Starting phenix.real_space_refine on Wed Sep 17 11:08:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yb4_39108/09_2025/8yb4_39108.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yb4_39108/09_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_39108/09_2025/8yb4_39108.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yb4_39108/09_2025/8yb4_39108.map" model { file = "/net/cci-nas-00/data/ceres_data/8yb4_39108/09_2025/8yb4_39108.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yb4_39108/09_2025/8yb4_39108.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.20, per 1000 atoms: 0.26 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: 0.86 Conformation dependent library (CDL) restraints added in 367.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.33 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: 1.36 Time building geometry restraints manager: 1.09 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 1201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 9.690 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.520 ------------------------------------------------------------------------------- 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 8570 Z= 0.182 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (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 ARG 0.005 0.000 ARG B 320 TYR 0.009 0.001 TYR A 487 PHE 0.015 0.001 PHE A 551 TRP 0.009 0.001 TRP B 191 HIS 0.005 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 8568) covalent geometry : angle 0.61945 (11595) hydrogen bonds : bond 0.15267 ( 448) hydrogen bonds : angle 5.16320 ( 1239) Misc. bond : bond 0.00077 ( 2) *********************** 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 : 0.319 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: 0.1094 time to fit residues: 16.6120 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 : 0.328 ------------------------------------------------------------------------------- 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 49 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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 = 0.3747 r_free = 0.3747 target = 0.139549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.099888 restraints weight = 11131.390| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.95 r_work: 0.3093 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.0814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8570 Z= 0.137 Angle : 0.565 10.101 11595 Z= 0.281 Chirality : 0.039 0.150 1295 Planarity : 0.004 0.053 1487 Dihedral : 7.203 88.321 1241 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.09 % Allowed : 26.13 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.27), residues: 1047 helix: 2.15 (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 ARG 0.004 0.000 ARG A 547 TYR 0.010 0.001 TYR B 83 PHE 0.014 0.001 PHE A 551 TRP 0.009 0.001 TRP A 397 HIS 0.005 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8568) covalent geometry : angle 0.56454 (11595) hydrogen bonds : bond 0.04901 ( 448) hydrogen bonds : angle 4.28331 ( 1239) Misc. bond : bond 0.00096 ( 2) *********************** 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: 28 poor density : 107 time to evaluate : 0.317 Fit side-chains REVERT: B 109 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8322 (mt0) REVERT: B 220 ARG cc_start: 0.8577 (ttm170) cc_final: 0.8243 (mmm-85) REVERT: A 532 LEU cc_start: 0.6637 (OUTLIER) cc_final: 0.6391 (mm) outliers start: 28 outliers final: 14 residues processed: 130 average time/residue: 0.1033 time to fit residues: 18.1296 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 : 0.325 ------------------------------------------------------------------------------- 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 543 TYR 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 75 optimal weight: 0.9980 chunk 44 optimal weight: 0.0050 chunk 100 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.138556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.098987 restraints weight = 11093.353| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.91 r_work: 0.3082 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8570 Z= 0.137 Angle : 0.547 10.156 11595 Z= 0.276 Chirality : 0.039 0.136 1295 Planarity : 0.004 0.056 1487 Dihedral : 6.430 84.895 1241 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.20 % Allowed : 26.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.27), residues: 1047 helix: 2.38 (0.25), residues: 430 sheet: -0.13 (0.38), residues: 189 loop : -1.52 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 320 TYR 0.011 0.001 TYR A 416 PHE 0.014 0.001 PHE B 117 TRP 0.009 0.001 TRP A 397 HIS 0.005 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 8568) covalent geometry : angle 0.54749 (11595) hydrogen bonds : bond 0.04760 ( 448) hydrogen bonds : angle 4.11549 ( 1239) Misc. bond : bond 0.00063 ( 2) *********************** 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 136 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 0.309 Fit side-chains REVERT: B 109 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8090 (mt0) REVERT: A 532 LEU cc_start: 0.6697 (OUTLIER) cc_final: 0.6453 (mm) outliers start: 29 outliers final: 18 residues processed: 132 average time/residue: 0.1061 time to fit residues: 19.0768 Evaluate side-chains 122 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 31 optimal weight: 0.0670 chunk 40 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 overall best weight: 1.3120 ------------------------------------------------------------------------------- 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 = 0.3736 r_free = 0.3736 target = 0.138729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.098912 restraints weight = 11391.816| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.97 r_work: 0.3084 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8570 Z= 0.131 Angle : 0.536 10.139 11595 Z= 0.269 Chirality : 0.039 0.136 1295 Planarity : 0.004 0.059 1487 Dihedral : 6.205 83.410 1241 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.82 % Favored : 96.08 % Rotamer: Outliers : 3.53 % Allowed : 25.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.27), residues: 1047 helix: 2.45 (0.25), residues: 430 sheet: 0.01 (0.39), residues: 192 loop : -1.47 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 320 TYR 0.010 0.001 TYR A 416 PHE 0.014 0.001 PHE B 117 TRP 0.008 0.001 TRP B 191 HIS 0.005 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8568) covalent geometry : angle 0.53632 (11595) hydrogen bonds : bond 0.04597 ( 448) hydrogen bonds : angle 4.02371 ( 1239) Misc. bond : bond 0.00063 ( 2) *********************** 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 141 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.256 Fit side-chains REVERT: B 466 GLN cc_start: 0.7985 (mp10) cc_final: 0.7556 (mp10) REVERT: A 532 LEU cc_start: 0.6751 (OUTLIER) cc_final: 0.6517 (mm) REVERT: C 55 ASN cc_start: 0.8833 (t0) cc_final: 0.8589 (t0) outliers start: 32 outliers final: 24 residues processed: 137 average time/residue: 0.1093 time to fit residues: 20.3788 Evaluate side-chains 128 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 205 LEU 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 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 340 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 73 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 9 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 ** 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 = 0.3734 r_free = 0.3734 target = 0.138783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.099007 restraints weight = 11244.461| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.94 r_work: 0.3082 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8570 Z= 0.126 Angle : 0.527 10.055 11595 Z= 0.266 Chirality : 0.039 0.134 1295 Planarity : 0.004 0.060 1487 Dihedral : 5.975 80.649 1238 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.63 % Favored : 96.28 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.27), residues: 1047 helix: 2.48 (0.26), residues: 431 sheet: 0.10 (0.39), residues: 192 loop : -1.41 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 547 TYR 0.025 0.001 TYR A 487 PHE 0.014 0.001 PHE B 117 TRP 0.008 0.001 TRP B 191 HIS 0.005 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8568) covalent geometry : angle 0.52690 (11595) hydrogen bonds : bond 0.04479 ( 448) hydrogen bonds : angle 3.94863 ( 1239) Misc. bond : bond 0.00057 ( 2) *********************** 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 139 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 107 time to evaluate : 0.330 Fit side-chains REVERT: A 532 LEU cc_start: 0.6713 (OUTLIER) cc_final: 0.6470 (mm) REVERT: A 582 ARG cc_start: 0.7293 (ttm-80) cc_final: 0.7074 (mtt-85) REVERT: A 614 LEU cc_start: 0.8904 (mm) cc_final: 0.8695 (mm) REVERT: C 55 ASN cc_start: 0.8841 (t0) cc_final: 0.8571 (t0) outliers start: 32 outliers final: 27 residues processed: 134 average time/residue: 0.1040 time to fit residues: 18.9167 Evaluate side-chains 133 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 90 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 87 optimal weight: 0.0030 chunk 68 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- 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 = 0.3755 r_free = 0.3755 target = 0.140762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.101101 restraints weight = 11100.944| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.91 r_work: 0.3112 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8570 Z= 0.101 Angle : 0.510 9.102 11595 Z= 0.257 Chirality : 0.038 0.137 1295 Planarity : 0.004 0.059 1487 Dihedral : 5.850 77.808 1238 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.63 % Favored : 96.28 % Rotamer: Outliers : 3.53 % Allowed : 26.13 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.27), residues: 1047 helix: 2.72 (0.25), residues: 425 sheet: 0.11 (0.38), residues: 197 loop : -1.23 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 547 TYR 0.022 0.001 TYR A 487 PHE 0.013 0.001 PHE A 551 TRP 0.008 0.001 TRP B 191 HIS 0.004 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 8568) covalent geometry : angle 0.51037 (11595) hydrogen bonds : bond 0.04011 ( 448) hydrogen bonds : angle 3.82960 ( 1239) Misc. bond : bond 0.00037 ( 2) *********************** 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 141 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.340 Fit side-chains REVERT: B 466 GLN cc_start: 0.7946 (mp10) cc_final: 0.7543 (mp10) REVERT: A 532 LEU cc_start: 0.6674 (OUTLIER) cc_final: 0.6432 (mm) REVERT: A 582 ARG cc_start: 0.7305 (ttm-80) cc_final: 0.6976 (mtt-85) REVERT: A 614 LEU cc_start: 0.8891 (mm) cc_final: 0.8681 (mm) REVERT: C 55 ASN cc_start: 0.8768 (t0) cc_final: 0.8478 (t0) outliers start: 32 outliers final: 26 residues processed: 136 average time/residue: 0.1099 time to fit residues: 20.2143 Evaluate side-chains 133 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 TYR 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 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: 3.9990 chunk 1 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 44 optimal weight: 0.0370 chunk 32 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.6860 ------------------------------------------------------------------------------- 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 = 0.3762 r_free = 0.3762 target = 0.141458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.101561 restraints weight = 11250.220| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.96 r_work: 0.3119 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8570 Z= 0.100 Angle : 0.503 8.805 11595 Z= 0.254 Chirality : 0.038 0.136 1295 Planarity : 0.004 0.059 1487 Dihedral : 5.775 73.964 1238 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.53 % Favored : 96.37 % Rotamer: Outliers : 3.75 % Allowed : 25.91 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.27), residues: 1047 helix: 2.81 (0.25), residues: 425 sheet: 0.26 (0.38), residues: 192 loop : -1.20 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 547 TYR 0.019 0.001 TYR A 487 PHE 0.014 0.001 PHE A 551 TRP 0.007 0.001 TRP B 191 HIS 0.004 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 8568) covalent geometry : angle 0.50339 (11595) hydrogen bonds : bond 0.03867 ( 448) hydrogen bonds : angle 3.76866 ( 1239) Misc. bond : bond 0.00036 ( 2) *********************** 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: 34 poor density : 106 time to evaluate : 0.325 Fit side-chains REVERT: B 258 ASP cc_start: 0.8287 (m-30) cc_final: 0.8065 (m-30) REVERT: B 466 GLN cc_start: 0.7954 (mp10) cc_final: 0.7529 (mp10) REVERT: A 532 LEU cc_start: 0.6734 (OUTLIER) cc_final: 0.6498 (mm) REVERT: A 539 MET cc_start: 0.8692 (ttp) cc_final: 0.8342 (tmm) REVERT: A 547 ARG cc_start: 0.5741 (mtm-85) cc_final: 0.5435 (mtm-85) REVERT: A 582 ARG cc_start: 0.7303 (ttm-80) cc_final: 0.6935 (mtt-85) REVERT: A 614 LEU cc_start: 0.8898 (mm) cc_final: 0.8684 (mm) REVERT: C 55 ASN cc_start: 0.8765 (t0) cc_final: 0.8468 (t0) outliers start: 34 outliers final: 28 residues processed: 135 average time/residue: 0.1034 time to fit residues: 18.9513 Evaluate side-chains 133 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 31 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 92 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 65 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 38 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 = 0.3731 r_free = 0.3731 target = 0.138549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.098695 restraints weight = 11226.190| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.94 r_work: 0.3075 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8570 Z= 0.149 Angle : 0.541 10.614 11595 Z= 0.273 Chirality : 0.039 0.132 1295 Planarity : 0.004 0.062 1487 Dihedral : 5.850 70.945 1238 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.82 % Favored : 96.08 % Rotamer: Outliers : 3.53 % Allowed : 26.46 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.27), residues: 1047 helix: 2.58 (0.25), residues: 432 sheet: 0.13 (0.38), residues: 197 loop : -1.23 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 320 TYR 0.017 0.002 TYR A 487 PHE 0.013 0.001 PHE B 117 TRP 0.009 0.001 TRP B 397 HIS 0.005 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 8568) covalent geometry : angle 0.54054 (11595) hydrogen bonds : bond 0.04562 ( 448) hydrogen bonds : angle 3.90180 ( 1239) Misc. bond : bond 0.00068 ( 2) *********************** 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 140 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 108 time to evaluate : 0.390 Fit side-chains REVERT: B 466 GLN cc_start: 0.7923 (mp10) cc_final: 0.7360 (mp10) REVERT: A 532 LEU cc_start: 0.6777 (OUTLIER) cc_final: 0.6511 (mm) REVERT: A 547 ARG cc_start: 0.5853 (mtm-85) cc_final: 0.5591 (mtm-85) REVERT: A 614 LEU cc_start: 0.8922 (mm) cc_final: 0.8689 (mm) REVERT: C 55 ASN cc_start: 0.8839 (t0) cc_final: 0.8518 (t0) outliers start: 32 outliers final: 24 residues processed: 134 average time/residue: 0.1000 time to fit residues: 18.2786 Evaluate side-chains 129 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 14 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 86 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3748 r_free = 0.3748 target = 0.140193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.100500 restraints weight = 11124.822| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.93 r_work: 0.3103 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8570 Z= 0.113 Angle : 0.528 9.628 11595 Z= 0.268 Chirality : 0.038 0.147 1295 Planarity : 0.004 0.058 1487 Dihedral : 5.813 70.634 1238 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.63 % Favored : 96.28 % Rotamer: Outliers : 3.20 % Allowed : 26.68 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.27), residues: 1047 helix: 2.75 (0.25), residues: 426 sheet: 0.15 (0.38), residues: 197 loop : -1.12 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 320 TYR 0.017 0.001 TYR A 487 PHE 0.013 0.001 PHE A 551 TRP 0.008 0.001 TRP B 191 HIS 0.004 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 8568) covalent geometry : angle 0.52817 (11595) hydrogen bonds : bond 0.04106 ( 448) hydrogen bonds : angle 3.79971 ( 1239) Misc. bond : bond 0.00041 ( 2) *********************** 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 140 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.364 Fit side-chains REVERT: B 258 ASP cc_start: 0.8298 (m-30) cc_final: 0.8094 (m-30) REVERT: B 448 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.7396 (tp-100) REVERT: B 466 GLN cc_start: 0.7932 (mp10) cc_final: 0.7364 (mp10) REVERT: A 139 GLU cc_start: 0.8318 (tp30) cc_final: 0.7675 (tp30) REVERT: A 159 MET cc_start: 0.8292 (tpp) cc_final: 0.7959 (tpt) REVERT: A 532 LEU cc_start: 0.6753 (OUTLIER) cc_final: 0.6495 (mm) REVERT: A 539 MET cc_start: 0.8699 (ttp) cc_final: 0.8316 (tmm) REVERT: A 547 ARG cc_start: 0.5840 (mtm-85) cc_final: 0.5603 (mtm-85) REVERT: A 614 LEU cc_start: 0.8907 (mm) cc_final: 0.8669 (mm) REVERT: A 615 ARG cc_start: 0.8543 (mmm-85) cc_final: 0.8278 (mmm-85) REVERT: C 55 ASN cc_start: 0.8768 (t0) cc_final: 0.8444 (t0) outliers start: 29 outliers final: 23 residues processed: 135 average time/residue: 0.1123 time to fit residues: 20.2408 Evaluate side-chains 131 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 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 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 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 0 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 39 optimal weight: 0.1980 chunk 19 optimal weight: 0.3980 chunk 58 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 4 optimal weight: 0.0470 chunk 85 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.4078 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.142432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.102943 restraints weight = 11061.137| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.92 r_work: 0.3139 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8570 Z= 0.097 Angle : 0.516 8.400 11595 Z= 0.261 Chirality : 0.038 0.164 1295 Planarity : 0.004 0.054 1487 Dihedral : 5.731 72.132 1238 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.25 % Favored : 96.66 % Rotamer: Outliers : 2.98 % Allowed : 26.46 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.27), residues: 1047 helix: 2.88 (0.25), residues: 426 sheet: 0.25 (0.38), residues: 198 loop : -1.09 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 547 TYR 0.017 0.001 TYR A 487 PHE 0.017 0.001 PHE A 551 TRP 0.008 0.001 TRP B 191 HIS 0.004 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 8568) covalent geometry : angle 0.51562 (11595) hydrogen bonds : bond 0.03636 ( 448) hydrogen bonds : angle 3.70141 ( 1239) Misc. bond : bond 0.00022 ( 2) ********************** 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 135 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.344 Fit side-chains REVERT: B 258 ASP cc_start: 0.8251 (m-30) cc_final: 0.8027 (m-30) REVERT: B 448 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7398 (tp-100) REVERT: B 466 GLN cc_start: 0.7964 (mp10) cc_final: 0.7397 (mp10) REVERT: A 139 GLU cc_start: 0.8260 (tp30) cc_final: 0.7694 (tp30) REVERT: A 159 MET cc_start: 0.8295 (tpp) cc_final: 0.7970 (tpt) REVERT: A 532 LEU cc_start: 0.6745 (OUTLIER) cc_final: 0.6517 (mm) REVERT: A 582 ARG cc_start: 0.7343 (ttm-80) cc_final: 0.7072 (mtt-85) REVERT: A 614 LEU cc_start: 0.8893 (mm) cc_final: 0.8658 (mm) REVERT: A 615 ARG cc_start: 0.8564 (mmm-85) cc_final: 0.8314 (mmm-85) REVERT: C 55 ASN cc_start: 0.8755 (t0) cc_final: 0.8451 (t0) outliers start: 27 outliers final: 22 residues processed: 132 average time/residue: 0.1104 time to fit residues: 19.5656 Evaluate side-chains 132 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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 448 GLN Chi-restraints excluded: chain B residue 497 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 C residue 45 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 91 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 79 optimal weight: 9.9990 chunk 39 optimal weight: 0.0870 chunk 41 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 319 ASN A 404 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.134945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.095349 restraints weight = 11340.916| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.93 r_work: 0.3026 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 8570 Z= 0.255 Angle : 0.653 13.145 11595 Z= 0.330 Chirality : 0.043 0.166 1295 Planarity : 0.005 0.063 1487 Dihedral : 6.242 77.659 1238 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.68 % Favored : 95.22 % Rotamer: Outliers : 2.98 % Allowed : 26.46 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.27), residues: 1047 helix: 2.32 (0.25), residues: 432 sheet: 0.05 (0.38), residues: 199 loop : -1.30 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 547 TYR 0.021 0.002 TYR B 303 PHE 0.015 0.002 PHE B 117 TRP 0.014 0.002 TRP B 397 HIS 0.007 0.002 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00629 ( 8568) covalent geometry : angle 0.65333 (11595) hydrogen bonds : bond 0.05855 ( 448) hydrogen bonds : angle 4.22198 ( 1239) Misc. bond : bond 0.00116 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2182.87 seconds wall clock time: 38 minutes 10.77 seconds (2290.77 seconds total)