Starting phenix.real_space_refine on Wed Feb 12 20:20:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yb4_39108/02_2025/8yb4_39108.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yb4_39108/02_2025/8yb4_39108.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yb4_39108/02_2025/8yb4_39108.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yb4_39108/02_2025/8yb4_39108.map" model { file = "/net/cci-nas-00/data/ceres_data/8yb4_39108/02_2025/8yb4_39108.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yb4_39108/02_2025/8yb4_39108.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 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: 4 Type Number sf(0) Gaussians S 65 5.16 5 C 5321 2.51 5 N 1447 2.21 5 O 1567 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8400 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 4211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4211 Classifications: {'peptide': 542} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 518} Chain breaks: 3 Chain: "A" Number of atoms: 3701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3701 Classifications: {'peptide': 477} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 456} Chain breaks: 3 Chain: "C" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 402 Classifications: {'peptide': 48} Link IDs: {'TRANS': 47} Chain breaks: 1 Chain: "B" 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: 5.14, per 1000 atoms: 0.61 Number of scatterers: 8400 At special positions: 0 Unit cell: (73.95, 111.35, 122.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 65 16.00 O 1567 8.00 N 1447 7.00 C 5321 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.21 Conformation dependent library (CDL) restraints added in 1.0 seconds 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1994 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 7 sheets defined 45.6% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'B' and resid 55 through 77 removed outlier: 3.626A pdb=" N GLN B 59 " --> pdb=" O SER B 55 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR B 62 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL B 63 " --> pdb=" O GLN B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 90 Processing helix chain 'B' and resid 97 through 110 removed outlier: 3.835A pdb=" N ILE B 101 " --> pdb=" O PRO B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 142 removed outlier: 4.045A pdb=" N GLU B 139 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY B 142 " --> pdb=" O ARG B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 166 removed outlier: 3.522A pdb=" N LEU B 166 " --> pdb=" O VAL B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 180 Processing helix chain 'B' and resid 223 through 247 removed outlier: 3.609A pdb=" N ALA B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER B 234 " --> pdb=" O GLY B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 268 removed outlier: 3.609A pdb=" N GLU B 262 " --> pdb=" O ASP B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 removed outlier: 3.561A pdb=" N ASP B 307 " --> pdb=" O PRO B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 319 Processing helix chain 'B' and resid 355 through 366 Processing helix chain 'B' and resid 411 through 458 removed outlier: 4.065A pdb=" N ARG B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR B 416 " --> pdb=" O PHE B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 466 removed outlier: 3.693A pdb=" N GLN B 466 " --> pdb=" O GLY B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 473 Processing helix chain 'B' and resid 495 through 510 Processing helix chain 'B' and resid 520 through 525 removed outlier: 3.702A pdb=" N GLY B 525 " --> pdb=" O LEU B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 533 removed outlier: 3.538A pdb=" N GLY B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 561 Processing helix chain 'B' and resid 580 through 592 Processing helix chain 'B' and resid 600 through 621 removed outlier: 3.504A pdb=" N SER B 621 " --> pdb=" O SER B 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 141 Processing helix chain 'A' and resid 162 through 167 removed outlier: 3.656A pdb=" N PHE A 167 " --> pdb=" O ARG A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 181 Processing helix chain 'A' and resid 225 through 246 removed outlier: 3.653A pdb=" N ALA A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN A 235 " --> pdb=" O ALA A 231 " (cutoff:3.500A) 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 319 Processing helix chain 'A' and resid 355 through 366 Processing helix chain 'A' and resid 411 through 457 removed outlier: 3.861A pdb=" N GLN A 423 " --> pdb=" O GLU A 419 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 464 removed outlier: 3.830A pdb=" N ILE A 463 " --> pdb=" O PRO A 460 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL A 464 " --> pdb=" O ALA A 461 " (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 528 through 533 removed outlier: 3.880A pdb=" N LEU A 532 " --> pdb=" O GLY A 528 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 528 through 533' Processing helix chain 'A' and resid 580 through 592 removed outlier: 4.770A pdb=" N GLN A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LEU A 589 " --> pdb=" O PHE A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 621 Processing helix chain 'C' and resid 45 through 54 Processing sheet with id=AA1, first strand: chain 'B' and resid 113 through 114 removed outlier: 6.418A pdb=" N ILE B 130 " --> pdb=" O ASP B 124 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ASP B 124 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N MET B 120 " --> pdb=" O SER B 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 302 through 303 removed outlier: 6.644A pdb=" N VAL B 275 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLU B 289 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL B 273 " --> pdb=" O GLU B 289 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TRP B 397 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER B 393 " --> pdb=" O GLY B 379 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL B 375 " --> pdb=" O TRP B 397 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LEU B 399 " --> pdb=" O MET B 373 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N MET B 373 " --> pdb=" O LEU B 399 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N VAL B 401 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU B 371 " --> pdb=" O VAL B 401 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 486 through 491 removed outlier: 3.572A pdb=" N PHE B 549 " --> pdb=" O LEU B 482 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET B 539 " --> pdb=" O THR B 518 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR B 518 " --> pdb=" O MET B 539 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU B 516 " --> pdb=" O VAL B 541 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 113 through 114 removed outlier: 6.543A pdb=" N ALA A 122 " --> pdb=" O ILE A 131 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 302 through 303 removed outlier: 5.770A pdb=" N VAL A 286 " --> pdb=" O LYS A 277 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LYS A 277 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA A 288 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N TRP A 397 " --> pdb=" O PHE A 278 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL A 375 " --> pdb=" O TRP A 397 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LEU A 399 " --> pdb=" O MET A 373 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N MET A 373 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL A 401 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU A 371 " --> pdb=" O VAL A 401 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 486 through 491 removed outlier: 4.095A pdb=" N GLY A 478 " --> pdb=" O PHE A 553 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 18 through 23 448 hydrogen bonds defined for protein. 1239 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: 2.67 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2757 1.34 - 1.46: 1423 1.46 - 1.58: 4281 1.58 - 1.70: 0 1.70 - 1.82: 107 Bond restraints: 8568 Sorted by residual: bond pdb=" CAP O6E A1201 " pdb=" CBL O6E A1201 " ideal model delta sigma weight residual 1.448 1.385 0.063 2.00e-02 2.50e+03 9.77e+00 bond pdb=" CAP O6E B1201 " pdb=" CBL O6E B1201 " ideal model delta sigma weight residual 1.448 1.386 0.062 2.00e-02 2.50e+03 9.60e+00 bond pdb=" CAB O6E B1201 " pdb=" CBI O6E B1201 " ideal model delta sigma weight residual 1.449 1.388 0.061 2.00e-02 2.50e+03 9.35e+00 bond pdb=" N ASP A 209 " pdb=" CA ASP A 209 " ideal model delta sigma weight residual 1.457 1.497 -0.039 1.29e-02 6.01e+03 9.26e+00 bond pdb=" CAB O6E A1201 " pdb=" CBI O6E A1201 " ideal model delta sigma weight residual 1.449 1.389 0.060 2.00e-02 2.50e+03 9.06e+00 ... (remaining 8563 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 11461 2.50 - 5.00: 111 5.00 - 7.51: 20 7.51 - 10.01: 2 10.01 - 12.51: 1 Bond angle restraints: 11595 Sorted by residual: angle pdb=" C PRO A 411 " pdb=" N PHE A 412 " pdb=" CA PHE A 412 " ideal model delta sigma weight residual 120.26 125.58 -5.32 1.34e+00 5.57e-01 1.58e+01 angle pdb=" CA LEU A 614 " pdb=" CB LEU A 614 " pdb=" CG LEU A 614 " ideal model delta sigma weight residual 116.30 128.81 -12.51 3.50e+00 8.16e-02 1.28e+01 angle pdb=" C PHE A 585 " pdb=" N GLN A 586 " pdb=" CA GLN A 586 " ideal model delta sigma weight residual 121.54 128.15 -6.61 1.91e+00 2.74e-01 1.20e+01 angle pdb=" N VAL A 210 " pdb=" CA VAL A 210 " pdb=" C VAL A 210 " ideal model delta sigma weight residual 111.58 108.09 3.49 1.06e+00 8.90e-01 1.09e+01 angle pdb=" CA ASP A 209 " pdb=" CB ASP A 209 " pdb=" CG ASP A 209 " ideal model delta sigma weight residual 112.60 115.87 -3.27 1.00e+00 1.00e+00 1.07e+01 ... (remaining 11590 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 4336 17.74 - 35.47: 627 35.47 - 53.21: 180 53.21 - 70.94: 43 70.94 - 88.68: 14 Dihedral angle restraints: 5200 sinusoidal: 2114 harmonic: 3086 Sorted by residual: dihedral pdb=" CA GLN A 586 " pdb=" C GLN A 586 " pdb=" N ALA A 587 " pdb=" CA ALA A 587 " ideal model delta harmonic sigma weight residual 180.00 160.87 19.13 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA ARG A 292 " pdb=" C ARG A 292 " pdb=" N ASP A 293 " pdb=" CA ASP A 293 " ideal model delta harmonic sigma weight residual -180.00 -163.26 -16.74 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA ASN A 188 " pdb=" CB ASN A 188 " pdb=" CG ASN A 188 " pdb=" OD1 ASN A 188 " ideal model delta sinusoidal sigma weight residual 120.00 -169.21 -70.79 2 2.00e+01 2.50e-03 1.07e+01 ... (remaining 5197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1122 0.056 - 0.111: 149 0.111 - 0.167: 22 0.167 - 0.223: 1 0.223 - 0.279: 1 Chirality restraints: 1295 Sorted by residual: chirality pdb=" CG LEU A 614 " pdb=" CB LEU A 614 " pdb=" CD1 LEU A 614 " pdb=" CD2 LEU A 614 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CA VAL A 210 " pdb=" N VAL A 210 " pdb=" C VAL A 210 " pdb=" CB VAL A 210 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA VAL A 321 " pdb=" N VAL A 321 " pdb=" C VAL A 321 " pdb=" CB VAL A 321 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.45e-01 ... (remaining 1292 not shown) Planarity restraints: 1487 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAB O6E A1201 " 0.587 2.00e-02 2.50e+03 3.88e-01 3.76e+03 pdb=" CAP O6E A1201 " 0.053 2.00e-02 2.50e+03 pdb=" CAS O6E A1201 " -0.597 2.00e-02 2.50e+03 pdb=" CAW O6E A1201 " -0.220 2.00e-02 2.50e+03 pdb=" CBC O6E A1201 " -0.212 2.00e-02 2.50e+03 pdb=" CBI O6E A1201 " 0.150 2.00e-02 2.50e+03 pdb=" CBL O6E A1201 " 0.657 2.00e-02 2.50e+03 pdb=" CBM O6E A1201 " -0.055 2.00e-02 2.50e+03 pdb=" NAJ O6E A1201 " -0.486 2.00e-02 2.50e+03 pdb=" OAK O6E A1201 " 0.123 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAB O6E B1201 " -0.499 2.00e-02 2.50e+03 3.51e-01 3.09e+03 pdb=" CAP O6E B1201 " -0.023 2.00e-02 2.50e+03 pdb=" CAS O6E B1201 " 0.505 2.00e-02 2.50e+03 pdb=" CAW O6E B1201 " 0.214 2.00e-02 2.50e+03 pdb=" CBC O6E B1201 " 0.180 2.00e-02 2.50e+03 pdb=" CBI O6E B1201 " -0.130 2.00e-02 2.50e+03 pdb=" CBL O6E B1201 " -0.616 2.00e-02 2.50e+03 pdb=" CBM O6E B1201 " 0.044 2.00e-02 2.50e+03 pdb=" NAJ O6E B1201 " 0.479 2.00e-02 2.50e+03 pdb=" OAK O6E B1201 " -0.154 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAA O6E A1201 " -0.309 2.00e-02 2.50e+03 2.28e-01 1.29e+03 pdb=" CAO O6E A1201 " -0.041 2.00e-02 2.50e+03 pdb=" CAP O6E A1201 " -0.362 2.00e-02 2.50e+03 pdb=" CAR O6E A1201 " 0.430 2.00e-02 2.50e+03 pdb=" CAV O6E A1201 " 0.021 2.00e-02 2.50e+03 pdb=" CBB O6E A1201 " -0.103 2.00e-02 2.50e+03 pdb=" CBH O6E A1201 " 0.064 2.00e-02 2.50e+03 pdb=" CBL O6E A1201 " -0.089 2.00e-02 2.50e+03 pdb=" CBO O6E A1201 " 0.138 2.00e-02 2.50e+03 pdb=" NAE O6E A1201 " 0.251 2.00e-02 2.50e+03 ... (remaining 1484 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 807 2.74 - 3.28: 7861 3.28 - 3.82: 13389 3.82 - 4.36: 15170 4.36 - 4.90: 27360 Nonbonded interactions: 64587 Sorted by model distance: nonbonded pdb=" O ALA B 535 " pdb=" OG SER B 555 " model vdw 2.205 3.040 nonbonded pdb=" OG SER A 134 " pdb=" OD1 ASN A 136 " model vdw 2.207 3.040 nonbonded pdb=" O GLY B 379 " pdb=" OG SER B 393 " model vdw 2.209 3.040 nonbonded pdb=" NH1 ARG B 177 " pdb=" O GLU C 53 " model vdw 2.287 3.120 nonbonded pdb=" NH1 ARG B 129 " pdb=" O GLY B 160 " model vdw 2.313 3.120 ... (remaining 64582 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' selection = (chain 'B' and (resid 111 through 144 or resid 156 through 565 or resid 578 thro \ ugh 621 or resid 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: 0.600 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: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.010 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 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 : 0.004 0.063 8568 Z= 0.231 Angle : 0.619 12.512 11595 Z= 0.319 Chirality : 0.040 0.279 1295 Planarity : 0.016 0.388 1487 Dihedral : 18.652 88.678 3206 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.33 % Allowed : 29.99 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.27), residues: 1047 helix: 2.07 (0.26), residues: 435 sheet: -0.48 (0.38), residues: 187 loop : -1.60 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 191 HIS 0.005 0.001 HIS B 206 PHE 0.015 0.001 PHE A 551 TYR 0.009 0.001 TYR A 487 ARG 0.005 0.000 ARG B 320 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 109 time to evaluate : 0.980 Fit side-chains REVERT: B 109 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8418 (mt0) REVERT: B 220 ARG cc_start: 0.8043 (ttm170) cc_final: 0.7753 (mtt-85) outliers start: 3 outliers final: 1 residues processed: 112 average time/residue: 0.2321 time to fit residues: 35.0363 Evaluate side-chains 107 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 105 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 GLN Chi-restraints excluded: chain A residue 209 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 82 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 GLN B 319 ASN B 448 GLN B 580 HIS A 115 GLN A 336 GLN A 466 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.138891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.099274 restraints weight = 11070.628| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.93 r_work: 0.3082 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8568 Z= 0.227 Angle : 0.575 11.141 11595 Z= 0.285 Chirality : 0.039 0.146 1295 Planarity : 0.005 0.053 1487 Dihedral : 7.177 87.941 1241 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.20 % Allowed : 26.13 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.27), residues: 1047 helix: 2.11 (0.25), residues: 443 sheet: -0.27 (0.38), residues: 187 loop : -1.60 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 397 HIS 0.005 0.001 HIS B 206 PHE 0.014 0.001 PHE B 117 TYR 0.011 0.001 TYR B 276 ARG 0.004 0.000 ARG A 547 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 106 time to evaluate : 0.811 Fit side-chains REVERT: B 109 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8360 (mt0) REVERT: B 220 ARG cc_start: 0.8583 (ttm170) cc_final: 0.8245 (mmm-85) REVERT: A 532 LEU cc_start: 0.6628 (OUTLIER) cc_final: 0.6376 (mm) REVERT: A 586 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7707 (pt0) outliers start: 29 outliers final: 13 residues processed: 131 average time/residue: 0.2182 time to fit residues: 38.5825 Evaluate side-chains 119 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 TYR Chi-restraints excluded: chain B residue 109 GLN Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 586 GLN Chi-restraints excluded: chain A residue 612 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 98 optimal weight: 0.0070 chunk 84 optimal weight: 2.9990 chunk 93 optimal weight: 0.4980 chunk 38 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.141122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.101594 restraints weight = 11147.218| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.92 r_work: 0.3120 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8568 Z= 0.145 Angle : 0.515 8.767 11595 Z= 0.260 Chirality : 0.038 0.135 1295 Planarity : 0.004 0.054 1487 Dihedral : 6.255 85.762 1241 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.87 % Allowed : 26.68 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.27), residues: 1047 helix: 2.60 (0.25), residues: 424 sheet: -0.11 (0.38), residues: 189 loop : -1.42 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 191 HIS 0.004 0.001 HIS B 206 PHE 0.014 0.001 PHE A 551 TYR 0.008 0.001 TYR B 83 ARG 0.003 0.000 ARG B 320 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.895 Fit side-chains REVERT: A 120 MET cc_start: 0.8243 (tpp) cc_final: 0.8026 (tpp) REVERT: A 501 ASP cc_start: 0.8248 (t0) cc_final: 0.8040 (t0) REVERT: A 532 LEU cc_start: 0.6666 (OUTLIER) cc_final: 0.6451 (mm) outliers start: 26 outliers final: 18 residues processed: 129 average time/residue: 0.2184 time to fit residues: 38.4712 Evaluate side-chains 122 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 TYR Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 543 TYR Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain C residue 45 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 23 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 29 optimal weight: 0.0470 chunk 92 optimal weight: 20.0000 chunk 60 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 overall best weight: 1.3482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.139108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.099441 restraints weight = 11185.014| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.93 r_work: 0.3089 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8568 Z= 0.203 Angle : 0.525 9.783 11595 Z= 0.264 Chirality : 0.039 0.133 1295 Planarity : 0.004 0.058 1487 Dihedral : 5.994 84.651 1238 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.82 % Favored : 96.08 % Rotamer: Outliers : 3.31 % Allowed : 25.69 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.27), residues: 1047 helix: 2.53 (0.25), residues: 430 sheet: 0.05 (0.39), residues: 192 loop : -1.44 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 191 HIS 0.005 0.001 HIS B 206 PHE 0.014 0.001 PHE B 117 TYR 0.010 0.001 TYR A 416 ARG 0.003 0.000 ARG B 320 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 0.969 Fit side-chains REVERT: B 109 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.7988 (mt0) REVERT: B 466 GLN cc_start: 0.7988 (mp10) cc_final: 0.7547 (mp10) REVERT: A 501 ASP cc_start: 0.8308 (t0) cc_final: 0.8102 (t0) REVERT: A 532 LEU cc_start: 0.6716 (OUTLIER) cc_final: 0.6482 (mm) REVERT: C 55 ASN cc_start: 0.8849 (t0) cc_final: 0.8583 (t0) outliers start: 30 outliers final: 21 residues processed: 135 average time/residue: 0.2201 time to fit residues: 40.4259 Evaluate side-chains 125 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 TYR Chi-restraints excluded: chain B residue 109 GLN Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 46 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 0.0040 chunk 46 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 101 optimal weight: 0.0040 chunk 15 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 overall best weight: 0.7406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 GLN B 319 ASN ** B 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.140942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.101365 restraints weight = 11086.633| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.93 r_work: 0.3115 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8568 Z= 0.148 Angle : 0.506 9.056 11595 Z= 0.255 Chirality : 0.038 0.133 1295 Planarity : 0.004 0.057 1487 Dihedral : 5.877 83.834 1238 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.53 % Favored : 96.37 % Rotamer: Outliers : 3.09 % Allowed : 26.24 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.27), residues: 1047 helix: 2.73 (0.25), residues: 425 sheet: 0.20 (0.39), residues: 192 loop : -1.33 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 191 HIS 0.004 0.001 HIS B 206 PHE 0.014 0.001 PHE A 551 TYR 0.025 0.001 TYR A 487 ARG 0.006 0.000 ARG A 547 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.965 Fit side-chains REVERT: A 532 LEU cc_start: 0.6685 (OUTLIER) cc_final: 0.6468 (mm) REVERT: A 582 ARG cc_start: 0.7296 (ttm-80) cc_final: 0.7078 (mtt-85) REVERT: C 55 ASN cc_start: 0.8806 (t0) cc_final: 0.8511 (t0) outliers start: 28 outliers final: 25 residues processed: 130 average time/residue: 0.2244 time to fit residues: 39.6358 Evaluate side-chains 130 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 TYR Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 543 TYR Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain C residue 45 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 74 optimal weight: 0.0770 chunk 96 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 23 optimal weight: 0.2980 chunk 21 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 319 ASN ** B 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.141881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.102474 restraints weight = 11059.936| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.93 r_work: 0.3131 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8568 Z= 0.138 Angle : 0.493 8.501 11595 Z= 0.249 Chirality : 0.038 0.133 1295 Planarity : 0.004 0.058 1487 Dihedral : 5.797 81.737 1238 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.44 % Favored : 96.47 % Rotamer: Outliers : 3.97 % Allowed : 25.47 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.27), residues: 1047 helix: 2.83 (0.25), residues: 425 sheet: 0.21 (0.38), residues: 198 loop : -1.23 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 191 HIS 0.004 0.001 HIS B 206 PHE 0.013 0.001 PHE A 551 TYR 0.021 0.001 TYR A 487 ARG 0.006 0.000 ARG A 547 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 110 time to evaluate : 0.930 Fit side-chains REVERT: B 129 ARG cc_start: 0.7262 (ttm-80) cc_final: 0.6934 (mmt-90) REVERT: B 258 ASP cc_start: 0.8287 (m-30) cc_final: 0.8059 (m-30) REVERT: B 344 MET cc_start: 0.8442 (mmt) cc_final: 0.8224 (mmm) REVERT: B 448 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7405 (tp-100) REVERT: B 466 GLN cc_start: 0.7967 (mp10) cc_final: 0.7566 (mp10) REVERT: A 532 LEU cc_start: 0.6706 (OUTLIER) cc_final: 0.6490 (mm) REVERT: A 547 ARG cc_start: 0.5756 (mtm-85) cc_final: 0.5445 (mtm-85) REVERT: A 582 ARG cc_start: 0.7335 (ttm-80) cc_final: 0.6957 (mtt-85) REVERT: C 55 ASN cc_start: 0.8794 (t0) cc_final: 0.8494 (t0) outliers start: 36 outliers final: 27 residues processed: 142 average time/residue: 0.2284 time to fit residues: 44.1802 Evaluate side-chains 136 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 TYR Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 543 TYR Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 46 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 13 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 83 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 49 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 319 ASN ** B 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.139832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.100104 restraints weight = 11132.114| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.92 r_work: 0.3097 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8568 Z= 0.200 Angle : 0.530 9.775 11595 Z= 0.265 Chirality : 0.039 0.152 1295 Planarity : 0.004 0.060 1487 Dihedral : 5.812 78.943 1238 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.63 % Favored : 96.28 % Rotamer: Outliers : 3.42 % Allowed : 25.91 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.27), residues: 1047 helix: 2.75 (0.25), residues: 426 sheet: 0.12 (0.38), residues: 203 loop : -1.15 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 397 HIS 0.005 0.001 HIS B 206 PHE 0.013 0.001 PHE B 117 TYR 0.019 0.001 TYR A 487 ARG 0.004 0.000 ARG B 320 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 1.029 Fit side-chains REVERT: B 466 GLN cc_start: 0.7959 (mp10) cc_final: 0.7530 (mp10) REVERT: A 532 LEU cc_start: 0.6742 (OUTLIER) cc_final: 0.6503 (mm) REVERT: A 547 ARG cc_start: 0.5819 (mtm-85) cc_final: 0.5529 (mtm-85) REVERT: A 582 ARG cc_start: 0.7373 (ttm-80) cc_final: 0.6999 (mtt-85) REVERT: C 55 ASN cc_start: 0.8819 (t0) cc_final: 0.8499 (t0) outliers start: 31 outliers final: 26 residues processed: 136 average time/residue: 0.2295 time to fit residues: 41.8476 Evaluate side-chains 131 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 TYR Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 543 TYR Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 46 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 60 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 319 ASN B 556 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.138984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.099354 restraints weight = 11212.062| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.93 r_work: 0.3085 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8568 Z= 0.213 Angle : 0.539 10.345 11595 Z= 0.271 Chirality : 0.039 0.132 1295 Planarity : 0.004 0.060 1487 Dihedral : 5.842 76.510 1238 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.92 % Favored : 95.99 % Rotamer: Outliers : 3.42 % Allowed : 26.13 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.27), residues: 1047 helix: 2.70 (0.25), residues: 426 sheet: 0.10 (0.38), residues: 203 loop : -1.13 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 397 HIS 0.005 0.001 HIS B 206 PHE 0.014 0.001 PHE A 551 TYR 0.018 0.001 TYR A 487 ARG 0.004 0.000 ARG B 320 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 0.968 Fit side-chains REVERT: B 466 GLN cc_start: 0.7942 (mp10) cc_final: 0.7476 (mp10) REVERT: A 139 GLU cc_start: 0.8317 (tp30) cc_final: 0.7670 (tp30) REVERT: A 532 LEU cc_start: 0.6778 (OUTLIER) cc_final: 0.6514 (mm) REVERT: A 539 MET cc_start: 0.8699 (ttp) cc_final: 0.8309 (tmm) REVERT: A 547 ARG cc_start: 0.5836 (mtm-85) cc_final: 0.5544 (mtm-85) REVERT: C 55 ASN cc_start: 0.8817 (t0) cc_final: 0.8490 (t0) outliers start: 31 outliers final: 25 residues processed: 135 average time/residue: 0.2273 time to fit residues: 42.0147 Evaluate side-chains 132 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 TYR Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 46 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 81 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 319 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.139700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.100167 restraints weight = 11234.905| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.93 r_work: 0.3095 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8568 Z= 0.185 Angle : 0.532 9.982 11595 Z= 0.269 Chirality : 0.039 0.136 1295 Planarity : 0.004 0.058 1487 Dihedral : 5.821 74.440 1238 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.01 % Favored : 95.89 % Rotamer: Outliers : 3.31 % Allowed : 26.57 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.27), residues: 1047 helix: 2.71 (0.25), residues: 426 sheet: 0.11 (0.38), residues: 203 loop : -1.11 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 397 HIS 0.005 0.001 HIS B 206 PHE 0.014 0.001 PHE A 551 TYR 0.017 0.001 TYR A 487 ARG 0.003 0.000 ARG A 547 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: B 448 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7402 (tp-100) REVERT: B 466 GLN cc_start: 0.7944 (mp10) cc_final: 0.7377 (mp10) REVERT: A 139 GLU cc_start: 0.8317 (tp30) cc_final: 0.7676 (tp30) REVERT: A 532 LEU cc_start: 0.6767 (OUTLIER) cc_final: 0.6530 (mm) REVERT: A 547 ARG cc_start: 0.5845 (mtm-85) cc_final: 0.5573 (mtm-85) REVERT: A 582 ARG cc_start: 0.7344 (ttm-80) cc_final: 0.7070 (mtt-85) REVERT: C 55 ASN cc_start: 0.8811 (t0) cc_final: 0.8482 (t0) outliers start: 30 outliers final: 27 residues processed: 131 average time/residue: 0.2285 time to fit residues: 40.6329 Evaluate side-chains 134 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 TYR Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 46 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 59 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 4 optimal weight: 0.3980 chunk 24 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 67 optimal weight: 0.0170 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 319 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.141224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.101591 restraints weight = 11091.051| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.94 r_work: 0.3122 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8568 Z= 0.147 Angle : 0.521 10.717 11595 Z= 0.261 Chirality : 0.038 0.139 1295 Planarity : 0.004 0.056 1487 Dihedral : 5.755 71.252 1238 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.53 % Favored : 96.37 % Rotamer: Outliers : 3.64 % Allowed : 26.24 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.27), residues: 1047 helix: 2.79 (0.25), residues: 426 sheet: 0.26 (0.38), residues: 198 loop : -1.09 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 191 HIS 0.004 0.001 HIS B 206 PHE 0.014 0.001 PHE A 551 TYR 0.017 0.001 TYR A 487 ARG 0.003 0.000 ARG A 547 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 108 time to evaluate : 0.895 Fit side-chains revert: symmetry clash REVERT: B 448 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7396 (tp-100) REVERT: B 466 GLN cc_start: 0.7955 (mp10) cc_final: 0.7387 (mp10) REVERT: A 139 GLU cc_start: 0.8272 (tp30) cc_final: 0.7698 (tp30) REVERT: A 532 LEU cc_start: 0.6771 (OUTLIER) cc_final: 0.6540 (mm) REVERT: A 539 MET cc_start: 0.8705 (ttp) cc_final: 0.8322 (tmm) REVERT: A 547 ARG cc_start: 0.5858 (mtm-85) cc_final: 0.5583 (mtm-85) REVERT: A 582 ARG cc_start: 0.7344 (ttm-80) cc_final: 0.7082 (mtt-85) REVERT: C 55 ASN cc_start: 0.8757 (t0) cc_final: 0.8440 (t0) outliers start: 33 outliers final: 27 residues processed: 135 average time/residue: 0.2177 time to fit residues: 39.8760 Evaluate side-chains 134 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 TYR Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 543 TYR Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 46 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 20 optimal weight: 0.2980 chunk 53 optimal weight: 0.7980 chunk 17 optimal weight: 0.2980 chunk 78 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 319 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.141815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.102070 restraints weight = 11235.030| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.96 r_work: 0.3128 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8568 Z= 0.151 Angle : 0.524 10.212 11595 Z= 0.263 Chirality : 0.038 0.139 1295 Planarity : 0.004 0.053 1487 Dihedral : 5.711 71.335 1238 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.53 % Favored : 96.37 % Rotamer: Outliers : 3.31 % Allowed : 26.79 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.27), residues: 1047 helix: 2.81 (0.25), residues: 426 sheet: 0.28 (0.38), residues: 198 loop : -1.05 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 191 HIS 0.004 0.001 HIS B 206 PHE 0.017 0.001 PHE A 551 TYR 0.017 0.001 TYR A 487 ARG 0.003 0.000 ARG A 547 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3913.75 seconds wall clock time: 70 minutes 12.18 seconds (4212.18 seconds total)