Starting phenix.real_space_refine on Sun Aug 24 00:41:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9itf_60860/08_2025/9itf_60860_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9itf_60860/08_2025/9itf_60860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9itf_60860/08_2025/9itf_60860_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9itf_60860/08_2025/9itf_60860_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9itf_60860/08_2025/9itf_60860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9itf_60860/08_2025/9itf_60860.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.059 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 61 5.16 5 C 5042 2.51 5 N 1368 2.21 5 O 1459 1.98 5 H 7836 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15766 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 7135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 7135 Classifications: {'peptide': 459} Link IDs: {'PTRANS': 20, 'TRANS': 438} Chain breaks: 7 Chain: "A" Number of atoms: 7898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 7898 Classifications: {'peptide': 508} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 487} Chain breaks: 9 Chain: "B" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 647 Classifications: {'peptide': 40} Link IDs: {'TRANS': 39} 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: 2.82, per 1000 atoms: 0.18 Number of scatterers: 15766 At special positions: 0 Unit cell: (67.2, 118.44, 120.12, 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 61 16.00 O 1459 8.00 N 1368 7.00 C 5042 6.00 H 7836 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: 1.03 Conformation dependent library (CDL) restraints added in 423.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1882 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 7 sheets defined 46.2% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'C' and resid 136 through 141 Processing helix chain 'C' and resid 162 through 167 removed outlier: 3.603A pdb=" N SER C 165 " --> pdb=" O ASP C 162 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE C 167 " --> pdb=" O ARG C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 181 Processing helix chain 'C' and resid 183 through 188 removed outlier: 3.648A pdb=" N ASN C 188 " --> pdb=" O THR C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 248 removed outlier: 4.102A pdb=" N GLN C 235 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA C 238 " --> pdb=" O SER C 234 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN C 244 " --> pdb=" O ARG C 240 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 269 Processing helix chain 'C' and resid 304 through 308 Processing helix chain 'C' and resid 309 through 316 Processing helix chain 'C' and resid 355 through 366 Processing helix chain 'C' and resid 411 through 456 Processing helix chain 'C' and resid 461 through 465 Processing helix chain 'C' and resid 495 through 510 Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.783A pdb=" N GLY C 525 " --> pdb=" O LEU C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 592 Processing helix chain 'C' and resid 600 through 613 removed outlier: 3.716A pdb=" N ILE C 613 " --> pdb=" O SER C 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 78 removed outlier: 4.151A pdb=" N TYR A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N THR A 62 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 3.877A 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 111 Processing helix chain 'A' and resid 136 through 141 Processing helix chain 'A' and resid 162 through 166 Processing helix chain 'A' and resid 168 through 181 Processing helix chain 'A' and resid 223 through 247 Processing helix chain 'A' and resid 253 through 269 Processing helix chain 'A' and resid 304 through 308 Processing helix chain 'A' and resid 309 through 317 removed outlier: 3.668A pdb=" N LYS A 317 " --> pdb=" O ARG A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 366 Processing helix chain 'A' and resid 411 through 454 removed outlier: 3.600A pdb=" N ARG A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 473 Processing helix chain 'A' and resid 495 through 510 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 526 through 533 removed outlier: 4.578A pdb=" N ALA A 530 " --> pdb=" O PRO A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 561 Processing helix chain 'A' and resid 580 through 592 Processing helix chain 'A' and resid 600 through 615 Processing helix chain 'B' and resid 45 through 54 Processing sheet with id=AA1, first strand: chain 'C' and resid 113 through 114 removed outlier: 6.594A pdb=" N ALA C 122 " --> pdb=" O ILE C 131 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N TYR C 133 " --> pdb=" O MET C 120 " (cutoff:3.500A) removed outlier: 6.807A 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: 6.475A pdb=" N VAL C 275 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU C 289 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL C 273 " --> pdb=" O GLU C 289 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TRP C 397 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL C 375 " --> pdb=" O TRP C 397 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU C 399 " --> pdb=" O MET C 373 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N MET C 373 " --> pdb=" O LEU C 399 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL C 401 " --> pdb=" O LEU C 371 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU C 371 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N HIS C 403 " --> pdb=" O ALA C 369 " (cutoff:3.500A) removed outlier: 6.808A 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: 6.201A pdb=" N ILE A 130 " --> pdb=" O ASP A 124 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ASP A 124 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY A 132 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N MET A 120 " --> pdb=" O SER A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 302 through 303 removed outlier: 3.799A pdb=" N TYR A 303 " --> pdb=" O GLY A 284 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL A 275 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLU A 289 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL A 273 " --> pdb=" O GLU A 289 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N LEU A 396 " --> pdb=" O ILE A 377 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE A 377 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY A 398 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N HIS A 404 " --> pdb=" O ALA A 369 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 488 through 491 Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 23 449 hydrogen bonds defined for protein. 1215 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: 2.75 Time building geometry restraints manager: 1.43 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: 7814 1.04 - 1.23: 579 1.23 - 1.43: 2864 1.43 - 1.63: 4559 1.63 - 1.83: 100 Bond restraints: 15916 Sorted by residual: bond pdb=" CAP O6E A1201 " pdb=" CBL O6E A1201 " ideal model delta sigma weight residual 1.448 1.352 0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" CAP O6E C1201 " pdb=" CBL O6E C1201 " ideal model delta sigma weight residual 1.448 1.364 0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" CAQ O6E C1201 " pdb=" CBN O6E C1201 " ideal model delta sigma weight residual 1.346 1.420 -0.074 2.00e-02 2.50e+03 1.35e+01 bond pdb=" CAB O6E A1201 " pdb=" CBI O6E A1201 " ideal model delta sigma weight residual 1.449 1.390 0.059 2.00e-02 2.50e+03 8.78e+00 bond pdb=" CAQ O6E A1201 " pdb=" CBN O6E A1201 " ideal model delta sigma weight residual 1.346 1.404 -0.058 2.00e-02 2.50e+03 8.29e+00 ... (remaining 15911 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 28585 2.77 - 5.54: 107 5.54 - 8.32: 2 8.32 - 11.09: 3 11.09 - 13.86: 1 Bond angle restraints: 28698 Sorted by residual: angle pdb=" CAC O6E A1201 " pdb=" CBJ O6E A1201 " pdb=" CBN O6E A1201 " ideal model delta sigma weight residual 111.76 97.90 13.86 3.00e+00 1.11e-01 2.13e+01 angle pdb=" C ASN B 24 " pdb=" CA ASN B 24 " pdb=" CB ASN B 24 " ideal model delta sigma weight residual 116.54 112.19 4.35 1.15e+00 7.56e-01 1.43e+01 angle pdb=" CB MET A 454 " pdb=" CG MET A 454 " pdb=" SD MET A 454 " ideal model delta sigma weight residual 112.70 122.62 -9.92 3.00e+00 1.11e-01 1.09e+01 angle pdb=" N ALA C 558 " pdb=" CA ALA C 558 " pdb=" C ALA C 558 " ideal model delta sigma weight residual 114.64 109.79 4.85 1.52e+00 4.33e-01 1.02e+01 angle pdb=" CAC O6E C1201 " pdb=" CBJ O6E C1201 " pdb=" CBN O6E C1201 " ideal model delta sigma weight residual 111.76 103.11 8.65 3.00e+00 1.11e-01 8.32e+00 ... (remaining 28693 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.54: 7120 27.54 - 55.08: 355 55.08 - 82.63: 31 82.63 - 110.17: 5 110.17 - 137.71: 1 Dihedral angle restraints: 7512 sinusoidal: 4131 harmonic: 3381 Sorted by residual: dihedral pdb=" CAG O6E A1201 " pdb=" CAB O6E A1201 " pdb=" CBI O6E A1201 " pdb=" CBC O6E A1201 " ideal model delta sinusoidal sigma weight residual 180.11 42.40 137.71 1 3.00e+01 1.11e-03 1.86e+01 dihedral pdb=" CA ILE C 208 " pdb=" C ILE C 208 " pdb=" N ASP C 209 " pdb=" CA ASP C 209 " ideal model delta harmonic sigma weight residual 180.00 159.48 20.52 0 5.00e+00 4.00e-02 1.68e+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 180.00 161.69 18.31 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 7509 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1039 0.052 - 0.104: 148 0.104 - 0.157: 41 0.157 - 0.209: 2 0.209 - 0.261: 2 Chirality restraints: 1232 Sorted by residual: chirality pdb=" CBJ O6E A1201 " pdb=" CAC O6E A1201 " pdb=" CBD O6E A1201 " pdb=" CBN O6E A1201 " both_signs ideal model delta sigma weight residual False 2.70 2.96 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CBD O6E A1201 " pdb=" CAT O6E A1201 " pdb=" CAX O6E A1201 " pdb=" CBJ O6E A1201 " both_signs ideal model delta sigma weight residual False -2.69 -2.48 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CBD O6E C1201 " pdb=" CAT O6E C1201 " pdb=" CAX O6E C1201 " pdb=" CBJ O6E C1201 " both_signs ideal model delta sigma weight residual False -2.69 -2.53 -0.16 2.00e-01 2.50e+01 6.67e-01 ... (remaining 1229 not shown) Planarity restraints: 2334 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAA O6E C1201 " -0.473 2.00e-02 2.50e+03 3.13e-01 2.45e+03 pdb=" CAO O6E C1201 " 0.305 2.00e-02 2.50e+03 pdb=" CAP O6E C1201 " -0.126 2.00e-02 2.50e+03 pdb=" CAR O6E C1201 " 0.627 2.00e-02 2.50e+03 pdb=" CAV O6E C1201 " -0.067 2.00e-02 2.50e+03 pdb=" CBB O6E C1201 " -0.155 2.00e-02 2.50e+03 pdb=" CBH O6E C1201 " 0.115 2.00e-02 2.50e+03 pdb=" CBL O6E C1201 " -0.142 2.00e-02 2.50e+03 pdb=" CBO O6E C1201 " 0.265 2.00e-02 2.50e+03 pdb=" NAE O6E C1201 " -0.347 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAB O6E C1201 " 0.361 2.00e-02 2.50e+03 1.76e-01 7.71e+02 pdb=" CAP O6E C1201 " -0.022 2.00e-02 2.50e+03 pdb=" CAS O6E C1201 " -0.245 2.00e-02 2.50e+03 pdb=" CAW O6E C1201 " -0.057 2.00e-02 2.50e+03 pdb=" CBC O6E C1201 " -0.082 2.00e-02 2.50e+03 pdb=" CBI O6E C1201 " 0.093 2.00e-02 2.50e+03 pdb=" CBL O6E C1201 " 0.252 2.00e-02 2.50e+03 pdb=" CBM O6E C1201 " -0.060 2.00e-02 2.50e+03 pdb=" NAJ O6E C1201 " -0.077 2.00e-02 2.50e+03 pdb=" OAK O6E C1201 " -0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAA O6E A1201 " 0.210 2.00e-02 2.50e+03 1.31e-01 4.30e+02 pdb=" CAO O6E A1201 " -0.159 2.00e-02 2.50e+03 pdb=" CAP O6E A1201 " 0.085 2.00e-02 2.50e+03 pdb=" CAR O6E A1201 " -0.262 2.00e-02 2.50e+03 pdb=" CAV O6E A1201 " 0.018 2.00e-02 2.50e+03 pdb=" CBB O6E A1201 " 0.087 2.00e-02 2.50e+03 pdb=" CBH O6E A1201 " -0.045 2.00e-02 2.50e+03 pdb=" CBL O6E A1201 " 0.044 2.00e-02 2.50e+03 pdb=" CBO O6E A1201 " -0.075 2.00e-02 2.50e+03 pdb=" NAE O6E A1201 " 0.096 2.00e-02 2.50e+03 ... (remaining 2331 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 267 2.09 - 2.72: 26040 2.72 - 3.34: 44680 3.34 - 3.97: 56721 3.97 - 4.60: 90325 Nonbonded interactions: 218033 Sorted by model distance: nonbonded pdb=" OE1 GLU C 280 " pdb=" H GLU C 280 " model vdw 1.459 2.450 nonbonded pdb=" OE1 GLU A 496 " pdb=" H GLU A 496 " model vdw 1.524 2.450 nonbonded pdb=" OE1 GLN A 577 " pdb=" H GLN A 577 " model vdw 1.550 2.450 nonbonded pdb=" O HIS C 279 " pdb=" H GLU C 282 " model vdw 1.556 2.450 nonbonded pdb=" OE2 GLU A 125 " pdb="HH11 ARG A 207 " model vdw 1.572 2.450 ... (remaining 218028 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 142 or (resid 159 and (name N or name CA or \ name C or name O or name CB or name CG or name SD or name CE or name HA or name \ HB2 or name HB3 or name HG2 or name HG3 or name HE1 or name HE2 or name HE3)) o \ r resid 160 through 249 or (resid 250 and (name N or name CA or name C or name O \ or name HA2 or name HA3)) or resid 252 through 565 or (resid 578 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name NE or name \ CZ or name NH1 or name NH2 or name HA or name HB2 or name HB3 or name HG2 or na \ me HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 \ or name HH22)) or resid 579 through 614 or resid 1201)) selection = (chain 'C' and (resid 111 through 142 or resid 159 through 251 or (resid 252 and \ (name N or name CA or name C or name O or name CB or name CG or name OD1 or nam \ e OD2 or name HA or name HB2 or name HB3)) or resid 253 through 336 or resid 339 \ through 454 or (resid 461 and (name N or name CA or name C or name O or name CB \ or name HA or name HB1 or name HB2 or name HB3)) or resid 462 through 483 or (r \ esid 486 and (name N or name CA or name C or name O or name CB or name CG or nam \ e CD or name CE or name NZ or name HA or name HB2 or name HB3 or name HG2 or nam \ e HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ1 or name HZ2 or \ name HZ3)) or resid 487 through 1201)) } 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: 0.060 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.670 Find NCS groups from input model: 0.210 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:8.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 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 8082 Z= 0.234 Angle : 0.676 13.861 10922 Z= 0.351 Chirality : 0.041 0.261 1232 Planarity : 0.012 0.313 1386 Dihedral : 15.664 137.712 3009 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.76 % Allowed : 20.89 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.27), residues: 967 helix: 2.15 (0.26), residues: 404 sheet: -0.25 (0.33), residues: 195 loop : -1.35 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 339 TYR 0.016 0.002 TYR A 416 PHE 0.015 0.001 PHE A 412 TRP 0.010 0.001 TRP A 191 HIS 0.005 0.001 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.00453 ( 8080) covalent geometry : angle 0.67576 (10922) hydrogen bonds : bond 0.13163 ( 449) hydrogen bonds : angle 5.71995 ( 1215) Misc. bond : bond 0.06090 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 138 ARG cc_start: 0.7773 (ttt180) cc_final: 0.6982 (ttm110) REVERT: C 562 LYS cc_start: 0.7655 (mmtt) cc_final: 0.7357 (mtmp) REVERT: A 412 PHE cc_start: 0.7664 (t80) cc_final: 0.7222 (t80) REVERT: A 445 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8107 (tt) REVERT: A 520 SER cc_start: 0.8633 (t) cc_final: 0.8333 (m) REVERT: A 582 ARG cc_start: 0.7378 (mtm-85) cc_final: 0.6957 (mtp85) REVERT: B 18 MET cc_start: 0.8084 (mtm) cc_final: 0.7311 (mmt) REVERT: B 30 LYS cc_start: 0.8159 (ttmt) cc_final: 0.7936 (tttm) outliers start: 15 outliers final: 10 residues processed: 140 average time/residue: 1.0444 time to fit residues: 155.0518 Evaluate side-chains 136 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 357 CYS Chi-restraints excluded: chain C residue 373 MET Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 445 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 448 GLN B 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.147182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.119881 restraints weight = 30897.892| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.44 r_work: 0.3501 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8082 Z= 0.176 Angle : 0.565 8.722 10922 Z= 0.289 Chirality : 0.040 0.156 1232 Planarity : 0.005 0.052 1386 Dihedral : 6.810 72.335 1174 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.82 % Allowed : 18.66 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.27), residues: 967 helix: 2.22 (0.26), residues: 414 sheet: -0.21 (0.34), residues: 195 loop : -1.36 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 339 TYR 0.012 0.002 TYR C 416 PHE 0.012 0.001 PHE A 117 TRP 0.009 0.001 TRP C 191 HIS 0.006 0.001 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 8080) covalent geometry : angle 0.56525 (10922) hydrogen bonds : bond 0.05011 ( 449) hydrogen bonds : angle 4.91565 ( 1215) Misc. bond : bond 0.00099 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 138 ARG cc_start: 0.7853 (ttt180) cc_final: 0.7098 (ttm110) REVERT: C 373 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8705 (mtp) REVERT: C 428 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.7303 (tt0) REVERT: C 499 ILE cc_start: 0.8555 (tp) cc_final: 0.8336 (mm) REVERT: C 562 LYS cc_start: 0.7714 (mmtt) cc_final: 0.7499 (mtmp) REVERT: A 412 PHE cc_start: 0.7578 (t80) cc_final: 0.7373 (t80) REVERT: A 445 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8085 (tt) REVERT: A 490 LEU cc_start: 0.8022 (tp) cc_final: 0.7601 (mt) REVERT: A 582 ARG cc_start: 0.7505 (mtm-85) cc_final: 0.7064 (mtp85) REVERT: B 19 GLU cc_start: 0.7425 (tt0) cc_final: 0.6789 (mt-10) REVERT: B 30 LYS cc_start: 0.7885 (ttmt) cc_final: 0.7457 (tttm) outliers start: 24 outliers final: 11 residues processed: 154 average time/residue: 1.1243 time to fit residues: 182.9211 Evaluate side-chains 136 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 357 CYS Chi-restraints excluded: chain C residue 373 MET Chi-restraints excluded: chain C residue 428 GLN Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 517 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 73 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 21 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.147209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.120875 restraints weight = 30656.927| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.37 r_work: 0.3510 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8082 Z= 0.168 Angle : 0.549 8.234 10922 Z= 0.279 Chirality : 0.040 0.154 1232 Planarity : 0.005 0.062 1386 Dihedral : 6.598 79.271 1166 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.17 % Allowed : 18.54 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.27), residues: 967 helix: 2.26 (0.26), residues: 413 sheet: -0.22 (0.34), residues: 195 loop : -1.45 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 339 TYR 0.013 0.001 TYR C 298 PHE 0.012 0.001 PHE A 117 TRP 0.008 0.001 TRP C 191 HIS 0.006 0.001 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 8080) covalent geometry : angle 0.54883 (10922) hydrogen bonds : bond 0.04745 ( 449) hydrogen bonds : angle 4.68342 ( 1215) Misc. bond : bond 0.00032 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 138 ARG cc_start: 0.7846 (ttt180) cc_final: 0.7106 (ttm110) REVERT: C 428 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.7319 (tt0) REVERT: C 499 ILE cc_start: 0.8524 (tp) cc_final: 0.8291 (mm) REVERT: A 138 ARG cc_start: 0.7961 (tpp-160) cc_final: 0.7537 (mtm-85) REVERT: A 445 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8031 (tt) REVERT: A 490 LEU cc_start: 0.8115 (tp) cc_final: 0.7768 (mt) REVERT: A 582 ARG cc_start: 0.7517 (mtm-85) cc_final: 0.7110 (mtp85) REVERT: B 19 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.6849 (pm20) REVERT: B 23 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7580 (mt-10) REVERT: B 27 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7590 (mm) REVERT: B 30 LYS cc_start: 0.7805 (ttmt) cc_final: 0.7251 (tttm) outliers start: 27 outliers final: 17 residues processed: 149 average time/residue: 0.9978 time to fit residues: 157.9801 Evaluate side-chains 145 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 357 CYS Chi-restraints excluded: chain C residue 428 GLN Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 357 CYS Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 27 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 19 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 85 optimal weight: 0.1980 chunk 56 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.145540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.118920 restraints weight = 30824.373| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.38 r_work: 0.3494 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8082 Z= 0.190 Angle : 0.565 8.031 10922 Z= 0.287 Chirality : 0.040 0.152 1232 Planarity : 0.005 0.048 1386 Dihedral : 6.522 83.410 1163 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.82 % Allowed : 19.84 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.27), residues: 967 helix: 2.15 (0.26), residues: 414 sheet: -0.26 (0.34), residues: 194 loop : -1.54 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 129 TYR 0.014 0.002 TYR C 416 PHE 0.013 0.001 PHE A 117 TRP 0.009 0.002 TRP C 191 HIS 0.005 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 8080) covalent geometry : angle 0.56513 (10922) hydrogen bonds : bond 0.04811 ( 449) hydrogen bonds : angle 4.66849 ( 1215) Misc. bond : bond 0.00042 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 138 ARG cc_start: 0.7827 (ttt180) cc_final: 0.7063 (ttm110) REVERT: C 159 MET cc_start: 0.5486 (tpt) cc_final: 0.4916 (tpt) REVERT: C 164 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7761 (mtp85) REVERT: C 428 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7358 (tt0) REVERT: A 138 ARG cc_start: 0.7995 (tpp-160) cc_final: 0.7579 (mtm-85) REVERT: A 445 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8051 (tt) REVERT: A 490 LEU cc_start: 0.8108 (tp) cc_final: 0.7834 (mt) REVERT: A 582 ARG cc_start: 0.7483 (mtm-85) cc_final: 0.7071 (mtp85) REVERT: B 19 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6715 (mt-10) REVERT: B 30 LYS cc_start: 0.7879 (ttmt) cc_final: 0.7448 (tttm) outliers start: 24 outliers final: 14 residues processed: 148 average time/residue: 1.0069 time to fit residues: 158.3430 Evaluate side-chains 144 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 357 CYS Chi-restraints excluded: chain C residue 428 GLN Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 357 CYS Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain B residue 19 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 55 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 25 optimal weight: 0.2980 chunk 75 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.147470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.121292 restraints weight = 30465.423| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.35 r_work: 0.3509 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8082 Z= 0.148 Angle : 0.540 7.814 10922 Z= 0.273 Chirality : 0.039 0.152 1232 Planarity : 0.005 0.047 1386 Dihedral : 6.357 85.011 1163 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.58 % Allowed : 19.95 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.27), residues: 967 helix: 2.31 (0.26), residues: 414 sheet: -0.19 (0.34), residues: 199 loop : -1.48 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 129 TYR 0.011 0.001 TYR C 416 PHE 0.013 0.001 PHE A 117 TRP 0.008 0.001 TRP C 397 HIS 0.005 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 8080) covalent geometry : angle 0.53981 (10922) hydrogen bonds : bond 0.04464 ( 449) hydrogen bonds : angle 4.51455 ( 1215) Misc. bond : bond 0.00024 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 138 ARG cc_start: 0.7852 (ttt180) cc_final: 0.7045 (ttm110) REVERT: C 159 MET cc_start: 0.5545 (tpt) cc_final: 0.5081 (tpt) REVERT: C 164 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7720 (mtp85) REVERT: C 428 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.7317 (tt0) REVERT: A 445 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8015 (tt) REVERT: A 490 LEU cc_start: 0.8100 (tp) cc_final: 0.7844 (mt) REVERT: A 582 ARG cc_start: 0.7472 (mtm-85) cc_final: 0.7077 (mtp85) REVERT: B 19 GLU cc_start: 0.7417 (tt0) cc_final: 0.6753 (mt-10) REVERT: B 27 ILE cc_start: 0.8067 (OUTLIER) cc_final: 0.7662 (mm) REVERT: B 30 LYS cc_start: 0.7821 (ttmt) cc_final: 0.7416 (tttm) outliers start: 22 outliers final: 13 residues processed: 148 average time/residue: 0.9406 time to fit residues: 148.0214 Evaluate side-chains 141 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 357 CYS Chi-restraints excluded: chain C residue 428 GLN Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain B residue 27 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 0.0020 chunk 36 optimal weight: 0.0470 chunk 15 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.9290 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.147836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.121400 restraints weight = 30422.640| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.37 r_work: 0.3526 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8082 Z= 0.118 Angle : 0.513 7.567 10922 Z= 0.259 Chirality : 0.039 0.148 1232 Planarity : 0.004 0.047 1386 Dihedral : 6.102 86.057 1163 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.00 % Allowed : 21.13 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.27), residues: 967 helix: 2.50 (0.26), residues: 414 sheet: -0.13 (0.35), residues: 200 loop : -1.44 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 129 TYR 0.010 0.001 TYR C 303 PHE 0.012 0.001 PHE A 117 TRP 0.009 0.001 TRP C 191 HIS 0.004 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8080) covalent geometry : angle 0.51262 (10922) hydrogen bonds : bond 0.04099 ( 449) hydrogen bonds : angle 4.35549 ( 1215) Misc. bond : bond 0.00014 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 138 ARG cc_start: 0.7822 (ttt180) cc_final: 0.6999 (ttm110) REVERT: C 159 MET cc_start: 0.5451 (tpt) cc_final: 0.4949 (tpt) REVERT: C 164 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7797 (mpp80) REVERT: A 182 ARG cc_start: 0.7049 (ttt-90) cc_final: 0.6404 (ttp-170) REVERT: A 445 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.8004 (tt) REVERT: A 490 LEU cc_start: 0.8087 (tp) cc_final: 0.7873 (mt) REVERT: A 582 ARG cc_start: 0.7424 (mtm-85) cc_final: 0.7041 (mtp85) REVERT: B 19 GLU cc_start: 0.7422 (tt0) cc_final: 0.6765 (mt-10) REVERT: B 30 LYS cc_start: 0.7852 (ttmt) cc_final: 0.7451 (tttm) outliers start: 17 outliers final: 12 residues processed: 143 average time/residue: 0.8899 time to fit residues: 135.4650 Evaluate side-chains 135 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 357 CYS Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 357 CYS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 614 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 4 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 77 optimal weight: 0.2980 chunk 53 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.146163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.119779 restraints weight = 30394.804| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.35 r_work: 0.3501 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8082 Z= 0.163 Angle : 0.551 7.739 10922 Z= 0.279 Chirality : 0.039 0.150 1232 Planarity : 0.004 0.047 1386 Dihedral : 6.376 87.007 1163 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.46 % Allowed : 21.01 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.27), residues: 967 helix: 2.40 (0.26), residues: 414 sheet: -0.13 (0.35), residues: 199 loop : -1.43 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 129 TYR 0.013 0.001 TYR C 416 PHE 0.011 0.001 PHE A 117 TRP 0.008 0.001 TRP C 191 HIS 0.005 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 8080) covalent geometry : angle 0.55136 (10922) hydrogen bonds : bond 0.04424 ( 449) hydrogen bonds : angle 4.43724 ( 1215) Misc. bond : bond 0.00038 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 138 ARG cc_start: 0.7812 (ttt180) cc_final: 0.7003 (ttm110) REVERT: C 159 MET cc_start: 0.5521 (tpt) cc_final: 0.5095 (tpt) REVERT: C 164 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7828 (mpp80) REVERT: C 428 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.7305 (tt0) REVERT: A 445 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8011 (tt) REVERT: A 548 ASP cc_start: 0.8110 (m-30) cc_final: 0.7908 (m-30) REVERT: A 582 ARG cc_start: 0.7461 (mtm-85) cc_final: 0.7084 (mtp85) REVERT: B 19 GLU cc_start: 0.7384 (tt0) cc_final: 0.6709 (mt-10) REVERT: B 30 LYS cc_start: 0.7880 (ttmt) cc_final: 0.7474 (tttm) outliers start: 21 outliers final: 13 residues processed: 140 average time/residue: 0.9085 time to fit residues: 136.0691 Evaluate side-chains 137 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 357 CYS Chi-restraints excluded: chain C residue 428 GLN Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 357 CYS Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 614 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 35 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.147208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.120827 restraints weight = 30734.738| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.37 r_work: 0.3512 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8082 Z= 0.131 Angle : 0.527 7.487 10922 Z= 0.266 Chirality : 0.039 0.143 1232 Planarity : 0.004 0.047 1386 Dihedral : 6.145 88.212 1163 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.35 % Allowed : 21.36 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.27), residues: 967 helix: 2.52 (0.26), residues: 414 sheet: -0.07 (0.35), residues: 200 loop : -1.41 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 129 TYR 0.011 0.001 TYR C 303 PHE 0.012 0.001 PHE A 117 TRP 0.008 0.001 TRP C 191 HIS 0.004 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 8080) covalent geometry : angle 0.52747 (10922) hydrogen bonds : bond 0.04150 ( 449) hydrogen bonds : angle 4.32667 ( 1215) Misc. bond : bond 0.00025 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 138 ARG cc_start: 0.7790 (ttt180) cc_final: 0.6948 (ttm110) REVERT: C 159 MET cc_start: 0.5551 (tpt) cc_final: 0.5216 (tpt) REVERT: C 164 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7811 (mpp80) REVERT: A 445 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8016 (tt) REVERT: A 541 VAL cc_start: 0.7989 (OUTLIER) cc_final: 0.7774 (t) REVERT: A 548 ASP cc_start: 0.8107 (m-30) cc_final: 0.7889 (m-30) REVERT: A 582 ARG cc_start: 0.7444 (mtm-85) cc_final: 0.7055 (mtp85) REVERT: B 19 GLU cc_start: 0.7460 (tt0) cc_final: 0.6763 (mt-10) REVERT: B 30 LYS cc_start: 0.7887 (ttmt) cc_final: 0.7482 (tttm) outliers start: 20 outliers final: 15 residues processed: 141 average time/residue: 0.9489 time to fit residues: 142.3562 Evaluate side-chains 138 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 357 CYS Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 357 CYS Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 614 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 0 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.147229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.121124 restraints weight = 30367.661| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.35 r_work: 0.3511 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8082 Z= 0.156 Angle : 0.549 7.572 10922 Z= 0.277 Chirality : 0.039 0.147 1232 Planarity : 0.004 0.046 1386 Dihedral : 6.279 89.048 1163 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.23 % Allowed : 21.48 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.27), residues: 967 helix: 2.46 (0.25), residues: 414 sheet: -0.12 (0.35), residues: 199 loop : -1.44 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 129 TYR 0.013 0.001 TYR C 416 PHE 0.011 0.001 PHE A 117 TRP 0.009 0.001 TRP C 191 HIS 0.005 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 8080) covalent geometry : angle 0.54879 (10922) hydrogen bonds : bond 0.04321 ( 449) hydrogen bonds : angle 4.38529 ( 1215) Misc. bond : bond 0.00048 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 138 ARG cc_start: 0.7823 (ttt180) cc_final: 0.7023 (ttm110) REVERT: C 164 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7730 (mpp80) REVERT: A 445 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7991 (tt) REVERT: A 541 VAL cc_start: 0.7992 (OUTLIER) cc_final: 0.7788 (t) REVERT: A 548 ASP cc_start: 0.8070 (m-30) cc_final: 0.7823 (m-30) REVERT: A 582 ARG cc_start: 0.7456 (mtm-85) cc_final: 0.7089 (mtp85) REVERT: B 18 MET cc_start: 0.8203 (mtm) cc_final: 0.7026 (mmt) REVERT: B 19 GLU cc_start: 0.7406 (tt0) cc_final: 0.6692 (mt-10) REVERT: B 30 LYS cc_start: 0.7954 (ttmt) cc_final: 0.7484 (tttm) outliers start: 19 outliers final: 15 residues processed: 141 average time/residue: 0.9711 time to fit residues: 145.6759 Evaluate side-chains 140 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 357 CYS Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 357 CYS Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 614 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 63 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 80 optimal weight: 0.0170 chunk 32 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 overall best weight: 0.9420 ------------------------------------------------------------------------------- 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 = 0.3983 r_free = 0.3983 target = 0.148570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.122540 restraints weight = 30306.861| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.35 r_work: 0.3528 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8082 Z= 0.120 Angle : 0.528 7.387 10922 Z= 0.266 Chirality : 0.039 0.142 1232 Planarity : 0.005 0.089 1386 Dihedral : 6.035 89.544 1163 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.23 % Allowed : 21.71 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.00 (0.28), residues: 967 helix: 2.64 (0.26), residues: 414 sheet: -0.08 (0.35), residues: 200 loop : -1.37 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 352 TYR 0.013 0.001 TYR A 416 PHE 0.013 0.001 PHE A 117 TRP 0.008 0.001 TRP A 191 HIS 0.004 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 8080) covalent geometry : angle 0.52777 (10922) hydrogen bonds : bond 0.04016 ( 449) hydrogen bonds : angle 4.28178 ( 1215) Misc. bond : bond 0.00035 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 138 ARG cc_start: 0.7794 (ttt180) cc_final: 0.6976 (ttm110) REVERT: C 164 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7737 (mpp80) REVERT: C 428 GLN cc_start: 0.7494 (OUTLIER) cc_final: 0.7236 (tt0) REVERT: A 445 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8012 (tt) REVERT: A 541 VAL cc_start: 0.7988 (OUTLIER) cc_final: 0.7774 (t) REVERT: A 548 ASP cc_start: 0.8106 (m-30) cc_final: 0.7872 (m-30) REVERT: A 582 ARG cc_start: 0.7427 (mtm-85) cc_final: 0.7042 (mtp85) REVERT: B 19 GLU cc_start: 0.7331 (tt0) cc_final: 0.6627 (mt-10) REVERT: B 30 LYS cc_start: 0.7936 (ttmt) cc_final: 0.7525 (tttm) outliers start: 19 outliers final: 12 residues processed: 141 average time/residue: 0.9950 time to fit residues: 149.6665 Evaluate side-chains 137 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 357 CYS Chi-restraints excluded: chain C residue 428 GLN Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 357 CYS Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 614 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 8 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.147064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.120826 restraints weight = 30319.507| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.34 r_work: 0.3501 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8082 Z= 0.165 Angle : 0.558 7.587 10922 Z= 0.281 Chirality : 0.040 0.150 1232 Planarity : 0.005 0.072 1386 Dihedral : 6.278 89.950 1163 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.11 % Allowed : 21.71 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.27), residues: 967 helix: 2.51 (0.25), residues: 414 sheet: -0.15 (0.35), residues: 199 loop : -1.40 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 352 TYR 0.016 0.002 TYR A 416 PHE 0.011 0.001 PHE A 117 TRP 0.008 0.001 TRP C 191 HIS 0.005 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 8080) covalent geometry : angle 0.55761 (10922) hydrogen bonds : bond 0.04342 ( 449) hydrogen bonds : angle 4.38724 ( 1215) Misc. bond : bond 0.00069 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4821.96 seconds wall clock time: 82 minutes 4.76 seconds (4924.76 seconds total)