Starting phenix.real_space_refine on Thu Mar 14 18:50:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqx_26701/03_2024/7uqx_26701_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqx_26701/03_2024/7uqx_26701.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqx_26701/03_2024/7uqx_26701.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqx_26701/03_2024/7uqx_26701.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqx_26701/03_2024/7uqx_26701_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqx_26701/03_2024/7uqx_26701_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.034 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 Mn 1 7.51 5 P 4 5.49 5 S 46 5.16 5 C 6100 2.51 5 N 1593 2.21 5 O 1747 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 320": "OE1" <-> "OE2" Residue "B ASP 540": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9491 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4759 Classifications: {'peptide': 583} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 555} Chain breaks: 3 Chain: "B" Number of atoms: 4628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4628 Classifications: {'peptide': 571} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 35, 'TRANS': 535} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'UDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {' MN': 1, 'UDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.54, per 1000 atoms: 0.58 Number of scatterers: 9491 At special positions: 0 Unit cell: (102.672, 86.94, 110.124, 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) Mn 1 24.99 S 46 16.00 P 4 15.00 O 1747 8.00 N 1593 7.00 C 6100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 103 " distance=2.03 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 355 " distance=2.03 Simple disulfide: pdb=" SG CYS A 652 " - pdb=" SG CYS A 704 " distance=2.03 Simple disulfide: pdb=" SG CYS B 85 " - pdb=" SG CYS B 90 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 151 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 339 " distance=2.03 Simple disulfide: pdb=" SG CYS B 626 " - pdb=" SG CYS B 676 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG A 802 " - " ASN A 330 " " NAG C 1 " - " ASN B 637 " Time building additional restraints: 3.84 Conformation dependent library (CDL) restraints added in 1.7 seconds 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2204 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 13 sheets defined 33.7% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 106 through 111 Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 174 through 179 removed outlier: 3.786A pdb=" N GLN A 179 " --> pdb=" O ARG A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 278 through 281 No H-bonds generated for 'chain 'A' and resid 278 through 281' Processing helix chain 'A' and resid 283 through 286 No H-bonds generated for 'chain 'A' and resid 283 through 286' Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 325 through 328 No H-bonds generated for 'chain 'A' and resid 325 through 328' Processing helix chain 'A' and resid 345 through 352 Processing helix chain 'A' and resid 383 through 385 No H-bonds generated for 'chain 'A' and resid 383 through 385' Processing helix chain 'A' and resid 389 through 395 Processing helix chain 'A' and resid 398 through 415 Processing helix chain 'A' and resid 419 through 432 Processing helix chain 'A' and resid 442 through 446 removed outlier: 3.838A pdb=" N ASN A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 442 through 446' Processing helix chain 'A' and resid 462 through 464 No H-bonds generated for 'chain 'A' and resid 462 through 464' Processing helix chain 'A' and resid 496 through 505 removed outlier: 3.557A pdb=" N VAL A 502 " --> pdb=" O LEU A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 550 No H-bonds generated for 'chain 'A' and resid 548 through 550' Processing helix chain 'A' and resid 572 through 584 removed outlier: 3.830A pdb=" N SER A 584 " --> pdb=" O THR A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 623 No H-bonds generated for 'chain 'A' and resid 621 through 623' Processing helix chain 'A' and resid 628 through 636 Processing helix chain 'A' and resid 640 through 649 Processing helix chain 'A' and resid 653 through 665 Processing helix chain 'A' and resid 697 through 712 removed outlier: 3.774A pdb=" N ARG A 701 " --> pdb=" O HIS A 697 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN A 702 " --> pdb=" O PHE A 698 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER A 703 " --> pdb=" O ALA A 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 90 No H-bonds generated for 'chain 'B' and resid 87 through 90' Processing helix chain 'B' and resid 128 through 138 Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 167 through 177 Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 235 through 239 Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 308 through 314 removed outlier: 3.943A pdb=" N LEU B 312 " --> pdb=" O TYR B 308 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLN B 313 " --> pdb=" O PRO B 309 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU B 314 " --> pdb=" O GLN B 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 308 through 314' Processing helix chain 'B' and resid 329 through 337 Processing helix chain 'B' and resid 358 through 360 No H-bonds generated for 'chain 'B' and resid 358 through 360' Processing helix chain 'B' and resid 367 through 369 No H-bonds generated for 'chain 'B' and resid 367 through 369' Processing helix chain 'B' and resid 373 through 379 removed outlier: 3.532A pdb=" N SER B 379 " --> pdb=" O SER B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 399 Processing helix chain 'B' and resid 403 through 418 Processing helix chain 'B' and resid 420 through 422 No H-bonds generated for 'chain 'B' and resid 420 through 422' Processing helix chain 'B' and resid 426 through 430 Processing helix chain 'B' and resid 433 through 438 Processing helix chain 'B' and resid 467 through 478 removed outlier: 3.631A pdb=" N ARG B 471 " --> pdb=" O GLU B 467 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS B 478 " --> pdb=" O THR B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 523 removed outlier: 4.029A pdb=" N ARG B 522 " --> pdb=" O LEU B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 558 removed outlier: 3.799A pdb=" N GLU B 558 " --> pdb=" O GLU B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 610 Processing helix chain 'B' and resid 616 through 623 Processing helix chain 'B' and resid 627 through 639 Processing helix chain 'B' and resid 671 through 684 Processing sheet with id= A, first strand: chain 'A' and resid 116 through 118 removed outlier: 6.660A pdb=" N LEU A 153 " --> pdb=" O TYR A 117 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 191 through 194 removed outlier: 6.740A pdb=" N MET A 215 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ASN A 194 " --> pdb=" O MET A 215 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ALA A 217 " --> pdb=" O ASN A 194 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 264 through 267 Processing sheet with id= D, first strand: chain 'A' and resid 333 through 336 removed outlier: 6.047A pdb=" N VAL A 356 " --> pdb=" O CYS A 334 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL A 336 " --> pdb=" O VAL A 356 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL A 358 " --> pdb=" O VAL A 336 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 623 through 627 removed outlier: 3.818A pdb=" N ALA A 624 " --> pdb=" O SER A 563 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ALA A 482 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE A 513 " --> pdb=" O ALA A 482 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE A 484 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL A 515 " --> pdb=" O ILE A 484 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA A 486 " --> pdb=" O VAL A 515 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TRP A 517 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 671 through 673 removed outlier: 3.680A pdb=" N THR A 673 " --> pdb=" O LEU A 724 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 106 through 108 removed outlier: 6.767A pdb=" N LEU B 152 " --> pdb=" O TYR B 107 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 187 through 189 removed outlier: 6.804A pdb=" N LEU B 211 " --> pdb=" O LEU B 188 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 254 through 257 removed outlier: 3.695A pdb=" N SER B 256 " --> pdb=" O LEU B 281 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 298 through 301 Processing sheet with id= K, first strand: chain 'B' and resid 317 through 320 removed outlier: 5.877A pdb=" N VAL B 340 " --> pdb=" O CYS B 318 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL B 320 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N VAL B 342 " --> pdb=" O VAL B 320 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 598 through 601 removed outlier: 3.647A pdb=" N ALA B 598 " --> pdb=" O ALA B 536 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 536 " --> pdb=" O ALA B 598 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR B 600 " --> pdb=" O VAL B 534 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N THR B 457 " --> pdb=" O LEU B 535 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ILE B 537 " --> pdb=" O THR B 457 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ILE B 459 " --> pdb=" O ILE B 537 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ALA B 458 " --> pdb=" O SER B 483 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU B 485 " --> pdb=" O ALA B 458 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N VAL B 460 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N VAL B 487 " --> pdb=" O VAL B 460 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N THR B 462 " --> pdb=" O VAL B 487 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N TRP B 489 " --> pdb=" O THR B 462 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL B 487 " --> pdb=" O PRO B 508 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LYS B 510 " --> pdb=" O VAL B 487 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N TRP B 489 " --> pdb=" O LYS B 510 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL B 512 " --> pdb=" O TRP B 489 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 570 through 574 removed outlier: 3.647A pdb=" N LEU B 570 " --> pdb=" O GLU B 583 " (cutoff:3.500A) 221 hydrogen bonds defined for protein. 630 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.50 Time building geometry restraints manager: 4.14 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: 3002 1.34 - 1.46: 2265 1.46 - 1.58: 4402 1.58 - 1.70: 5 1.70 - 1.82: 72 Bond restraints: 9746 Sorted by residual: bond pdb=" O1A UDP B 801 " pdb=" PA UDP B 801 " ideal model delta sigma weight residual 1.482 1.526 -0.044 1.00e-02 1.00e+04 1.91e+01 bond pdb=" N ILE B 616 " pdb=" CA ILE B 616 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.17e-02 7.31e+03 8.38e+00 bond pdb=" N ASP B 615 " pdb=" CA ASP B 615 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.78e+00 bond pdb=" N TYR A 324 " pdb=" CA TYR A 324 " ideal model delta sigma weight residual 1.459 1.491 -0.031 1.19e-02 7.06e+03 6.91e+00 bond pdb=" O2A UDP B 801 " pdb=" PA UDP B 801 " ideal model delta sigma weight residual 1.527 1.481 0.046 1.80e-02 3.09e+03 6.52e+00 ... (remaining 9741 not shown) Histogram of bond angle deviations from ideal: 99.94 - 106.75: 354 106.75 - 113.56: 5228 113.56 - 120.37: 3536 120.37 - 127.18: 3994 127.18 - 134.00: 140 Bond angle restraints: 13252 Sorted by residual: angle pdb=" O5' UDP B 801 " pdb=" PA UDP B 801 " pdb=" O1A UDP B 801 " ideal model delta sigma weight residual 106.70 111.06 -4.36 1.00e+00 1.00e+00 1.90e+01 angle pdb=" O2A UDP B 801 " pdb=" PA UDP B 801 " pdb=" O3A UDP B 801 " ideal model delta sigma weight residual 105.97 110.21 -4.24 1.00e+00 1.00e+00 1.80e+01 angle pdb=" O5' UDP B 801 " pdb=" PA UDP B 801 " pdb=" O2A UDP B 801 " ideal model delta sigma weight residual 110.83 107.01 3.82 1.00e+00 1.00e+00 1.46e+01 angle pdb=" O1A UDP B 801 " pdb=" PA UDP B 801 " pdb=" O3A UDP B 801 " ideal model delta sigma weight residual 109.95 106.28 3.67 1.00e+00 1.00e+00 1.35e+01 angle pdb=" CA GLU A 320 " pdb=" C GLU A 320 " pdb=" O GLU A 320 " ideal model delta sigma weight residual 121.28 117.36 3.92 1.07e+00 8.73e-01 1.34e+01 ... (remaining 13247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.77: 5638 21.77 - 43.53: 222 43.53 - 65.30: 29 65.30 - 87.06: 11 87.06 - 108.83: 4 Dihedral angle restraints: 5904 sinusoidal: 2493 harmonic: 3411 Sorted by residual: dihedral pdb=" O4 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C5 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sinusoidal sigma weight residual 288.71 179.88 108.83 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" C3 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C5 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sinusoidal sigma weight residual 47.62 -59.25 106.87 1 3.00e+01 1.11e-03 1.38e+01 dihedral pdb=" C6 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C5 BMA C 3 " pdb=" O4 BMA C 3 " ideal model delta sinusoidal sigma weight residual -163.34 -60.34 -103.00 1 3.00e+01 1.11e-03 1.31e+01 ... (remaining 5901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1205 0.054 - 0.108: 200 0.108 - 0.162: 36 0.162 - 0.216: 4 0.216 - 0.270: 3 Chirality restraints: 1448 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA ILE B 542 " pdb=" N ILE B 542 " pdb=" C ILE B 542 " pdb=" CB ILE B 542 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ILE B 537 " pdb=" N ILE B 537 " pdb=" C ILE B 537 " pdb=" CB ILE B 537 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1445 not shown) Planarity restraints: 1677 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 399 " -0.019 2.00e-02 2.50e+03 1.01e-02 2.05e+00 pdb=" CG TYR B 399 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR B 399 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 399 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR B 399 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 399 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 399 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 399 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 479 " -0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO B 480 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 480 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 480 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 448 " -0.021 5.00e-02 4.00e+02 3.16e-02 1.60e+00 pdb=" N PRO A 449 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 449 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 449 " -0.016 5.00e-02 4.00e+02 ... (remaining 1674 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 24 2.38 - 3.01: 5236 3.01 - 3.64: 14435 3.64 - 4.27: 22268 4.27 - 4.90: 36615 Nonbonded interactions: 78578 Sorted by model distance: nonbonded pdb=" O1A UDP B 801 " pdb="MN MN B 802 " model vdw 1.752 2.320 nonbonded pdb=" O ALA A 377 " pdb=" OG1 THR A 408 " model vdw 2.205 2.440 nonbonded pdb=" OG SER A 547 " pdb=" OD1 ASP A 647 " model vdw 2.215 2.440 nonbonded pdb=" OH TYR B 130 " pdb=" O PRO B 155 " model vdw 2.217 2.440 nonbonded pdb=" O GLU A 587 " pdb=" OH TYR A 630 " model vdw 2.237 2.440 ... (remaining 78573 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: 0.770 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: 3.780 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 28.420 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 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 : 0.003 0.046 9746 Z= 0.175 Angle : 0.524 6.152 13252 Z= 0.297 Chirality : 0.045 0.270 1448 Planarity : 0.003 0.035 1675 Dihedral : 11.926 108.829 3673 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.19 % Allowed : 5.24 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.26), residues: 1138 helix: 1.40 (0.28), residues: 358 sheet: -1.03 (0.44), residues: 142 loop : -0.17 (0.26), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 396 HIS 0.002 0.001 HIS B 623 PHE 0.009 0.001 PHE B 400 TYR 0.019 0.001 TYR B 399 ARG 0.001 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 284 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.7296 (mmtt) cc_final: 0.6898 (mmtt) REVERT: A 142 ARG cc_start: 0.8325 (ptt90) cc_final: 0.7889 (ptt90) REVERT: A 210 ASP cc_start: 0.7744 (t70) cc_final: 0.7176 (t70) REVERT: A 394 ARG cc_start: 0.7952 (mtm-85) cc_final: 0.7750 (ptp-170) REVERT: A 546 MET cc_start: 0.4384 (ppp) cc_final: 0.3916 (ppp) REVERT: A 600 ASP cc_start: 0.7023 (t0) cc_final: 0.6633 (t0) REVERT: A 603 LYS cc_start: 0.7372 (ttpt) cc_final: 0.7049 (tttt) REVERT: A 615 ASP cc_start: 0.7169 (m-30) cc_final: 0.6816 (p0) REVERT: A 645 MET cc_start: 0.6936 (tpp) cc_final: 0.6621 (tpp) REVERT: A 706 ASN cc_start: 0.7586 (m-40) cc_final: 0.7096 (m-40) REVERT: B 131 ASN cc_start: 0.7903 (t0) cc_final: 0.7389 (t0) REVERT: B 268 ASP cc_start: 0.7180 (t0) cc_final: 0.6926 (t0) REVERT: B 275 LYS cc_start: 0.8500 (tmtt) cc_final: 0.8002 (tmtt) REVERT: B 310 GLN cc_start: 0.7566 (mp10) cc_final: 0.7079 (mp10) REVERT: B 370 MET cc_start: 0.7553 (tpt) cc_final: 0.7156 (tpp) REVERT: B 372 ASP cc_start: 0.7385 (t0) cc_final: 0.6721 (t0) REVERT: B 427 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6578 (mm-30) REVERT: B 431 ASP cc_start: 0.6963 (m-30) cc_final: 0.6503 (m-30) REVERT: B 435 VAL cc_start: 0.7715 (m) cc_final: 0.7509 (p) REVERT: B 566 TYR cc_start: 0.7004 (m-80) cc_final: 0.6513 (m-80) REVERT: B 583 GLU cc_start: 0.5957 (tm-30) cc_final: 0.5460 (tm-30) REVERT: B 589 GLU cc_start: 0.6544 (pm20) cc_final: 0.6222 (pm20) REVERT: B 646 VAL cc_start: 0.7834 (t) cc_final: 0.7180 (m) outliers start: 2 outliers final: 1 residues processed: 286 average time/residue: 0.2673 time to fit residues: 99.7436 Evaluate side-chains 254 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 253 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.0030 chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 46 optimal weight: 0.0870 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 67 optimal weight: 5.9990 chunk 104 optimal weight: 0.0370 overall best weight: 0.3448 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 HIS A 406 GLN A 431 GLN A 658 ASN B 430 ASN B 517 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9746 Z= 0.148 Angle : 0.506 8.495 13252 Z= 0.251 Chirality : 0.042 0.165 1448 Planarity : 0.004 0.034 1675 Dihedral : 8.999 86.040 1414 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.04 % Allowed : 10.57 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.31 (0.25), residues: 1138 helix: 1.34 (0.28), residues: 359 sheet: -0.82 (0.43), residues: 140 loop : -0.13 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 711 HIS 0.004 0.001 HIS A 287 PHE 0.020 0.001 PHE B 551 TYR 0.022 0.001 TYR A 319 ARG 0.006 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 256 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ASP cc_start: 0.7756 (t70) cc_final: 0.7176 (t70) REVERT: A 267 LYS cc_start: 0.6605 (tttp) cc_final: 0.6388 (tttm) REVERT: A 436 LYS cc_start: 0.8436 (mmmm) cc_final: 0.7932 (mmtt) REVERT: A 546 MET cc_start: 0.4608 (ppp) cc_final: 0.4066 (ppp) REVERT: A 595 ARG cc_start: 0.7147 (mmt-90) cc_final: 0.6883 (mmt-90) REVERT: A 600 ASP cc_start: 0.7042 (t0) cc_final: 0.6644 (t0) REVERT: A 603 LYS cc_start: 0.7416 (ttpt) cc_final: 0.7119 (ttpt) REVERT: A 615 ASP cc_start: 0.7165 (m-30) cc_final: 0.6821 (p0) REVERT: A 645 MET cc_start: 0.6921 (tpp) cc_final: 0.6605 (tpp) REVERT: A 706 ASN cc_start: 0.7558 (m-40) cc_final: 0.7136 (m110) REVERT: B 131 ASN cc_start: 0.7866 (t0) cc_final: 0.6823 (t0) REVERT: B 135 MET cc_start: 0.7091 (OUTLIER) cc_final: 0.6394 (mpp) REVERT: B 182 ARG cc_start: 0.8152 (mmm-85) cc_final: 0.7852 (mtp85) REVERT: B 268 ASP cc_start: 0.7207 (t0) cc_final: 0.6992 (t0) REVERT: B 275 LYS cc_start: 0.8494 (tmtt) cc_final: 0.7977 (tmtt) REVERT: B 310 GLN cc_start: 0.7601 (mp10) cc_final: 0.7159 (mp10) REVERT: B 344 ILE cc_start: 0.6918 (OUTLIER) cc_final: 0.6710 (mm) REVERT: B 370 MET cc_start: 0.7547 (tpt) cc_final: 0.7126 (tpp) REVERT: B 372 ASP cc_start: 0.7544 (t0) cc_final: 0.6978 (t0) REVERT: B 427 GLU cc_start: 0.7042 (mm-30) cc_final: 0.6671 (mm-30) REVERT: B 431 ASP cc_start: 0.6978 (m-30) cc_final: 0.6551 (m-30) REVERT: B 566 TYR cc_start: 0.7273 (m-80) cc_final: 0.7027 (m-80) REVERT: B 583 GLU cc_start: 0.6015 (tm-30) cc_final: 0.5371 (tm-30) REVERT: B 589 GLU cc_start: 0.6576 (pm20) cc_final: 0.6250 (pm20) REVERT: B 693 GLU cc_start: 0.7406 (mp0) cc_final: 0.7041 (mp0) outliers start: 21 outliers final: 13 residues processed: 267 average time/residue: 0.2513 time to fit residues: 89.1961 Evaluate side-chains 265 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 250 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 539 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 0.4980 chunk 32 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 93 optimal weight: 0.0970 chunk 103 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 HIS B 412 GLN ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 517 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9746 Z= 0.208 Angle : 0.527 8.492 13252 Z= 0.261 Chirality : 0.043 0.169 1448 Planarity : 0.004 0.031 1675 Dihedral : 8.088 87.604 1414 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.52 % Allowed : 12.42 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.16 (0.25), residues: 1138 helix: 1.12 (0.28), residues: 370 sheet: -0.98 (0.43), residues: 139 loop : -0.16 (0.26), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 374 HIS 0.004 0.001 HIS A 448 PHE 0.027 0.002 PHE A 577 TYR 0.019 0.001 TYR A 319 ARG 0.005 0.001 ARG B 383 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 255 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8433 (mm) REVERT: A 210 ASP cc_start: 0.7817 (t70) cc_final: 0.7231 (t70) REVERT: A 216 LEU cc_start: 0.6696 (pt) cc_final: 0.6354 (mt) REVERT: A 223 THR cc_start: 0.8198 (p) cc_final: 0.7861 (t) REVERT: A 436 LYS cc_start: 0.8458 (mmmm) cc_final: 0.7986 (mmtt) REVERT: A 546 MET cc_start: 0.4627 (ppp) cc_final: 0.4069 (ppp) REVERT: A 600 ASP cc_start: 0.7080 (t0) cc_final: 0.6652 (t0) REVERT: A 603 LYS cc_start: 0.7455 (ttpt) cc_final: 0.7093 (ttpt) REVERT: A 614 ASN cc_start: 0.7723 (t0) cc_final: 0.7523 (t0) REVERT: A 615 ASP cc_start: 0.7214 (m-30) cc_final: 0.6979 (p0) REVERT: A 645 MET cc_start: 0.6946 (tpp) cc_final: 0.6612 (tpp) REVERT: A 706 ASN cc_start: 0.7654 (m-40) cc_final: 0.7198 (m110) REVERT: B 131 ASN cc_start: 0.7845 (t0) cc_final: 0.6849 (t0) REVERT: B 135 MET cc_start: 0.7117 (OUTLIER) cc_final: 0.6419 (mpp) REVERT: B 182 ARG cc_start: 0.8146 (mmm-85) cc_final: 0.7867 (mtp85) REVERT: B 268 ASP cc_start: 0.7283 (t0) cc_final: 0.7082 (t0) REVERT: B 275 LYS cc_start: 0.8506 (tmtt) cc_final: 0.7958 (tmtt) REVERT: B 310 GLN cc_start: 0.7709 (mp10) cc_final: 0.7264 (mp10) REVERT: B 370 MET cc_start: 0.7548 (tpt) cc_final: 0.7181 (tpp) REVERT: B 372 ASP cc_start: 0.7579 (t0) cc_final: 0.7038 (t0) REVERT: B 386 GLU cc_start: 0.7268 (mt-10) cc_final: 0.7026 (mt-10) REVERT: B 427 GLU cc_start: 0.7112 (mm-30) cc_final: 0.6822 (mm-30) REVERT: B 428 GLU cc_start: 0.7211 (tm-30) cc_final: 0.6803 (tm-30) REVERT: B 431 ASP cc_start: 0.7051 (m-30) cc_final: 0.6799 (m-30) REVERT: B 541 ILE cc_start: 0.7522 (OUTLIER) cc_final: 0.7246 (mm) REVERT: B 559 PHE cc_start: 0.7591 (m-10) cc_final: 0.7289 (m-80) REVERT: B 566 TYR cc_start: 0.7359 (m-80) cc_final: 0.7065 (m-80) REVERT: B 583 GLU cc_start: 0.6139 (tm-30) cc_final: 0.5734 (tm-30) REVERT: B 589 GLU cc_start: 0.6601 (pm20) cc_final: 0.6244 (pm20) REVERT: B 638 VAL cc_start: 0.8117 (t) cc_final: 0.7721 (m) REVERT: B 644 ILE cc_start: 0.8704 (mm) cc_final: 0.8483 (mt) REVERT: B 693 GLU cc_start: 0.7418 (mp0) cc_final: 0.7093 (mp0) outliers start: 26 outliers final: 16 residues processed: 268 average time/residue: 0.2443 time to fit residues: 87.0781 Evaluate side-chains 261 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 242 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 541 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 11 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 104 optimal weight: 0.0000 chunk 111 optimal weight: 2.9990 chunk 99 optimal weight: 0.2980 chunk 29 optimal weight: 0.4980 chunk 92 optimal weight: 0.2980 overall best weight: 0.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 GLN B 430 ASN B 517 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9746 Z= 0.144 Angle : 0.504 7.067 13252 Z= 0.253 Chirality : 0.042 0.244 1448 Planarity : 0.004 0.032 1675 Dihedral : 7.371 86.819 1414 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.91 % Allowed : 12.61 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.16 (0.25), residues: 1138 helix: 1.19 (0.28), residues: 364 sheet: -0.91 (0.43), residues: 139 loop : -0.22 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 396 HIS 0.005 0.001 HIS A 241 PHE 0.034 0.001 PHE A 577 TYR 0.020 0.001 TYR A 714 ARG 0.006 0.000 ARG B 383 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 240 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ASP cc_start: 0.7824 (t70) cc_final: 0.7219 (t70) REVERT: A 216 LEU cc_start: 0.6662 (pt) cc_final: 0.6339 (mt) REVERT: A 223 THR cc_start: 0.8123 (p) cc_final: 0.7896 (t) REVERT: A 436 LYS cc_start: 0.8416 (mmmm) cc_final: 0.8029 (mmtt) REVERT: A 546 MET cc_start: 0.4663 (ppp) cc_final: 0.4069 (ppp) REVERT: A 600 ASP cc_start: 0.7092 (t0) cc_final: 0.6671 (t0) REVERT: A 603 LYS cc_start: 0.7436 (ttpt) cc_final: 0.7082 (ttpt) REVERT: A 615 ASP cc_start: 0.7204 (m-30) cc_final: 0.6995 (p0) REVERT: A 645 MET cc_start: 0.6939 (tpp) cc_final: 0.6587 (tpp) REVERT: A 706 ASN cc_start: 0.7637 (m-40) cc_final: 0.7163 (m-40) REVERT: B 131 ASN cc_start: 0.7827 (t0) cc_final: 0.6836 (t0) REVERT: B 135 MET cc_start: 0.7098 (OUTLIER) cc_final: 0.6388 (mpp) REVERT: B 182 ARG cc_start: 0.8134 (mmm-85) cc_final: 0.7849 (mtp85) REVERT: B 275 LYS cc_start: 0.8474 (tmtt) cc_final: 0.7950 (tmtt) REVERT: B 282 VAL cc_start: 0.8817 (OUTLIER) cc_final: 0.8548 (p) REVERT: B 310 GLN cc_start: 0.7650 (mp10) cc_final: 0.7194 (mp10) REVERT: B 344 ILE cc_start: 0.7119 (OUTLIER) cc_final: 0.6839 (mm) REVERT: B 372 ASP cc_start: 0.7543 (t0) cc_final: 0.6971 (t0) REVERT: B 386 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6973 (mt-10) REVERT: B 541 ILE cc_start: 0.7493 (OUTLIER) cc_final: 0.7272 (mm) REVERT: B 566 TYR cc_start: 0.7254 (m-80) cc_final: 0.6933 (m-80) REVERT: B 583 GLU cc_start: 0.6086 (tm-30) cc_final: 0.5487 (tm-30) REVERT: B 589 GLU cc_start: 0.6586 (pm20) cc_final: 0.6253 (pm20) REVERT: B 633 PHE cc_start: 0.7609 (m-80) cc_final: 0.7297 (m-80) REVERT: B 638 VAL cc_start: 0.8083 (t) cc_final: 0.7695 (m) REVERT: B 644 ILE cc_start: 0.8736 (mm) cc_final: 0.8508 (mt) REVERT: B 693 GLU cc_start: 0.7377 (mp0) cc_final: 0.7020 (mp0) outliers start: 30 outliers final: 19 residues processed: 257 average time/residue: 0.2472 time to fit residues: 85.1308 Evaluate side-chains 259 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 236 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 541 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 0 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 99 optimal weight: 0.0470 chunk 28 optimal weight: 0.0020 chunk 37 optimal weight: 0.6980 overall best weight: 0.4886 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 HIS A 352 GLN B 430 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9746 Z= 0.162 Angle : 0.514 8.624 13252 Z= 0.256 Chirality : 0.043 0.247 1448 Planarity : 0.004 0.031 1675 Dihedral : 7.044 87.694 1414 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.78 % Allowed : 12.61 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.13 (0.25), residues: 1138 helix: 1.22 (0.28), residues: 359 sheet: -0.88 (0.43), residues: 139 loop : -0.27 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 396 HIS 0.003 0.001 HIS A 241 PHE 0.034 0.001 PHE A 577 TYR 0.020 0.001 TYR A 319 ARG 0.006 0.000 ARG B 383 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 242 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8434 (mm) REVERT: A 210 ASP cc_start: 0.7817 (t70) cc_final: 0.7197 (t70) REVERT: A 216 LEU cc_start: 0.6647 (pt) cc_final: 0.6326 (mt) REVERT: A 436 LYS cc_start: 0.8389 (mmmm) cc_final: 0.8016 (mmtt) REVERT: A 546 MET cc_start: 0.4678 (ppp) cc_final: 0.4065 (ppp) REVERT: A 600 ASP cc_start: 0.7099 (t0) cc_final: 0.6672 (t0) REVERT: A 603 LYS cc_start: 0.7449 (ttpt) cc_final: 0.7075 (ttpt) REVERT: A 615 ASP cc_start: 0.7276 (m-30) cc_final: 0.6968 (p0) REVERT: A 645 MET cc_start: 0.6919 (tpp) cc_final: 0.6636 (tpp) REVERT: A 706 ASN cc_start: 0.7588 (m-40) cc_final: 0.7157 (m110) REVERT: B 131 ASN cc_start: 0.7820 (t0) cc_final: 0.7357 (t0) REVERT: B 135 MET cc_start: 0.7123 (OUTLIER) cc_final: 0.6774 (mpp) REVERT: B 182 ARG cc_start: 0.8137 (mmm-85) cc_final: 0.7864 (mtp85) REVERT: B 251 GLN cc_start: 0.7588 (pt0) cc_final: 0.7336 (pt0) REVERT: B 275 LYS cc_start: 0.8490 (tmtt) cc_final: 0.7948 (tmtt) REVERT: B 282 VAL cc_start: 0.8820 (OUTLIER) cc_final: 0.8547 (p) REVERT: B 310 GLN cc_start: 0.7666 (mp10) cc_final: 0.7203 (mp10) REVERT: B 344 ILE cc_start: 0.7091 (OUTLIER) cc_final: 0.6843 (mm) REVERT: B 370 MET cc_start: 0.7478 (tpt) cc_final: 0.7197 (tpp) REVERT: B 372 ASP cc_start: 0.7561 (t0) cc_final: 0.6992 (t0) REVERT: B 416 ASP cc_start: 0.7752 (m-30) cc_final: 0.7278 (m-30) REVERT: B 541 ILE cc_start: 0.7441 (OUTLIER) cc_final: 0.7191 (mm) REVERT: B 566 TYR cc_start: 0.7238 (m-80) cc_final: 0.6938 (m-80) REVERT: B 583 GLU cc_start: 0.6100 (tm-30) cc_final: 0.5511 (tm-30) REVERT: B 589 GLU cc_start: 0.6581 (pm20) cc_final: 0.6234 (pm20) REVERT: B 638 VAL cc_start: 0.8100 (t) cc_final: 0.7718 (m) REVERT: B 693 GLU cc_start: 0.7365 (mp0) cc_final: 0.7062 (mp0) outliers start: 39 outliers final: 27 residues processed: 266 average time/residue: 0.2375 time to fit residues: 85.0907 Evaluate side-chains 265 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 233 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 539 ASP Chi-restraints excluded: chain B residue 541 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 0.0270 chunk 21 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 0.0570 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9746 Z= 0.191 Angle : 0.519 6.849 13252 Z= 0.260 Chirality : 0.043 0.242 1448 Planarity : 0.004 0.032 1675 Dihedral : 6.931 88.800 1414 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.78 % Allowed : 13.19 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.06 (0.25), residues: 1138 helix: 1.10 (0.27), residues: 365 sheet: -0.88 (0.43), residues: 139 loop : -0.30 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 374 HIS 0.004 0.001 HIS B 88 PHE 0.028 0.001 PHE A 577 TYR 0.022 0.001 TYR A 319 ARG 0.006 0.000 ARG B 383 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 238 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.8301 (m-80) cc_final: 0.7851 (m-80) REVERT: A 181 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8422 (mm) REVERT: A 210 ASP cc_start: 0.7828 (t70) cc_final: 0.7198 (t70) REVERT: A 216 LEU cc_start: 0.6624 (pt) cc_final: 0.6366 (mt) REVERT: A 223 THR cc_start: 0.8405 (t) cc_final: 0.8146 (t) REVERT: A 436 LYS cc_start: 0.8394 (mmmm) cc_final: 0.8036 (mmtt) REVERT: A 546 MET cc_start: 0.4650 (ppp) cc_final: 0.4023 (ppp) REVERT: A 600 ASP cc_start: 0.7089 (t0) cc_final: 0.6566 (t0) REVERT: A 603 LYS cc_start: 0.7463 (ttpt) cc_final: 0.7166 (ttpt) REVERT: A 615 ASP cc_start: 0.7302 (m-30) cc_final: 0.6963 (p0) REVERT: A 645 MET cc_start: 0.6930 (tpp) cc_final: 0.6633 (tpp) REVERT: A 706 ASN cc_start: 0.7641 (m-40) cc_final: 0.7207 (m-40) REVERT: B 131 ASN cc_start: 0.7879 (t0) cc_final: 0.7447 (t0) REVERT: B 135 MET cc_start: 0.7106 (OUTLIER) cc_final: 0.6771 (mpp) REVERT: B 182 ARG cc_start: 0.8140 (mmm-85) cc_final: 0.7861 (mtp85) REVERT: B 251 GLN cc_start: 0.7622 (pt0) cc_final: 0.7360 (pt0) REVERT: B 275 LYS cc_start: 0.8495 (tmtt) cc_final: 0.7955 (tmtt) REVERT: B 282 VAL cc_start: 0.8806 (t) cc_final: 0.8568 (p) REVERT: B 310 GLN cc_start: 0.7706 (mp10) cc_final: 0.7219 (mp10) REVERT: B 344 ILE cc_start: 0.7192 (OUTLIER) cc_final: 0.6917 (mm) REVERT: B 370 MET cc_start: 0.7411 (tpt) cc_final: 0.7185 (tpp) REVERT: B 372 ASP cc_start: 0.7560 (t0) cc_final: 0.6993 (t0) REVERT: B 386 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6940 (mt-10) REVERT: B 428 GLU cc_start: 0.7167 (tm-30) cc_final: 0.6899 (tm-30) REVERT: B 541 ILE cc_start: 0.7464 (OUTLIER) cc_final: 0.7230 (mm) REVERT: B 566 TYR cc_start: 0.7285 (m-80) cc_final: 0.6985 (m-80) REVERT: B 583 GLU cc_start: 0.6138 (tm-30) cc_final: 0.5522 (tm-30) REVERT: B 589 GLU cc_start: 0.6578 (pm20) cc_final: 0.6209 (pm20) REVERT: B 633 PHE cc_start: 0.7611 (m-80) cc_final: 0.7240 (m-80) REVERT: B 638 VAL cc_start: 0.8106 (t) cc_final: 0.7726 (m) REVERT: B 693 GLU cc_start: 0.7370 (mp0) cc_final: 0.7115 (mp0) outliers start: 39 outliers final: 31 residues processed: 263 average time/residue: 0.2454 time to fit residues: 86.7703 Evaluate side-chains 271 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 236 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 539 ASP Chi-restraints excluded: chain B residue 541 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 68 optimal weight: 0.0020 chunk 44 optimal weight: 0.6980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9746 Z= 0.185 Angle : 0.533 8.736 13252 Z= 0.267 Chirality : 0.043 0.226 1448 Planarity : 0.004 0.032 1675 Dihedral : 6.762 89.980 1414 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.69 % Allowed : 13.97 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.09 (0.25), residues: 1138 helix: 1.14 (0.27), residues: 359 sheet: -0.89 (0.43), residues: 140 loop : -0.27 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 374 HIS 0.003 0.001 HIS A 241 PHE 0.024 0.001 PHE A 577 TYR 0.019 0.001 TYR A 319 ARG 0.007 0.000 ARG B 383 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 241 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.8304 (m-80) cc_final: 0.7855 (m-80) REVERT: A 181 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8420 (mm) REVERT: A 210 ASP cc_start: 0.7834 (t70) cc_final: 0.7202 (t70) REVERT: A 216 LEU cc_start: 0.6599 (pt) cc_final: 0.6379 (mt) REVERT: A 223 THR cc_start: 0.8419 (t) cc_final: 0.8176 (t) REVERT: A 436 LYS cc_start: 0.8389 (mmmm) cc_final: 0.8029 (mmtt) REVERT: A 546 MET cc_start: 0.4674 (ppp) cc_final: 0.4040 (ppp) REVERT: A 600 ASP cc_start: 0.7111 (t0) cc_final: 0.6584 (t0) REVERT: A 603 LYS cc_start: 0.7476 (ttpt) cc_final: 0.7165 (ttpt) REVERT: A 615 ASP cc_start: 0.7292 (m-30) cc_final: 0.6957 (p0) REVERT: A 645 MET cc_start: 0.6926 (tpp) cc_final: 0.6629 (tpp) REVERT: A 706 ASN cc_start: 0.7640 (m-40) cc_final: 0.7206 (m-40) REVERT: B 131 ASN cc_start: 0.7910 (t0) cc_final: 0.7468 (t0) REVERT: B 135 MET cc_start: 0.7108 (OUTLIER) cc_final: 0.6776 (mpp) REVERT: B 182 ARG cc_start: 0.8141 (mmm-85) cc_final: 0.7863 (mtp85) REVERT: B 251 GLN cc_start: 0.7647 (pt0) cc_final: 0.7366 (pt0) REVERT: B 275 LYS cc_start: 0.8493 (tmtt) cc_final: 0.7958 (tmtt) REVERT: B 282 VAL cc_start: 0.8811 (t) cc_final: 0.8570 (p) REVERT: B 310 GLN cc_start: 0.7717 (mp10) cc_final: 0.7240 (mp10) REVERT: B 344 ILE cc_start: 0.7270 (OUTLIER) cc_final: 0.6991 (mm) REVERT: B 372 ASP cc_start: 0.7563 (t0) cc_final: 0.6997 (t0) REVERT: B 541 ILE cc_start: 0.7440 (OUTLIER) cc_final: 0.7238 (mm) REVERT: B 566 TYR cc_start: 0.7278 (m-80) cc_final: 0.6945 (m-80) REVERT: B 583 GLU cc_start: 0.6126 (tm-30) cc_final: 0.5470 (tm-30) REVERT: B 589 GLU cc_start: 0.6560 (pm20) cc_final: 0.6213 (pm20) REVERT: B 638 VAL cc_start: 0.8098 (t) cc_final: 0.7728 (m) REVERT: B 693 GLU cc_start: 0.7395 (mp0) cc_final: 0.7098 (mp0) outliers start: 38 outliers final: 33 residues processed: 266 average time/residue: 0.2384 time to fit residues: 85.1037 Evaluate side-chains 271 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 234 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 539 ASP Chi-restraints excluded: chain B residue 541 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 87 optimal weight: 0.0030 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9746 Z= 0.202 Angle : 0.542 7.650 13252 Z= 0.272 Chirality : 0.043 0.215 1448 Planarity : 0.004 0.041 1675 Dihedral : 6.673 88.617 1414 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.78 % Allowed : 14.45 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.05 (0.25), residues: 1138 helix: 1.06 (0.27), residues: 359 sheet: -0.91 (0.43), residues: 141 loop : -0.26 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 374 HIS 0.009 0.001 HIS A 631 PHE 0.018 0.001 PHE A 577 TYR 0.018 0.001 TYR A 319 ARG 0.008 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 236 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.8322 (m-80) cc_final: 0.7877 (m-80) REVERT: A 181 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8418 (mm) REVERT: A 210 ASP cc_start: 0.7851 (t70) cc_final: 0.7198 (t70) REVERT: A 223 THR cc_start: 0.8426 (t) cc_final: 0.8194 (t) REVERT: A 436 LYS cc_start: 0.8393 (mmmm) cc_final: 0.8047 (mmtt) REVERT: A 546 MET cc_start: 0.4691 (ppp) cc_final: 0.4051 (ppp) REVERT: A 600 ASP cc_start: 0.7120 (t0) cc_final: 0.6612 (t0) REVERT: A 603 LYS cc_start: 0.7483 (ttpt) cc_final: 0.7166 (ttpt) REVERT: A 615 ASP cc_start: 0.7309 (m-30) cc_final: 0.7003 (p0) REVERT: A 645 MET cc_start: 0.6931 (tpp) cc_final: 0.6633 (tpp) REVERT: A 706 ASN cc_start: 0.7641 (m-40) cc_final: 0.7179 (m-40) REVERT: A 715 MET cc_start: 0.6532 (tpp) cc_final: 0.5981 (tpp) REVERT: B 106 VAL cc_start: 0.8314 (m) cc_final: 0.8094 (t) REVERT: B 131 ASN cc_start: 0.7944 (t0) cc_final: 0.7538 (t0) REVERT: B 135 MET cc_start: 0.7114 (OUTLIER) cc_final: 0.6804 (mpp) REVERT: B 182 ARG cc_start: 0.8140 (mmm-85) cc_final: 0.7867 (mtp85) REVERT: B 275 LYS cc_start: 0.8483 (tmtt) cc_final: 0.7955 (tmtt) REVERT: B 282 VAL cc_start: 0.8820 (t) cc_final: 0.8586 (p) REVERT: B 310 GLN cc_start: 0.7750 (mp10) cc_final: 0.7246 (mp10) REVERT: B 344 ILE cc_start: 0.7350 (OUTLIER) cc_final: 0.7087 (mm) REVERT: B 359 LYS cc_start: 0.7807 (mppt) cc_final: 0.7305 (mppt) REVERT: B 372 ASP cc_start: 0.7588 (t0) cc_final: 0.6999 (t0) REVERT: B 416 ASP cc_start: 0.7844 (m-30) cc_final: 0.7366 (m-30) REVERT: B 541 ILE cc_start: 0.7454 (OUTLIER) cc_final: 0.7247 (mm) REVERT: B 566 TYR cc_start: 0.7304 (m-80) cc_final: 0.6970 (m-80) REVERT: B 583 GLU cc_start: 0.6136 (tm-30) cc_final: 0.5491 (tm-30) REVERT: B 589 GLU cc_start: 0.6567 (pm20) cc_final: 0.6205 (pm20) REVERT: B 638 VAL cc_start: 0.8097 (t) cc_final: 0.7734 (m) REVERT: B 672 GLU cc_start: 0.6582 (tp30) cc_final: 0.6214 (tm-30) REVERT: B 693 GLU cc_start: 0.7365 (mp0) cc_final: 0.7108 (mp0) outliers start: 39 outliers final: 34 residues processed: 261 average time/residue: 0.2494 time to fit residues: 87.6406 Evaluate side-chains 270 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 232 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 539 ASP Chi-restraints excluded: chain B residue 541 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 97 optimal weight: 0.0970 chunk 102 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9746 Z= 0.195 Angle : 0.549 9.356 13252 Z= 0.276 Chirality : 0.043 0.198 1448 Planarity : 0.004 0.049 1675 Dihedral : 6.608 87.590 1414 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.88 % Allowed : 14.35 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.12 (0.25), residues: 1138 helix: 1.10 (0.28), residues: 353 sheet: -0.84 (0.44), residues: 140 loop : -0.21 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 711 HIS 0.012 0.001 HIS A 631 PHE 0.025 0.002 PHE A 143 TYR 0.019 0.001 TYR A 319 ARG 0.008 0.001 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 235 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.8327 (m-80) cc_final: 0.7886 (m-80) REVERT: A 131 TYR cc_start: 0.6991 (t80) cc_final: 0.6785 (t80) REVERT: A 142 ARG cc_start: 0.8492 (ptt90) cc_final: 0.8253 (ptt-90) REVERT: A 181 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8435 (mm) REVERT: A 210 ASP cc_start: 0.8015 (t70) cc_final: 0.7340 (t70) REVERT: A 223 THR cc_start: 0.8429 (t) cc_final: 0.8225 (t) REVERT: A 436 LYS cc_start: 0.8388 (mmmm) cc_final: 0.8048 (mmtt) REVERT: A 546 MET cc_start: 0.4699 (ppp) cc_final: 0.4064 (ppp) REVERT: A 600 ASP cc_start: 0.7118 (t0) cc_final: 0.6606 (t0) REVERT: A 603 LYS cc_start: 0.7487 (ttpt) cc_final: 0.7165 (ttpt) REVERT: A 615 ASP cc_start: 0.7281 (m-30) cc_final: 0.6977 (p0) REVERT: A 645 MET cc_start: 0.6916 (tpp) cc_final: 0.6644 (tpp) REVERT: A 706 ASN cc_start: 0.7623 (m-40) cc_final: 0.7193 (m-40) REVERT: A 715 MET cc_start: 0.6516 (tpp) cc_final: 0.6020 (tpp) REVERT: B 106 VAL cc_start: 0.8312 (m) cc_final: 0.8098 (t) REVERT: B 135 MET cc_start: 0.7117 (OUTLIER) cc_final: 0.6798 (mpp) REVERT: B 275 LYS cc_start: 0.8498 (tmtt) cc_final: 0.7966 (tmtt) REVERT: B 282 VAL cc_start: 0.8819 (t) cc_final: 0.8571 (p) REVERT: B 310 GLN cc_start: 0.7747 (mp10) cc_final: 0.7248 (mp10) REVERT: B 344 ILE cc_start: 0.7399 (OUTLIER) cc_final: 0.7102 (mm) REVERT: B 359 LYS cc_start: 0.7814 (mppt) cc_final: 0.7299 (mppt) REVERT: B 372 ASP cc_start: 0.7595 (t0) cc_final: 0.7013 (t0) REVERT: B 416 ASP cc_start: 0.7837 (m-30) cc_final: 0.7474 (m-30) REVERT: B 566 TYR cc_start: 0.7291 (m-80) cc_final: 0.6960 (m-80) REVERT: B 583 GLU cc_start: 0.6113 (tm-30) cc_final: 0.5457 (tm-30) REVERT: B 589 GLU cc_start: 0.6559 (pm20) cc_final: 0.6195 (pm20) REVERT: B 638 VAL cc_start: 0.8119 (t) cc_final: 0.7742 (m) REVERT: B 672 GLU cc_start: 0.6555 (tp30) cc_final: 0.6207 (tm-30) REVERT: B 693 GLU cc_start: 0.7363 (mp0) cc_final: 0.7056 (mp0) outliers start: 40 outliers final: 32 residues processed: 261 average time/residue: 0.2358 time to fit residues: 82.3698 Evaluate side-chains 266 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 231 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 539 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 55 optimal weight: 0.0170 chunk 72 optimal weight: 0.6980 chunk 97 optimal weight: 0.0370 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 597 HIS ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9746 Z= 0.195 Angle : 0.547 8.260 13252 Z= 0.276 Chirality : 0.043 0.189 1448 Planarity : 0.004 0.037 1675 Dihedral : 6.564 86.686 1414 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.59 % Allowed : 14.74 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.13 (0.25), residues: 1138 helix: 1.14 (0.28), residues: 347 sheet: -0.88 (0.43), residues: 141 loop : -0.19 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 711 HIS 0.003 0.001 HIS A 241 PHE 0.025 0.002 PHE A 143 TYR 0.019 0.001 TYR A 319 ARG 0.007 0.000 ARG B 383 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 236 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.8328 (m-80) cc_final: 0.7892 (m-80) REVERT: A 131 TYR cc_start: 0.6993 (t80) cc_final: 0.6762 (t80) REVERT: A 142 ARG cc_start: 0.8501 (ptt90) cc_final: 0.8279 (ptt-90) REVERT: A 147 ASP cc_start: 0.7335 (t0) cc_final: 0.7026 (t70) REVERT: A 181 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8433 (mm) REVERT: A 210 ASP cc_start: 0.8014 (t70) cc_final: 0.7333 (t70) REVERT: A 223 THR cc_start: 0.8488 (t) cc_final: 0.8271 (t) REVERT: A 436 LYS cc_start: 0.8389 (mmmm) cc_final: 0.8047 (mmtt) REVERT: A 546 MET cc_start: 0.4692 (ppp) cc_final: 0.4062 (ppp) REVERT: A 595 ARG cc_start: 0.7186 (mmt-90) cc_final: 0.6849 (mmt-90) REVERT: A 600 ASP cc_start: 0.7117 (t0) cc_final: 0.6613 (t0) REVERT: A 603 LYS cc_start: 0.7491 (ttpt) cc_final: 0.7170 (ttpt) REVERT: A 615 ASP cc_start: 0.7261 (m-30) cc_final: 0.6978 (p0) REVERT: A 645 MET cc_start: 0.6910 (tpp) cc_final: 0.6667 (tpp) REVERT: A 706 ASN cc_start: 0.7639 (m-40) cc_final: 0.7223 (m-40) REVERT: A 715 MET cc_start: 0.6509 (tpp) cc_final: 0.6019 (tpp) REVERT: B 106 VAL cc_start: 0.8322 (m) cc_final: 0.8108 (t) REVERT: B 135 MET cc_start: 0.7113 (OUTLIER) cc_final: 0.6707 (mpp) REVERT: B 275 LYS cc_start: 0.8492 (tmtt) cc_final: 0.7975 (tmtt) REVERT: B 282 VAL cc_start: 0.8808 (t) cc_final: 0.8576 (p) REVERT: B 310 GLN cc_start: 0.7758 (mp10) cc_final: 0.7263 (mp10) REVERT: B 344 ILE cc_start: 0.7431 (OUTLIER) cc_final: 0.7158 (mm) REVERT: B 359 LYS cc_start: 0.7832 (mppt) cc_final: 0.7315 (mppt) REVERT: B 372 ASP cc_start: 0.7579 (t0) cc_final: 0.6997 (t0) REVERT: B 566 TYR cc_start: 0.7306 (m-80) cc_final: 0.6976 (m-80) REVERT: B 583 GLU cc_start: 0.6116 (tm-30) cc_final: 0.5467 (tm-30) REVERT: B 589 GLU cc_start: 0.6559 (pm20) cc_final: 0.6185 (pm20) REVERT: B 638 VAL cc_start: 0.8122 (t) cc_final: 0.7748 (m) REVERT: B 672 GLU cc_start: 0.6539 (tp30) cc_final: 0.6222 (tm-30) REVERT: B 693 GLU cc_start: 0.7372 (mp0) cc_final: 0.7080 (mp0) outliers start: 37 outliers final: 33 residues processed: 259 average time/residue: 0.2594 time to fit residues: 89.5645 Evaluate side-chains 272 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 236 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 539 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 0.6980 chunk 84 optimal weight: 0.3980 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 38 optimal weight: 0.0370 chunk 93 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.0670 chunk 80 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.151380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.130551 restraints weight = 14296.797| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.51 r_work: 0.3549 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9746 Z= 0.164 Angle : 0.540 9.545 13252 Z= 0.271 Chirality : 0.043 0.184 1448 Planarity : 0.004 0.035 1675 Dihedral : 6.461 86.259 1414 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.20 % Allowed : 15.13 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.17 (0.25), residues: 1138 helix: 1.27 (0.28), residues: 340 sheet: -0.83 (0.43), residues: 141 loop : -0.22 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 711 HIS 0.003 0.001 HIS A 241 PHE 0.025 0.001 PHE A 143 TYR 0.018 0.001 TYR A 319 ARG 0.008 0.001 ARG B 182 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2685.80 seconds wall clock time: 48 minutes 34.52 seconds (2914.52 seconds total)