Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 01:23:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrk_14917/04_2023/7zrk_14917_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrk_14917/04_2023/7zrk_14917.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/7zrk_14917/04_2023/7zrk_14917.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrk_14917/04_2023/7zrk_14917.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrk_14917/04_2023/7zrk_14917_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrk_14917/04_2023/7zrk_14917_updated.pdb" } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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: 6 Type Number sf(0) Gaussians K 12 8.98 5 P 8 5.49 5 S 62 5.16 5 C 7133 2.51 5 N 1826 2.21 5 O 2009 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 413": "OE1" <-> "OE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "B GLU 161": "OE1" <-> "OE2" Residue "B GLU 168": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 11050 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4155 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain: "C" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1431 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 13, 'TRANS': 176} Chain: "D" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 200 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "B" Number of atoms: 5025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5025 Classifications: {'peptide': 676} Link IDs: {'PTRANS': 26, 'TRANS': 649} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 211 Unusual residues: {' K': 11, 'CDL': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' K': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.09, per 1000 atoms: 0.55 Number of scatterers: 11050 At special positions: 0 Unit cell: (98.164, 116.38, 146.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 12 19.00 S 62 16.00 P 8 15.00 O 2009 8.00 N 1826 7.00 C 7133 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 - 3.50 Amino acid : False - 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=0, symmetry=0 Time building additional restraints: 4.89 Conformation dependent library (CDL) restraints added in 2.0 seconds 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2638 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 55 helices and 5 sheets defined 56.9% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 2 through 31 removed outlier: 3.860A pdb=" N ARG A 21 " --> pdb=" O MET A 17 " (cutoff:3.500A) Proline residue: A 22 - end of helix Processing helix chain 'A' and resid 42 through 50 Processing helix chain 'A' and resid 59 through 82 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 120 through 123 No H-bonds generated for 'chain 'A' and resid 120 through 123' Processing helix chain 'A' and resid 126 through 131 Processing helix chain 'A' and resid 133 through 156 removed outlier: 3.734A pdb=" N ALA A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 176 Processing helix chain 'A' and resid 178 through 192 Processing helix chain 'A' and resid 219 through 228 removed outlier: 3.655A pdb=" N ILE A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 241 No H-bonds generated for 'chain 'A' and resid 239 through 241' Processing helix chain 'A' and resid 249 through 273 removed outlier: 4.509A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Proline residue: A 263 - end of helix Processing helix chain 'A' and resid 277 through 304 Processing helix chain 'A' and resid 329 through 341 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 356 through 367 Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 378 through 398 Processing helix chain 'A' and resid 411 through 436 removed outlier: 4.503A pdb=" N THR A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix Processing helix chain 'A' and resid 439 through 442 No H-bonds generated for 'chain 'A' and resid 439 through 442' Processing helix chain 'A' and resid 450 through 464 Processing helix chain 'A' and resid 479 through 507 removed outlier: 4.691A pdb=" N VAL A 496 " --> pdb=" O GLY A 492 " (cutoff:3.500A) Proline residue: A 499 - end of helix Processing helix chain 'A' and resid 524 through 549 Proline residue: A 545 - end of helix Processing helix chain 'A' and resid 551 through 556 Processing helix chain 'C' and resid 4 through 20 Processing helix chain 'C' and resid 22 through 33 Processing helix chain 'C' and resid 35 through 39 Processing helix chain 'C' and resid 79 through 81 No H-bonds generated for 'chain 'C' and resid 79 through 81' Processing helix chain 'C' and resid 92 through 108 Processing helix chain 'C' and resid 118 through 121 No H-bonds generated for 'chain 'C' and resid 118 through 121' Processing helix chain 'C' and resid 134 through 148 Proline residue: C 142 - end of helix Processing helix chain 'C' and resid 152 through 161 Processing helix chain 'C' and resid 178 through 189 Processing helix chain 'D' and resid 3 through 24 Processing helix chain 'B' and resid 12 through 24 removed outlier: 3.656A pdb=" N GLU B 20 " --> pdb=" O GLN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 54 Processing helix chain 'B' and resid 62 through 98 Processing helix chain 'B' and resid 156 through 159 No H-bonds generated for 'chain 'B' and resid 156 through 159' Processing helix chain 'B' and resid 199 through 207 Processing helix chain 'B' and resid 216 through 246 removed outlier: 4.011A pdb=" N TRP B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) Proline residue: B 241 - end of helix removed outlier: 3.692A pdb=" N GLY B 246 " --> pdb=" O PHE B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 262 Processing helix chain 'B' and resid 265 through 285 removed outlier: 5.819A pdb=" N SER B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ALA B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 300 removed outlier: 3.817A pdb=" N GLY B 299 " --> pdb=" O VAL B 295 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASP B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 341 Processing helix chain 'B' and resid 347 through 360 removed outlier: 3.834A pdb=" N LYS B 357 " --> pdb=" O VAL B 353 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLN B 358 " --> pdb=" O ILE B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 407 Processing helix chain 'B' and resid 414 through 426 removed outlier: 4.338A pdb=" N GLN B 426 " --> pdb=" O GLN B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 462 Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 496 through 508 removed outlier: 4.017A pdb=" N LEU B 500 " --> pdb=" O PRO B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 Processing helix chain 'B' and resid 540 through 545 Processing helix chain 'B' and resid 555 through 594 removed outlier: 4.345A pdb=" N LEU B 558 " --> pdb=" O PRO B 555 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE B 559 " --> pdb=" O THR B 556 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS B 566 " --> pdb=" O HIS B 563 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET B 570 " --> pdb=" O GLN B 567 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY B 573 " --> pdb=" O MET B 570 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER B 574 " --> pdb=" O THR B 571 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN B 582 " --> pdb=" O SER B 579 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL B 584 " --> pdb=" O ALA B 581 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ILE B 591 " --> pdb=" O PHE B 588 " (cutoff:3.500A) Proline residue: B 592 - end of helix Processing helix chain 'B' and resid 600 through 605 removed outlier: 3.971A pdb=" N ALA B 604 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 637 removed outlier: 4.337A pdb=" N ILE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) Proline residue: B 633 - end of helix Processing helix chain 'B' and resid 646 through 679 removed outlier: 4.244A pdb=" N LEU B 659 " --> pdb=" O TRP B 655 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY B 660 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Proline residue: B 665 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 202 through 205 Processing sheet with id= B, first strand: chain 'B' and resid 130 through 134 removed outlier: 4.392A pdb=" N ASP B 130 " --> pdb=" O CYS B 191 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL B 134 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU B 187 " --> pdb=" O VAL B 134 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 152 through 154 removed outlier: 3.791A pdb=" N SER B 152 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 287 through 289 removed outlier: 3.779A pdb=" N MET B 548 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 531 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET B 535 " --> pdb=" O GLY B 517 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N VAL B 303 " --> pdb=" O ALA B 514 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N THR B 516 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU B 305 " --> pdb=" O THR B 516 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LYS B 466 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N LEU B 306 " --> pdb=" O LYS B 466 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL B 468 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASP B 489 " --> pdb=" O MET B 469 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N THR B 471 " --> pdb=" O ASP B 489 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N LEU B 491 " --> pdb=" O THR B 471 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 394 through 396 removed outlier: 3.768A pdb=" N ARG B 394 " --> pdb=" O VAL B 434 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 434 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY B 396 " --> pdb=" O VAL B 432 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL B 432 " --> pdb=" O GLY B 396 " (cutoff:3.500A) No H-bonds generated for sheet with id= E 563 hydrogen bonds defined for protein. 1602 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.01 Time building geometry restraints manager: 5.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1785 1.32 - 1.45: 2749 1.45 - 1.57: 6576 1.57 - 1.70: 16 1.70 - 1.82: 112 Bond restraints: 11238 Sorted by residual: bond pdb=" OD1 PHD B 307 " pdb=" P PHD B 307 " ideal model delta sigma weight residual 1.816 1.606 0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C ILE C 141 " pdb=" N PRO C 142 " ideal model delta sigma weight residual 1.335 1.383 -0.047 1.36e-02 5.41e+03 1.21e+01 bond pdb=" C51 CDL A 613 " pdb=" C52 CDL A 613 " ideal model delta sigma weight residual 1.523 1.479 0.044 1.50e-02 4.44e+03 8.66e+00 bond pdb=" OB3 CDL A 613 " pdb=" PB2 CDL A 613 " ideal model delta sigma weight residual 1.529 1.502 0.027 1.00e-02 1.00e+04 7.34e+00 bond pdb=" OA3 CDL A 612 " pdb=" PA1 CDL A 612 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.15e+00 ... (remaining 11233 not shown) Histogram of bond angle deviations from ideal: 98.82 - 106.31: 333 106.31 - 113.79: 6428 113.79 - 121.27: 5755 121.27 - 128.75: 2666 128.75 - 136.23: 74 Bond angle restraints: 15256 Sorted by residual: angle pdb=" N VAL A 496 " pdb=" CA VAL A 496 " pdb=" C VAL A 496 " ideal model delta sigma weight residual 112.96 107.91 5.05 1.00e+00 1.00e+00 2.55e+01 angle pdb=" CA TYR A 381 " pdb=" CB TYR A 381 " pdb=" CG TYR A 381 " ideal model delta sigma weight residual 113.90 121.13 -7.23 1.80e+00 3.09e-01 1.61e+01 angle pdb=" C MET B 392 " pdb=" N ILE B 393 " pdb=" CA ILE B 393 " ideal model delta sigma weight residual 120.69 126.14 -5.45 1.46e+00 4.69e-01 1.40e+01 angle pdb=" C ARG B 391 " pdb=" N MET B 392 " pdb=" CA MET B 392 " ideal model delta sigma weight residual 121.54 128.23 -6.69 1.91e+00 2.74e-01 1.23e+01 angle pdb=" C LEU A 380 " pdb=" N TYR A 381 " pdb=" CA TYR A 381 " ideal model delta sigma weight residual 121.14 115.60 5.54 1.75e+00 3.27e-01 1.00e+01 ... (remaining 15251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.80: 6246 24.80 - 49.59: 400 49.59 - 74.39: 50 74.39 - 99.19: 9 99.19 - 123.98: 1 Dihedral angle restraints: 6706 sinusoidal: 2600 harmonic: 4106 Sorted by residual: dihedral pdb=" O1B ADP B 701 " pdb=" O3A ADP B 701 " pdb=" PB ADP B 701 " pdb=" PA ADP B 701 " ideal model delta sinusoidal sigma weight residual -60.00 63.98 -123.98 1 2.00e+01 2.50e-03 3.74e+01 dihedral pdb=" CA ALA A 470 " pdb=" C ALA A 470 " pdb=" N PHE A 471 " pdb=" CA PHE A 471 " ideal model delta harmonic sigma weight residual 180.00 158.25 21.75 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA THR B 471 " pdb=" C THR B 471 " pdb=" N GLY B 472 " pdb=" CA GLY B 472 " ideal model delta harmonic sigma weight residual 180.00 -160.80 -19.20 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 6703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1394 0.051 - 0.101: 337 0.101 - 0.152: 70 0.152 - 0.203: 10 0.203 - 0.253: 4 Chirality restraints: 1815 Sorted by residual: chirality pdb=" CB4 CDL A 613 " pdb=" CB3 CDL A 613 " pdb=" CB6 CDL A 613 " pdb=" OB6 CDL A 613 " both_signs ideal model delta sigma weight residual False -2.57 -2.32 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA4 CDL A 612 " pdb=" CA3 CDL A 612 " pdb=" CA6 CDL A 612 " pdb=" OA6 CDL A 612 " both_signs ideal model delta sigma weight residual False -2.57 -2.34 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA4 CDL A 613 " pdb=" CA3 CDL A 613 " pdb=" CA6 CDL A 613 " pdb=" OA6 CDL A 613 " both_signs ideal model delta sigma weight residual False -2.57 -2.35 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 1812 not shown) Planarity restraints: 1910 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 163 " -0.055 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO B 164 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO B 164 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 164 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 495 " -0.042 5.00e-02 4.00e+02 6.33e-02 6.42e+00 pdb=" N PRO B 496 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 496 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 496 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 58 " -0.039 5.00e-02 4.00e+02 5.89e-02 5.55e+00 pdb=" N PRO B 59 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 59 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 59 " -0.033 5.00e-02 4.00e+02 ... (remaining 1907 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.83: 3307 2.83 - 3.41: 12662 3.41 - 3.98: 22251 3.98 - 4.56: 31271 4.56 - 5.14: 44819 Nonbonded interactions: 114310 Sorted by model distance: nonbonded pdb=" OE2 GLU C 119 " pdb=" OG1 THR C 133 " model vdw 2.251 2.440 nonbonded pdb=" O GLY B 149 " pdb=" OG SER B 169 " model vdw 2.290 2.440 nonbonded pdb=" OG1 THR B 47 " pdb=" OG SER B 69 " model vdw 2.301 2.440 nonbonded pdb=" OG SER B 615 " pdb=" OD1 ASP B 673 " model vdw 2.322 2.440 nonbonded pdb=" O LEU A 541 " pdb=" OH TYR B 587 " model vdw 2.324 2.440 ... (remaining 114305 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.720 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: 0.010 Extract box with map and model: 4.050 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 32.000 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.210 11238 Z= 0.312 Angle : 0.773 9.415 15256 Z= 0.390 Chirality : 0.047 0.253 1815 Planarity : 0.006 0.084 1910 Dihedral : 15.745 123.983 4068 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.25 (0.21), residues: 1436 helix: 0.67 (0.16), residues: 854 sheet: -0.82 (0.78), residues: 49 loop : -1.43 (0.25), residues: 533 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.257 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.2310 time to fit residues: 54.2128 Evaluate side-chains 134 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.284 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 37 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 112 optimal weight: 0.4980 chunk 43 optimal weight: 0.0170 chunk 68 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 129 optimal weight: 10.0000 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.0668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 11238 Z= 0.146 Angle : 0.507 7.385 15256 Z= 0.250 Chirality : 0.038 0.151 1815 Planarity : 0.004 0.055 1910 Dihedral : 10.556 110.584 1688 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.60 (0.22), residues: 1436 helix: 1.53 (0.18), residues: 850 sheet: -1.24 (0.68), residues: 56 loop : -1.31 (0.26), residues: 530 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 137 time to evaluate : 1.240 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 140 average time/residue: 0.2188 time to fit residues: 45.4742 Evaluate side-chains 136 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 132 time to evaluate : 1.110 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1057 time to fit residues: 2.5452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 5.9990 chunk 40 optimal weight: 0.1980 chunk 108 optimal weight: 6.9990 chunk 88 optimal weight: 30.0000 chunk 35 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 chunk 129 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 104 optimal weight: 0.0970 overall best weight: 3.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN D 25 ASN ** B 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 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 : 0.006 0.055 11238 Z= 0.398 Angle : 0.636 6.958 15256 Z= 0.315 Chirality : 0.044 0.185 1815 Planarity : 0.005 0.049 1910 Dihedral : 10.621 113.194 1688 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.19 (0.22), residues: 1436 helix: 1.06 (0.17), residues: 867 sheet: -1.00 (0.57), residues: 77 loop : -1.33 (0.26), residues: 492 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 139 time to evaluate : 1.166 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 144 average time/residue: 0.2148 time to fit residues: 46.0809 Evaluate side-chains 138 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 134 time to evaluate : 1.214 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1012 time to fit residues: 2.4048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS ** B 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 11238 Z= 0.210 Angle : 0.529 6.039 15256 Z= 0.262 Chirality : 0.039 0.162 1815 Planarity : 0.004 0.046 1910 Dihedral : 10.238 109.081 1688 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.53 (0.22), residues: 1436 helix: 1.38 (0.18), residues: 860 sheet: -0.86 (0.65), residues: 62 loop : -1.26 (0.26), residues: 514 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 137 time to evaluate : 1.282 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 140 average time/residue: 0.2199 time to fit residues: 45.7288 Evaluate side-chains 136 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 132 time to evaluate : 1.110 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1024 time to fit residues: 2.4423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 5.9990 chunk 78 optimal weight: 0.0870 chunk 2 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 95 optimal weight: 0.0570 chunk 0 optimal weight: 8.9990 chunk 70 optimal weight: 0.5980 chunk 124 optimal weight: 0.4980 chunk 34 optimal weight: 3.9990 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 528 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 11238 Z= 0.132 Angle : 0.493 7.036 15256 Z= 0.242 Chirality : 0.037 0.145 1815 Planarity : 0.004 0.047 1910 Dihedral : 9.644 104.505 1688 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.92 (0.22), residues: 1436 helix: 1.73 (0.18), residues: 863 sheet: -0.94 (0.64), residues: 63 loop : -1.16 (0.26), residues: 510 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 146 time to evaluate : 1.272 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 149 average time/residue: 0.2236 time to fit residues: 48.9668 Evaluate side-chains 136 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 1.236 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1325 time to fit residues: 1.8939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 5.9990 chunk 124 optimal weight: 0.5980 chunk 27 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 chunk 114 optimal weight: 20.0000 chunk 64 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 11238 Z= 0.182 Angle : 0.513 7.875 15256 Z= 0.250 Chirality : 0.039 0.154 1815 Planarity : 0.004 0.046 1910 Dihedral : 9.536 104.835 1688 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.92 (0.22), residues: 1436 helix: 1.70 (0.18), residues: 869 sheet: -0.85 (0.73), residues: 53 loop : -1.16 (0.26), residues: 514 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 138 time to evaluate : 1.271 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 140 average time/residue: 0.2232 time to fit residues: 46.1425 Evaluate side-chains 137 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 1.168 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1005 time to fit residues: 1.7695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 101 optimal weight: 0.0050 chunk 116 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 85 optimal weight: 9.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 11238 Z= 0.263 Angle : 0.568 8.213 15256 Z= 0.276 Chirality : 0.041 0.167 1815 Planarity : 0.004 0.045 1910 Dihedral : 9.657 106.113 1688 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.70 (0.22), residues: 1436 helix: 1.47 (0.18), residues: 871 sheet: -0.81 (0.74), residues: 53 loop : -1.16 (0.26), residues: 512 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 135 time to evaluate : 1.337 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 137 average time/residue: 0.2177 time to fit residues: 44.5607 Evaluate side-chains 134 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 133 time to evaluate : 1.142 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1020 time to fit residues: 1.8044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 0.5980 chunk 82 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 87 optimal weight: 20.0000 chunk 93 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 chunk 125 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 11238 Z= 0.165 Angle : 0.519 9.862 15256 Z= 0.251 Chirality : 0.038 0.155 1815 Planarity : 0.004 0.046 1910 Dihedral : 9.408 103.656 1688 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.90 (0.22), residues: 1436 helix: 1.65 (0.18), residues: 874 sheet: -0.72 (0.75), residues: 53 loop : -1.13 (0.27), residues: 509 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 139 time to evaluate : 1.177 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 142 average time/residue: 0.2306 time to fit residues: 47.8941 Evaluate side-chains 137 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 135 time to evaluate : 1.242 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1050 time to fit residues: 2.1565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 77 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 116 optimal weight: 8.9990 chunk 121 optimal weight: 0.9990 chunk 127 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 11238 Z= 0.169 Angle : 0.527 10.744 15256 Z= 0.254 Chirality : 0.038 0.154 1815 Planarity : 0.004 0.046 1910 Dihedral : 9.330 103.328 1688 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.95 (0.22), residues: 1436 helix: 1.68 (0.18), residues: 874 sheet: -0.61 (0.76), residues: 53 loop : -1.10 (0.27), residues: 509 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.280 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.2309 time to fit residues: 46.4139 Evaluate side-chains 136 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.162 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 94 optimal weight: 9.9990 chunk 142 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 69 optimal weight: 0.0060 chunk 90 optimal weight: 7.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 11238 Z= 0.182 Angle : 0.525 8.164 15256 Z= 0.254 Chirality : 0.039 0.156 1815 Planarity : 0.004 0.046 1910 Dihedral : 9.394 102.982 1688 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.94 (0.22), residues: 1436 helix: 1.67 (0.18), residues: 874 sheet: -0.63 (0.75), residues: 54 loop : -1.09 (0.27), residues: 508 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 132 time to evaluate : 1.122 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 133 average time/residue: 0.2210 time to fit residues: 43.8305 Evaluate side-chains 132 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 131 time to evaluate : 1.272 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1043 time to fit residues: 1.7865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 3.9990 chunk 34 optimal weight: 0.0570 chunk 104 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 113 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.142386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.099907 restraints weight = 13182.143| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.76 r_work: 0.2925 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 11238 Z= 0.164 Angle : 0.528 10.575 15256 Z= 0.253 Chirality : 0.038 0.153 1815 Planarity : 0.004 0.046 1910 Dihedral : 9.273 102.133 1688 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.99 (0.22), residues: 1436 helix: 1.72 (0.18), residues: 873 sheet: -0.63 (0.75), residues: 54 loop : -1.09 (0.27), residues: 509 =============================================================================== Job complete usr+sys time: 2246.49 seconds wall clock time: 41 minutes 38.80 seconds (2498.80 seconds total)