signs ideal model delta sigma weight residual False -2.69 -2.41 -0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 1276 not shown) Planarity restraints: 2464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 188 " -0.345 2.00e-02 2.50e+03 4.03e-01 2.43e+03 pdb=" CG ASN C 188 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN C 188 " 0.332 2.00e-02 2.50e+03 pdb=" ND2 ASN C 188 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN C 188 " -0.617 2.00e-02 2.50e+03 pdb="HD22 ASN C 188 " 0.603 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAB O6E A1001 " -0.276 2.00e-02 2.50e+03 1.77e-01 7.85e+02 pdb=" CAP O6E A1001 " -0.157 2.00e-02 2.50e+03 pdb=" CAS O6E A1001 " 0.215 2.00e-02 2.50e+03 pdb=" CAW O6E A1001 " 0.059 2.00e-02 2.50e+03 pdb=" CBC O6E A1001 " 0.056 2.00e-02 2.50e+03 pdb=" CBI O6E A1001 " -0.080 2.00e-02 2.50e+03 pdb=" CBL O6E A1001 " -0.193 2.00e-02 2.50e+03 pdb=" CBM O6E A1001 " 0.062 2.00e-02 2.50e+03 pdb=" NAJ O6E A1001 " 0.335 2.00e-02 2.50e+03 pdb=" OAK O6E A1001 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAA O6E C1001 " 0.252 2.00e-02 2.50e+03 1.55e-01 6.01e+02 pdb=" CAO O6E C1001 " -0.068 2.00e-02 2.50e+03 pdb=" CAP O6E C1001 " 0.285 2.00e-02 2.50e+03 pdb=" CAR O6E C1001 " -0.215 2.00e-02 2.50e+03 pdb=" CAV O6E C1001 " -0.073 2.00e-02 2.50e+03 pdb=" CBB O6E C1001 " 0.032 2.00e-02 2.50e+03 pdb=" CBH O6E C1001 " -0.081 2.00e-02 2.50e+03 pdb=" CBL O6E C1001 " 0.006 2.00e-02 2.50e+03 pdb=" CBO O6E C1001 " 0.036 2.00e-02 2.50e+03 pdb=" NAE O6E C1001 " -0.174 2.00e-02 2.50e+03 ... (remaining 2461 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.23: 1235 2.23 - 2.82: 34481 2.82 - 3.41: 40118 3.41 - 4.01: 55967 4.01 - 4.60: 87514 Nonbonded interactions: 219315 Sorted by model distance: nonbonded pdb=" O ILE C 470 " pdb=" HE1 TRP C 552 " model vdw 1.633 2.450 nonbonded pdb=" OE1 GLU A 98 " pdb=" H GLU A 98 " model vdw 1.639 2.450 nonbonded pdb=" OE2 GLU C 125 " pdb="HH12 ARG C 207 " model vdw 1.643 2.450 nonbonded pdb="HE21 GLN C 235 " pdb=" OE1 GLN A 235 " model vdw 1.719 2.450 nonbonded pdb=" OE1 GLU A 496 " pdb=" H GLU A 496 " model vdw 1.732 2.450 ... (remaining 219310 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 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 111 and (name N or name CA or name C or name O or name HA \ 2 or name HA3)) or resid 112 through 379 or (resid 393 and (name N or name CA or \ name C or name O or name CB or name OG or name HA or name HB2 or name HB3 or na \ me HG )) or resid 394 through 565 or (resid 577 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name OE1 or name NE2 or name HA o \ r name HB2 or name HB3 or name HG2 or name HG3 or name HE21 or name HE22)) or re \ sid 578 through 1001)) selection = (chain 'C' and (resid 111 through 143 or (resid 157 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2 or name HA or name \ HB2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 o \ r name HD22 or name HD23)) or resid 158 through 379 or resid 393 through 1001)) } 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: 1.900 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: 0.090 Extract box with map and model: 0.170 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.760 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 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 : 0.005 0.096 8444 Z= 0.269 Angle : 0.687 11.818 11424 Z= 0.378 Chirality : 0.044 0.342 1279 Planarity : 0.010 0.177 1463 Dihedral : 15.399 89.431 3154 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.12 % Allowed : 12.89 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.26), residues: 1032 helix: 2.54 (0.25), residues: 425 sheet: 0.86 (0.35), residues: 200 loop : -0.66 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 265 TYR 0.017 0.002 TYR C 416 PHE 0.019 0.002 PHE A 420 TRP 0.017 0.002 TRP C 191 HIS 0.007 0.002 HIS C 403 Details of bonding type rmsd covalent geometry : bond 0.00509 ( 8442) covalent geometry : angle 0.68731 (11424) hydrogen bonds : bond 0.14466 ( 457) hydrogen bonds : angle 4.94149 ( 1251) Misc. bond : bond 0.05504 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 144 MET cc_start: 0.4500 (mmm) cc_final: 0.3386 (ptp) REVERT: C 475 LYS cc_start: 0.8044 (tttp) cc_final: 0.7601 (ttpt) REVERT: C 582 ARG cc_start: 0.7680 (mtm-85) cc_final: 0.7405 (mtm-85) REVERT: A 451 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.6893 (mp) REVERT: B 30 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7823 (mtpm) outliers start: 10 outliers final: 7 residues processed: 119 average time/residue: 1.2000 time to fit residues: 151.5299 Evaluate side-chains 116 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 30 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.145530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.110435 restraints weight = 25175.773| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.84 r_work: 0.3148 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.0610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8444 Z= 0.153 Angle : 0.529 6.179 11424 Z= 0.282 Chirality : 0.040 0.149 1279 Planarity : 0.005 0.056 1463 Dihedral : 6.480 70.095 1231 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.47 % Allowed : 11.43 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.26), residues: 1032 helix: 2.46 (0.25), residues: 431 sheet: 1.12 (0.36), residues: 191 loop : -0.75 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 554 TYR 0.012 0.001 TYR A 416 PHE 0.015 0.002 PHE A 420 TRP 0.016 0.002 TRP C 191 HIS 0.007 0.002 HIS A 403 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 8442) covalent geometry : angle 0.52876 (11424) hydrogen bonds : bond 0.06972 ( 457) hydrogen bonds : angle 4.14847 ( 1251) Misc. bond : bond 0.00123 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 144 MET cc_start: 0.4443 (mmm) cc_final: 0.3409 (ptp) REVERT: C 439 MET cc_start: 0.7755 (mmm) cc_final: 0.7441 (mmm) REVERT: C 475 LYS cc_start: 0.8015 (tttp) cc_final: 0.7624 (ttpt) REVERT: C 582 ARG cc_start: 0.7720 (mtm-85) cc_final: 0.7463 (mtm-85) REVERT: C 591 VAL cc_start: 0.8156 (OUTLIER) cc_final: 0.7828 (m) REVERT: A 172 SER cc_start: 0.8351 (OUTLIER) cc_final: 0.8147 (m) outliers start: 22 outliers final: 9 residues processed: 125 average time/residue: 1.2799 time to fit residues: 169.4844 Evaluate side-chains 121 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 416 TYR Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 44 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 65 optimal weight: 0.4980 chunk 12 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.146286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.111117 restraints weight = 25109.801| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.83 r_work: 0.3091 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8444 Z= 0.143 Angle : 0.514 7.179 11424 Z= 0.272 Chirality : 0.039 0.146 1279 Planarity : 0.005 0.058 1463 Dihedral : 5.208 64.933 1220 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.02 % Allowed : 12.33 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.26), residues: 1032 helix: 2.52 (0.25), residues: 430 sheet: 1.15 (0.36), residues: 191 loop : -0.76 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 415 TYR 0.014 0.001 TYR A 416 PHE 0.014 0.002 PHE A 420 TRP 0.015 0.002 TRP C 191 HIS 0.007 0.001 HIS A 403 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8442) covalent geometry : angle 0.51431 (11424) hydrogen bonds : bond 0.06794 ( 457) hydrogen bonds : angle 4.00795 ( 1251) Misc. bond : bond 0.00033 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 144 MET cc_start: 0.4458 (mmm) cc_final: 0.3474 (ptp) REVERT: C 475 LYS cc_start: 0.8028 (tttp) cc_final: 0.7640 (ttpt) REVERT: C 582 ARG cc_start: 0.7696 (mtm-85) cc_final: 0.7487 (mtm-85) outliers start: 18 outliers final: 9 residues processed: 124 average time/residue: 1.2488 time to fit residues: 164.4760 Evaluate side-chains 119 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 416 TYR Chi-restraints excluded: chain B residue 13 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 88 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 70 optimal weight: 0.1980 chunk 6 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.146855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.110869 restraints weight = 25044.592| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.88 r_work: 0.3112 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8444 Z= 0.126 Angle : 0.489 7.069 11424 Z= 0.258 Chirality : 0.039 0.144 1279 Planarity : 0.005 0.057 1463 Dihedral : 5.061 63.369 1220 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.57 % Allowed : 12.67 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.27), residues: 1032 helix: 2.60 (0.25), residues: 430 sheet: 1.18 (0.37), residues: 190 loop : -0.74 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 554 TYR 0.012 0.001 TYR A 416 PHE 0.011 0.001 PHE A 420 TRP 0.013 0.001 TRP C 191 HIS 0.006 0.001 HIS A 403 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 8442) covalent geometry : angle 0.48872 (11424) hydrogen bonds : bond 0.06304 ( 457) hydrogen bonds : angle 3.89291 ( 1251) Misc. bond : bond 0.00034 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 144 MET cc_start: 0.4537 (mmm) cc_final: 0.3569 (ptp) REVERT: C 475 LYS cc_start: 0.8024 (tttp) cc_final: 0.7637 (ttpt) REVERT: C 582 ARG cc_start: 0.7676 (mtm-85) cc_final: 0.7427 (mtm-85) REVERT: A 294 ASP cc_start: 0.7866 (OUTLIER) cc_final: 0.7489 (p0) REVERT: B 30 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7209 (mtpm) outliers start: 14 outliers final: 8 residues processed: 124 average time/residue: 1.2080 time to fit residues: 159.0997 Evaluate side-chains 121 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 416 TYR Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain B residue 30 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 73 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.145630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.110330 restraints weight = 25047.909| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.84 r_work: 0.3107 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8444 Z= 0.149 Angle : 0.516 7.150 11424 Z= 0.272 Chirality : 0.039 0.145 1279 Planarity : 0.005 0.058 1463 Dihedral : 5.197 64.999 1220 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.13 % Allowed : 12.44 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.27), residues: 1032 helix: 2.53 (0.25), residues: 430 sheet: 1.11 (0.37), residues: 191 loop : -0.80 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 554 TYR 0.015 0.001 TYR A 416 PHE 0.014 0.002 PHE A 420 TRP 0.015 0.002 TRP C 191 HIS 0.008 0.001 HIS A 403 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 8442) covalent geometry : angle 0.51623 (11424) hydrogen bonds : bond 0.06765 ( 457) hydrogen bonds : angle 3.92574 ( 1251) Misc. bond : bond 0.00047 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 144 MET cc_start: 0.4987 (mmm) cc_final: 0.3662 (ptp) REVERT: C 475 LYS cc_start: 0.8035 (tttp) cc_final: 0.7644 (ttpt) REVERT: C 582 ARG cc_start: 0.7697 (mtm-85) cc_final: 0.7432 (mtm-85) REVERT: A 294 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7510 (p0) REVERT: B 30 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7207 (mtpm) outliers start: 19 outliers final: 8 residues processed: 124 average time/residue: 1.2680 time to fit residues: 166.5168 Evaluate side-chains 120 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain B residue 30 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 3 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.150435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.115700 restraints weight = 24938.643| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.77 r_work: 0.3165 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8444 Z= 0.143 Angle : 0.512 7.173 11424 Z= 0.269 Chirality : 0.039 0.144 1279 Planarity : 0.005 0.058 1463 Dihedral : 5.178 64.722 1220 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 1.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.91 % Allowed : 12.89 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.27), residues: 1032 helix: 2.54 (0.25), residues: 431 sheet: 1.15 (0.37), residues: 190 loop : -0.84 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 554 TYR 0.014 0.001 TYR A 416 PHE 0.012 0.001 PHE A 420 TRP 0.014 0.002 TRP C 191 HIS 0.006 0.001 HIS A 403 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 8442) covalent geometry : angle 0.51241 (11424) hydrogen bonds : bond 0.06608 ( 457) hydrogen bonds : angle 3.89719 ( 1251) Misc. bond : bond 0.00044 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 144 MET cc_start: 0.5165 (mmm) cc_final: 0.3873 (ptp) REVERT: C 475 LYS cc_start: 0.8058 (tttp) cc_final: 0.7682 (ttpt) REVERT: C 582 ARG cc_start: 0.7732 (mtm-85) cc_final: 0.7508 (mtm-85) REVERT: A 451 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7622 (mp) REVERT: B 30 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7344 (mtpm) outliers start: 17 outliers final: 9 residues processed: 124 average time/residue: 1.2979 time to fit residues: 170.2417 Evaluate side-chains 121 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 416 TYR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain B residue 30 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.149960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.115078 restraints weight = 24805.889| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.80 r_work: 0.3160 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8444 Z= 0.148 Angle : 0.519 7.186 11424 Z= 0.273 Chirality : 0.039 0.145 1279 Planarity : 0.005 0.058 1463 Dihedral : 5.233 65.032 1220 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.79 % Allowed : 13.00 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.27), residues: 1032 helix: 2.55 (0.25), residues: 431 sheet: 1.12 (0.37), residues: 191 loop : -0.88 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 554 TYR 0.014 0.001 TYR A 416 PHE 0.013 0.001 PHE A 420 TRP 0.014 0.002 TRP C 191 HIS 0.006 0.001 HIS A 403 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 8442) covalent geometry : angle 0.51948 (11424) hydrogen bonds : bond 0.06710 ( 457) hydrogen bonds : angle 3.91196 ( 1251) Misc. bond : bond 0.00052 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 144 MET cc_start: 0.5377 (mmm) cc_final: 0.3976 (ptp) REVERT: C 475 LYS cc_start: 0.8087 (tttp) cc_final: 0.7720 (ttpt) REVERT: C 582 ARG cc_start: 0.7723 (mtm-85) cc_final: 0.7506 (mtm-85) REVERT: A 294 ASP cc_start: 0.7862 (OUTLIER) cc_final: 0.7490 (p0) REVERT: A 451 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7554 (mp) REVERT: B 30 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7358 (mtpm) outliers start: 16 outliers final: 10 residues processed: 125 average time/residue: 1.2113 time to fit residues: 160.7962 Evaluate side-chains 123 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 556 HIS Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain B residue 30 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 99 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 30 optimal weight: 0.3980 chunk 69 optimal weight: 0.7980 chunk 39 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.150883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.116471 restraints weight = 24970.540| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.75 r_work: 0.3125 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8444 Z= 0.126 Angle : 0.494 7.093 11424 Z= 0.259 Chirality : 0.039 0.143 1279 Planarity : 0.005 0.058 1463 Dihedral : 5.081 63.675 1220 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.79 % Allowed : 13.34 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.27), residues: 1032 helix: 2.66 (0.25), residues: 431 sheet: 1.16 (0.37), residues: 190 loop : -0.83 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 415 TYR 0.012 0.001 TYR A 416 PHE 0.010 0.001 PHE A 420 TRP 0.012 0.001 TRP C 191 HIS 0.005 0.001 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 8442) covalent geometry : angle 0.49383 (11424) hydrogen bonds : bond 0.06198 ( 457) hydrogen bonds : angle 3.83034 ( 1251) Misc. bond : bond 0.00034 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 144 MET cc_start: 0.5336 (mmm) cc_final: 0.3939 (ptp) REVERT: C 475 LYS cc_start: 0.8070 (tttp) cc_final: 0.7664 (ttpt) REVERT: C 582 ARG cc_start: 0.7670 (mtm-85) cc_final: 0.7438 (mtm-85) REVERT: A 294 ASP cc_start: 0.7865 (OUTLIER) cc_final: 0.7492 (p0) REVERT: B 30 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7256 (mtpm) outliers start: 16 outliers final: 11 residues processed: 122 average time/residue: 1.2406 time to fit residues: 160.5711 Evaluate side-chains 121 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 556 HIS Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 416 TYR Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain B residue 30 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 56 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 99 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 2 optimal weight: 0.0020 chunk 81 optimal weight: 1.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.152362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.117753 restraints weight = 24929.070| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.01 r_work: 0.3191 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8444 Z= 0.108 Angle : 0.469 6.900 11424 Z= 0.246 Chirality : 0.038 0.139 1279 Planarity : 0.005 0.059 1463 Dihedral : 4.926 62.228 1220 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.57 % Allowed : 13.79 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.27), residues: 1032 helix: 2.82 (0.26), residues: 431 sheet: 1.19 (0.37), residues: 190 loop : -0.77 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 415 TYR 0.011 0.001 TYR A 416 PHE 0.011 0.001 PHE A 420 TRP 0.010 0.001 TRP C 191 HIS 0.004 0.001 HIS A 403 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 8442) covalent geometry : angle 0.46919 (11424) hydrogen bonds : bond 0.05678 ( 457) hydrogen bonds : angle 3.73662 ( 1251) Misc. bond : bond 0.00019 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 144 MET cc_start: 0.5382 (mmm) cc_final: 0.4112 (ptp) REVERT: C 475 LYS cc_start: 0.8083 (tttp) cc_final: 0.7699 (ttpt) REVERT: C 582 ARG cc_start: 0.7710 (mtm-85) cc_final: 0.7500 (mtm-85) REVERT: A 294 ASP cc_start: 0.7842 (OUTLIER) cc_final: 0.7472 (p0) REVERT: B 30 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7316 (mtpm) outliers start: 14 outliers final: 9 residues processed: 122 average time/residue: 1.2491 time to fit residues: 161.7397 Evaluate side-chains 117 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain B residue 30 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 69 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 556 HIS A 73 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.150939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.116474 restraints weight = 24752.063| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.75 r_work: 0.3124 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8444 Z= 0.132 Angle : 0.499 7.052 11424 Z= 0.262 Chirality : 0.039 0.142 1279 Planarity : 0.005 0.057 1463 Dihedral : 5.082 63.619 1220 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.46 % Allowed : 13.90 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.27), residues: 1032 helix: 2.75 (0.25), residues: 431 sheet: 1.17 (0.37), residues: 190 loop : -0.83 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 446 TYR 0.013 0.001 TYR A 416 PHE 0.013 0.001 PHE A 420 TRP 0.012 0.002 TRP C 191 HIS 0.005 0.001 HIS A 403 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8442) covalent geometry : angle 0.49902 (11424) hydrogen bonds : bond 0.06198 ( 457) hydrogen bonds : angle 3.78510 ( 1251) Misc. bond : bond 0.00038 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 144 MET cc_start: 0.5319 (mmm) cc_final: 0.3960 (ptp) REVERT: C 475 LYS cc_start: 0.8069 (tttp) cc_final: 0.7672 (ttpt) REVERT: C 582 ARG cc_start: 0.7669 (mtm-85) cc_final: 0.7436 (mtm-85) REVERT: A 294 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7473 (p0) REVERT: B 30 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7259 (mtpm) outliers start: 13 outliers final: 9 residues processed: 119 average time/residue: 1.2399 time to fit residues: 156.4246 Evaluate side-chains 120 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain B residue 30 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 91 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 556 HIS A 73 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.151849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.117519 restraints weight = 24743.000| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.75 r_work: 0.3134 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8444 Z= 0.116 Angle : 0.479 6.945 11424 Z= 0.252 Chirality : 0.039 0.140 1279 Planarity : 0.005 0.059 1463 Dihedral : 4.975 62.912 1220 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.68 % Allowed : 13.68 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.27), residues: 1032 helix: 2.82 (0.25), residues: 431 sheet: 1.19 (0.37), residues: 190 loop : -0.79 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 446 TYR 0.012 0.001 TYR A 416 PHE 0.010 0.001 PHE A 420 TRP 0.011 0.001 TRP C 191 HIS 0.004 0.001 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 8442) covalent geometry : angle 0.47942 (11424) hydrogen bonds : bond 0.05832 ( 457) hydrogen bonds : angle 3.73305 ( 1251) Misc. bond : bond 0.00029 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5589.53 seconds wall clock time: 95 minutes 0.11 seconds (5700.11 seconds total)