Starting phenix.real_space_refine on Thu Oct 10 18:05:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yb4_39108/10_2024/8yb4_39108.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yb4_39108/10_2024/8yb4_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yb4_39108/10_2024/8yb4_39108.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yb4_39108/10_2024/8yb4_39108.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yb4_39108/10_2024/8yb4_39108.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yb4_39108/10_2024/8yb4_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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: 5.50, per 1000 atoms: 0.65 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: 2.17 Conformation dependent library (CDL) restraints added in 952.3 milliseconds 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: 0.98 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: 2.61 Time building geometry restraints manager: 2.48 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: 0.850 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: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.520 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.030 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 3 poor density : 109 time to evaluate : 0.737 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: 0.2396 time to fit residues: 36.1264 Evaluate side-chains 107 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 105 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 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 fitting. rotamer outliers: 29 poor density : 106 time to evaluate : 0.977 Fit side-chains REVERT: B 220 ARG cc_start: 0.8091 (ttm170) cc_final: 0.7793 (mmm-85) REVERT: A 586 GLN cc_start: 0.6923 (OUTLIER) cc_final: 0.6654 (pt0) outliers start: 29 outliers final: 13 residues processed: 131 average time/residue: 0.2262 time to fit residues: 40.2602 Evaluate side-chains 118 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 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 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 52 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 103 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.1006 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= 0.187 Angle : 0.539 9.905 11595 Z= 0.271 Chirality : 0.039 0.136 1295 Planarity : 0.004 0.056 1487 Dihedral : 6.307 85.511 1238 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.76 % Allowed : 26.79 % 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: 0.66 (0.27), residues: 1047 helix: 2.50 (0.25), residues: 424 sheet: -0.13 (0.38), residues: 189 loop : -1.48 (0.29), residues: 434 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 A 551 TYR 0.010 0.001 TYR A 416 ARG 0.003 0.000 ARG A 129 *********************** 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 132 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 107 time to evaluate : 1.002 Fit side-chains REVERT: B 220 ARG cc_start: 0.8098 (ttm170) cc_final: 0.7777 (mtt-85) outliers start: 25 outliers final: 17 residues processed: 128 average time/residue: 0.2320 time to fit residues: 40.2805 Evaluate side-chains 118 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 101 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 371 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 490 LEU 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 94 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 64 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 101 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- 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 A 404 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 8568 Z= 0.378 Angle : 0.618 12.359 11595 Z= 0.311 Chirality : 0.041 0.138 1295 Planarity : 0.005 0.066 1487 Dihedral : 6.461 81.492 1238 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.97 % Favored : 94.94 % Rotamer: Outliers : 3.97 % Allowed : 25.80 % Favored : 70.23 % 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: 0.42 (0.27), residues: 1047 helix: 2.16 (0.26), residues: 432 sheet: -0.07 (0.39), residues: 189 loop : -1.61 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 397 HIS 0.006 0.001 HIS B 206 PHE 0.016 0.002 PHE B 117 TYR 0.017 0.002 TYR B 303 ARG 0.003 0.000 ARG A 129 *********************** 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 148 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 112 time to evaluate : 0.820 Fit side-chains outliers start: 36 outliers final: 29 residues processed: 139 average time/residue: 0.2182 time to fit residues: 41.3704 Evaluate side-chains 132 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 103 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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 168 THR 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 319 ASN Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 371 LEU 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 544 ILE 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 213 VAL 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 340 LEU Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain C residue 45 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 1 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 86 optimal weight: 20.0000 chunk 70 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8568 Z= 0.166 Angle : 0.536 9.951 11595 Z= 0.269 Chirality : 0.039 0.192 1295 Planarity : 0.004 0.058 1487 Dihedral : 6.130 79.296 1238 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.63 % Favored : 96.28 % Rotamer: Outliers : 2.76 % Allowed : 27.23 % Favored : 70.01 % 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: 2.48 (0.25), residues: 425 sheet: 0.04 (0.39), residues: 192 loop : -1.39 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 0.005 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 129 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 104 time to evaluate : 0.970 Fit side-chains REVERT: B 220 ARG cc_start: 0.8132 (ttm170) cc_final: 0.7829 (mtt-85) outliers start: 25 outliers final: 23 residues processed: 127 average time/residue: 0.2262 time to fit residues: 39.2127 Evaluate side-chains 123 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 100 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 168 THR 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 427 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 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 548 ASP 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 34 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 8 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 chunk 53 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.1354 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 : 0.526 10.586 11595 Z= 0.263 Chirality : 0.038 0.134 1295 Planarity : 0.004 0.060 1487 Dihedral : 5.886 73.558 1238 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.63 % Favored : 96.28 % Rotamer: Outliers : 3.42 % Allowed : 26.79 % Favored : 69.79 % 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: 0.96 (0.27), residues: 1047 helix: 2.65 (0.25), residues: 425 sheet: 0.18 (0.39), residues: 192 loop : -1.29 (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 0.013 0.001 PHE B 117 TYR 0.021 0.001 TYR A 487 ARG 0.005 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 135 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 104 time to evaluate : 0.990 Fit side-chains REVERT: B 220 ARG cc_start: 0.8128 (ttm170) cc_final: 0.7824 (mtt-85) outliers start: 31 outliers final: 26 residues processed: 130 average time/residue: 0.2283 time to fit residues: 40.2856 Evaluate side-chains 126 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 100 time to evaluate : 0.963 ------------------------------------------------------------------------------- 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 427 LEU 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 543 TYR Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain C residue 45 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 0.0980 chunk 11 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.1397 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= 0.192 Angle : 0.529 9.885 11595 Z= 0.267 Chirality : 0.039 0.133 1295 Planarity : 0.004 0.061 1487 Dihedral : 5.853 70.061 1238 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.82 % Favored : 96.08 % Rotamer: Outliers : 4.30 % Allowed : 26.13 % Favored : 69.57 % 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: 0.98 (0.27), residues: 1047 helix: 2.62 (0.25), residues: 426 sheet: 0.09 (0.38), residues: 197 loop : -1.21 (0.30), residues: 424 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 B 117 TYR 0.019 0.001 TYR A 487 ARG 0.005 0.000 ARG A 547 *********************** 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 142 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 103 time to evaluate : 0.964 Fit side-chains REVERT: B 220 ARG cc_start: 0.8145 (ttm170) cc_final: 0.7823 (mtt-85) outliers start: 39 outliers final: 30 residues processed: 135 average time/residue: 0.2211 time to fit residues: 40.6439 Evaluate side-chains 135 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 105 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 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 274 MET Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 454 MET 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 197 THR 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 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 543 TYR Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain C residue 45 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 0.0570 chunk 79 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 96 optimal weight: 8.9990 overall best weight: 0.9502 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.1461 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= 0.169 Angle : 0.541 13.068 11595 Z= 0.268 Chirality : 0.040 0.303 1295 Planarity : 0.004 0.060 1487 Dihedral : 5.800 70.505 1238 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.63 % Favored : 96.28 % Rotamer: Outliers : 4.08 % Allowed : 26.35 % Favored : 69.57 % 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: 1.12 (0.27), residues: 1047 helix: 2.77 (0.25), residues: 420 sheet: 0.25 (0.38), residues: 192 loop : -1.13 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 397 HIS 0.004 0.001 HIS B 206 PHE 0.013 0.001 PHE B 117 TYR 0.018 0.001 TYR A 487 ARG 0.006 0.000 ARG A 547 *********************** 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 144 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 107 time to evaluate : 0.969 Fit side-chains REVERT: B 220 ARG cc_start: 0.8150 (ttm170) cc_final: 0.7826 (mtt-85) REVERT: B 448 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.7454 (tp-100) REVERT: A 159 MET cc_start: 0.7368 (tpp) cc_final: 0.7105 (tpt) outliers start: 37 outliers final: 31 residues processed: 138 average time/residue: 0.2324 time to fit residues: 43.6477 Evaluate side-chains 135 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 103 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 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 274 MET Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 454 MET 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 197 THR 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 543 TYR 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 88 optimal weight: 9.9990 chunk 94 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8568 Z= 0.298 Angle : 0.596 11.849 11595 Z= 0.298 Chirality : 0.041 0.284 1295 Planarity : 0.005 0.059 1487 Dihedral : 5.982 74.337 1238 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.11 % Favored : 95.80 % Rotamer: Outliers : 3.53 % Allowed : 26.57 % 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: 0.85 (0.27), residues: 1047 helix: 2.44 (0.25), residues: 426 sheet: 0.15 (0.39), residues: 192 loop : -1.24 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 397 HIS 0.006 0.001 HIS B 206 PHE 0.015 0.001 PHE B 117 TYR 0.017 0.002 TYR A 487 ARG 0.006 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 139 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 107 time to evaluate : 1.040 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 28 residues processed: 132 average time/residue: 0.2328 time to fit residues: 41.7123 Evaluate side-chains 133 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 105 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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 168 THR Chi-restraints excluded: chain B residue 170 SER 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 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 197 THR 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 295 LEU 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 C residue 45 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 0.0980 chunk 60 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 69 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8568 Z= 0.227 Angle : 0.574 11.804 11595 Z= 0.287 Chirality : 0.040 0.283 1295 Planarity : 0.004 0.056 1487 Dihedral : 5.979 76.576 1238 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.01 % Favored : 95.89 % Rotamer: Outliers : 2.98 % Allowed : 27.23 % Favored : 69.79 % 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: 0.88 (0.27), residues: 1047 helix: 2.46 (0.25), residues: 425 sheet: 0.17 (0.39), residues: 192 loop : -1.21 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 397 HIS 0.005 0.001 HIS B 206 PHE 0.014 0.001 PHE B 117 TYR 0.017 0.001 TYR A 487 ARG 0.008 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 134 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 107 time to evaluate : 0.985 Fit side-chains REVERT: A 343 SER cc_start: 0.8880 (m) cc_final: 0.8383 (m) outliers start: 27 outliers final: 26 residues processed: 129 average time/residue: 0.2237 time to fit residues: 39.2593 Evaluate side-chains 129 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 103 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 168 THR 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 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 197 THR 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 C residue 45 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 76 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.139333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.099890 restraints weight = 11121.185| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.93 r_work: 0.3093 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8568 Z= 0.177 Angle : 0.576 11.894 11595 Z= 0.286 Chirality : 0.040 0.276 1295 Planarity : 0.004 0.054 1487 Dihedral : 5.889 77.992 1238 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.92 % Favored : 95.99 % Rotamer: Outliers : 3.53 % Allowed : 27.01 % Favored : 69.46 % 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: 1.01 (0.27), residues: 1047 helix: 2.57 (0.25), residues: 426 sheet: 0.26 (0.39), residues: 192 loop : -1.17 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 397 HIS 0.004 0.001 HIS B 206 PHE 0.014 0.001 PHE A 551 TYR 0.018 0.001 TYR A 487 ARG 0.007 0.000 ARG A 547 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2032.68 seconds wall clock time: 37 minutes 44.38 seconds (2264.38 seconds total)