Starting phenix.real_space_refine on Fri Mar 15 01:16:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sck_25037/03_2024/7sck_25037_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sck_25037/03_2024/7sck_25037.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sck_25037/03_2024/7sck_25037.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sck_25037/03_2024/7sck_25037.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sck_25037/03_2024/7sck_25037_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sck_25037/03_2024/7sck_25037_updated.pdb" } resolution = 2.8 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= 0.036 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 48 5.16 5 C 6583 2.51 5 N 1720 2.21 5 O 1894 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 606": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 10250 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 5239 Classifications: {'peptide': 642} Link IDs: {'PCIS': 2, 'PTRANS': 31, 'TRANS': 608} Chain breaks: 1 Chain: "B" Number of atoms: 4854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4854 Classifications: {'peptide': 598} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 39, 'TRANS': 558} 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: "D" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'BDP': 2, 'NDG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 6.40, per 1000 atoms: 0.62 Number of scatterers: 10250 At special positions: 0 Unit cell: (110.124, 88.596, 110.952, 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 48 16.00 P 4 15.00 O 1894 8.00 N 1720 7.00 C 6583 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 ALPHA1-4 " BDP D 2 " - " NDG D 3 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NDG D 1 " - " BDP D 2 " " NDG D 3 " - " BDP D 4 " NAG-ASN " NAG A 802 " - " ASN A 330 " " NAG C 1 " - " ASN B 637 " Time building additional restraints: 4.17 Conformation dependent library (CDL) restraints added in 1.6 seconds 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2372 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 12 sheets defined 30.9% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.24 Creating SS restraints... Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 129 through 139 Processing helix chain 'A' and resid 175 through 179 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 283 through 286 No H-bonds generated for 'chain 'A' and resid 283 through 286' Processing helix chain 'A' and resid 310 through 321 removed outlier: 4.123A pdb=" N ARG A 314 " --> pdb=" O SER A 310 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU A 320 " --> pdb=" O ASN A 316 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LYS A 321 " --> pdb=" O THR A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 removed outlier: 3.630A pdb=" N HIS A 329 " --> pdb=" O ARG A 325 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN A 330 " --> pdb=" O GLU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 389 through 394 Processing helix chain 'A' and resid 398 through 415 Processing helix chain 'A' and resid 419 through 433 removed outlier: 3.733A pdb=" N ARG A 433 " --> pdb=" O ILE A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 445 No H-bonds generated for 'chain 'A' and resid 442 through 445' 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 Processing helix chain 'A' and resid 526 through 528 No H-bonds generated for 'chain 'A' and resid 526 through 528' Processing helix chain 'A' and resid 546 through 550 removed outlier: 3.580A pdb=" N ARG A 549 " --> pdb=" O MET A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 584 removed outlier: 3.793A 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 629 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 696 through 712 Processing helix chain 'A' and resid 741 through 743 No H-bonds generated for 'chain 'A' and resid 741 through 743' 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 167 through 176 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 removed outlier: 3.832A pdb=" N GLU B 239 " --> pdb=" O LEU B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 308 through 314 removed outlier: 3.802A pdb=" N LEU B 312 " --> pdb=" O TYR B 308 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLN B 313 " --> pdb=" O PRO B 309 " (cutoff:3.500A) removed outlier: 3.719A 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 368 through 370 No H-bonds generated for 'chain 'B' and resid 368 through 370' Processing helix chain 'B' and resid 373 through 379 removed outlier: 3.537A pdb=" N SER B 379 " --> pdb=" O SER B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 398 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 427 through 430 No H-bonds generated for 'chain 'B' and resid 427 through 430' Processing helix chain 'B' and resid 433 through 438 Processing helix chain 'B' and resid 466 through 478 removed outlier: 3.925A pdb=" N ARG B 471 " --> pdb=" O GLU B 467 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS B 478 " --> pdb=" O THR B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 523 removed outlier: 3.658A pdb=" N ARG B 522 " --> pdb=" O LEU B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 558 Processing helix chain 'B' and resid 602 through 611 Processing helix chain 'B' and resid 616 through 623 Processing helix chain 'B' and resid 627 through 639 Processing helix chain 'B' and resid 669 through 684 Processing sheet with id= A, first strand: chain 'A' and resid 116 through 118 removed outlier: 6.271A 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: 6.950A pdb=" N MET A 215 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ASN A 194 " --> pdb=" O MET A 215 " (cutoff:3.500A) removed outlier: 6.126A 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 269 Processing sheet with id= D, first strand: chain 'A' and resid 333 through 336 removed outlier: 6.052A pdb=" N VAL A 356 " --> pdb=" O CYS A 334 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL A 336 " --> pdb=" O VAL A 356 " (cutoff:3.500A) removed outlier: 6.240A 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: 7.497A pdb=" N ALA A 482 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE A 513 " --> pdb=" O ALA A 482 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE A 484 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL A 515 " --> pdb=" O ILE A 484 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA A 486 " --> pdb=" O VAL A 515 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N TRP A 517 " --> pdb=" O ALA A 486 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N VAL A 515 " --> pdb=" O PRO A 535 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL A 537 " --> pdb=" O VAL A 515 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N TRP A 517 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE A 539 " --> pdb=" O TRP A 517 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 596 through 600 Processing sheet with id= G, first strand: chain 'B' and resid 106 through 108 removed outlier: 6.299A 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: 6.687A 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 280 through 283 removed outlier: 7.391A pdb=" N LEU B 254 " --> pdb=" O LEU B 281 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N LEU B 283 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N SER B 256 " --> pdb=" O LEU B 283 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N PHE B 317 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N SER B 257 " --> pdb=" O PHE B 317 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N VAL B 319 " --> pdb=" O SER B 257 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL B 340 " --> pdb=" O CYS B 318 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N VAL B 320 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N VAL B 342 " --> pdb=" O VAL B 320 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 298 through 300 Processing sheet with id= K, first strand: chain 'B' and resid 563 through 565 removed outlier: 3.806A pdb=" N LEU B 461 " --> pdb=" O ILE B 537 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ALA B 458 " --> pdb=" O SER B 483 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LEU B 485 " --> pdb=" O ALA B 458 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N VAL B 460 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL B 487 " --> pdb=" O VAL B 460 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N THR B 462 " --> pdb=" O VAL B 487 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N TRP B 489 " --> pdb=" O THR B 462 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N VAL B 487 " --> pdb=" O PRO B 508 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LYS B 510 " --> pdb=" O VAL B 487 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N TRP B 489 " --> pdb=" O LYS B 510 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL B 512 " --> pdb=" O TRP B 489 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 570 through 574 238 hydrogen bonds defined for protein. 675 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: 2.71 Time building geometry restraints manager: 4.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2584 1.33 - 1.45: 2239 1.45 - 1.58: 5626 1.58 - 1.70: 5 1.70 - 1.82: 74 Bond restraints: 10528 Sorted by residual: bond pdb=" C3 BDP D 2 " pdb=" O3 BDP D 2 " ideal model delta sigma weight residual 1.411 1.515 -0.104 2.00e-02 2.50e+03 2.73e+01 bond pdb=" C3 BDP D 4 " pdb=" O3 BDP D 4 " ideal model delta sigma weight residual 1.411 1.515 -0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" C1 BDP D 2 " pdb=" O5 BDP D 2 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C1 BDP D 4 " pdb=" O5 BDP D 4 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" O1B UDP B 901 " pdb=" PB UDP B 901 " ideal model delta sigma weight residual 1.530 1.492 0.038 1.00e-02 1.00e+04 1.48e+01 ... (remaining 10523 not shown) Histogram of bond angle deviations from ideal: 99.97 - 106.77: 395 106.77 - 113.58: 5725 113.58 - 120.39: 3867 120.39 - 127.20: 4175 127.20 - 134.00: 150 Bond angle restraints: 14312 Sorted by residual: angle pdb=" O1B UDP B 901 " pdb=" PB UDP B 901 " pdb=" O3A UDP B 901 " ideal model delta sigma weight residual 102.95 112.07 -9.12 1.00e+00 1.00e+00 8.33e+01 angle pdb=" O3A UDP B 901 " pdb=" PB UDP B 901 " pdb=" O3B UDP B 901 " ideal model delta sigma weight residual 112.01 103.15 8.86 1.00e+00 1.00e+00 7.86e+01 angle pdb=" CA ASP B 561 " pdb=" CB ASP B 561 " pdb=" CG ASP B 561 " ideal model delta sigma weight residual 112.60 116.16 -3.56 1.00e+00 1.00e+00 1.26e+01 angle pdb=" N ARG B 562 " pdb=" CA ARG B 562 " pdb=" CB ARG B 562 " ideal model delta sigma weight residual 110.49 104.68 5.81 1.69e+00 3.50e-01 1.18e+01 angle pdb=" C PRO B 560 " pdb=" N ASP B 561 " pdb=" CA ASP B 561 " ideal model delta sigma weight residual 122.49 117.30 5.19 1.57e+00 4.06e-01 1.09e+01 ... (remaining 14307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.95: 6182 21.95 - 43.91: 206 43.91 - 65.86: 33 65.86 - 87.81: 23 87.81 - 109.76: 12 Dihedral angle restraints: 6456 sinusoidal: 2786 harmonic: 3670 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 288.71 178.95 109.76 1 3.00e+01 1.11e-03 1.43e+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 -60.39 108.01 1 3.00e+01 1.11e-03 1.40e+01 dihedral pdb=" C3 NDG D 1 " pdb=" C4 NDG D 1 " pdb=" C5 NDG D 1 " pdb=" O5 NDG D 1 " ideal model delta sinusoidal sigma weight residual 53.31 -52.51 105.82 1 3.00e+01 1.11e-03 1.36e+01 ... (remaining 6453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1373 0.067 - 0.135: 187 0.135 - 0.202: 3 0.202 - 0.269: 5 0.269 - 0.336: 2 Chirality restraints: 1570 Sorted by residual: chirality pdb=" C4 NDG D 1 " pdb=" C3 NDG D 1 " pdb=" C5 NDG D 1 " pdb=" O4 NDG D 1 " both_signs ideal model delta sigma weight residual False -2.30 -2.64 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" C4 NDG D 3 " pdb=" C3 NDG D 3 " pdb=" C5 NDG D 3 " pdb=" O4 NDG D 3 " both_signs ideal model delta sigma weight residual False -2.30 -2.61 0.31 2.00e-01 2.50e+01 2.40e+00 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 -2.53 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 1567 not shown) Planarity restraints: 1808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 561 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.39e+00 pdb=" C ASP B 561 " -0.036 2.00e-02 2.50e+03 pdb=" O ASP B 561 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG B 562 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 399 " -0.025 2.00e-02 2.50e+03 1.31e-02 3.41e+00 pdb=" CG TYR B 399 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR B 399 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR B 399 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR B 399 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 399 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 399 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 399 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 479 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO B 480 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 480 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 480 " -0.023 5.00e-02 4.00e+02 ... (remaining 1805 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.38: 26 2.38 - 3.01: 5753 3.01 - 3.64: 15481 3.64 - 4.27: 24123 4.27 - 4.90: 40229 Nonbonded interactions: 85612 Sorted by model distance: nonbonded pdb=" O2A UDP B 901 " pdb="MN MN B 902 " model vdw 1.744 2.320 nonbonded pdb=" OH TYR B 130 " pdb=" O PRO B 155 " model vdw 2.229 2.440 nonbonded pdb=" NZ LYS B 484 " pdb=" O GLU B 528 " model vdw 2.241 2.520 nonbonded pdb=" O ARG B 209 " pdb=" OH TYR B 226 " model vdw 2.241 2.440 nonbonded pdb=" N ASP B 539 " pdb=" OD1 ASP B 539 " model vdw 2.252 2.520 ... (remaining 85607 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: 0.690 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: 3.890 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 31.620 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:13.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 10528 Z= 0.332 Angle : 0.615 9.125 14312 Z= 0.328 Chirality : 0.047 0.336 1570 Planarity : 0.004 0.042 1806 Dihedral : 13.394 109.764 4057 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.36 % Allowed : 5.49 % Favored : 94.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: -0.14 (0.24), residues: 1228 helix: 0.91 (0.28), residues: 382 sheet: -0.17 (0.48), residues: 122 loop : -0.60 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 556 HIS 0.003 0.001 HIS A 285 PHE 0.014 0.002 PHE B 306 TYR 0.025 0.002 TYR B 399 ARG 0.006 0.000 ARG B 562 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 335 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLU cc_start: 0.7327 (pm20) cc_final: 0.7094 (pm20) REVERT: A 269 LYS cc_start: 0.7811 (ptpp) cc_final: 0.7398 (ptpp) REVERT: A 305 GLN cc_start: 0.7284 (mp10) cc_final: 0.7018 (mp10) REVERT: A 321 LYS cc_start: 0.8021 (mmtm) cc_final: 0.7733 (mmtm) REVERT: A 447 LYS cc_start: 0.8047 (ttmm) cc_final: 0.7831 (ttmm) REVERT: A 458 TYR cc_start: 0.7805 (t80) cc_final: 0.7587 (t80) REVERT: A 547 SER cc_start: 0.7504 (p) cc_final: 0.7243 (m) REVERT: A 576 ASP cc_start: 0.5474 (m-30) cc_final: 0.5149 (m-30) REVERT: A 739 LYS cc_start: 0.7048 (ttpt) cc_final: 0.6727 (ttpt) REVERT: B 104 ILE cc_start: 0.8449 (tt) cc_final: 0.8217 (pt) REVERT: B 108 ILE cc_start: 0.8351 (mp) cc_final: 0.7949 (mt) REVERT: B 135 MET cc_start: 0.6573 (mmm) cc_final: 0.6252 (mmm) REVERT: B 144 THR cc_start: 0.8380 (p) cc_final: 0.8157 (m) REVERT: B 266 ARG cc_start: 0.7461 (tpp-160) cc_final: 0.7217 (ttm110) REVERT: B 268 ASP cc_start: 0.7218 (m-30) cc_final: 0.6991 (m-30) REVERT: B 281 LEU cc_start: 0.8276 (tp) cc_final: 0.8055 (tt) REVERT: B 348 TYR cc_start: 0.7755 (t80) cc_final: 0.7008 (t80) REVERT: B 359 LYS cc_start: 0.7259 (mmtm) cc_final: 0.6983 (tppp) REVERT: B 369 LYS cc_start: 0.7608 (tttp) cc_final: 0.7383 (tttp) REVERT: B 372 ASP cc_start: 0.7208 (m-30) cc_final: 0.6783 (m-30) REVERT: B 574 ASP cc_start: 0.6238 (t0) cc_final: 0.5805 (t0) REVERT: B 699 VAL cc_start: 0.7262 (m) cc_final: 0.6213 (p) outliers start: 4 outliers final: 1 residues processed: 339 average time/residue: 1.1093 time to fit residues: 405.8336 Evaluate side-chains 266 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 265 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN B 378 GLN B 430 ASN B 490 ASN ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 669 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10528 Z= 0.208 Angle : 0.584 7.716 14312 Z= 0.284 Chirality : 0.044 0.229 1570 Planarity : 0.005 0.048 1806 Dihedral : 11.773 97.771 1598 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.07 % Allowed : 13.67 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: -0.15 (0.24), residues: 1228 helix: 0.70 (0.27), residues: 389 sheet: -0.12 (0.49), residues: 115 loop : -0.50 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 396 HIS 0.004 0.001 HIS A 285 PHE 0.012 0.002 PHE A 250 TYR 0.020 0.001 TYR B 107 ARG 0.008 0.001 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 274 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLU cc_start: 0.7353 (pm20) cc_final: 0.7100 (pm20) REVERT: A 305 GLN cc_start: 0.7292 (mp10) cc_final: 0.7046 (mp10) REVERT: A 359 MET cc_start: 0.6994 (mpp) cc_final: 0.6745 (mpp) REVERT: A 458 TYR cc_start: 0.7797 (t80) cc_final: 0.7583 (t80) REVERT: A 648 GLN cc_start: 0.7361 (tm130) cc_final: 0.7150 (tm-30) REVERT: B 104 ILE cc_start: 0.8452 (tt) cc_final: 0.8197 (pt) REVERT: B 135 MET cc_start: 0.6552 (mmm) cc_final: 0.6063 (mmm) REVERT: B 139 ASP cc_start: 0.7450 (m-30) cc_final: 0.7088 (m-30) REVERT: B 266 ARG cc_start: 0.7454 (tpp-160) cc_final: 0.7212 (ttm110) REVERT: B 268 ASP cc_start: 0.7223 (m-30) cc_final: 0.6997 (m-30) REVERT: B 316 THR cc_start: 0.8259 (m) cc_final: 0.8036 (t) REVERT: B 348 TYR cc_start: 0.7717 (t80) cc_final: 0.6999 (t80) REVERT: B 364 VAL cc_start: 0.8255 (OUTLIER) cc_final: 0.7969 (m) REVERT: B 369 LYS cc_start: 0.7593 (tttp) cc_final: 0.7386 (tttp) REVERT: B 372 ASP cc_start: 0.7083 (m-30) cc_final: 0.6784 (m-30) REVERT: B 463 TYR cc_start: 0.6499 (t80) cc_final: 0.6202 (t80) REVERT: B 574 ASP cc_start: 0.6222 (t0) cc_final: 0.5871 (t0) REVERT: B 577 MET cc_start: 0.6470 (mtp) cc_final: 0.6032 (mtp) REVERT: B 592 MET cc_start: 0.6559 (mtp) cc_final: 0.6252 (mtp) REVERT: B 672 GLU cc_start: 0.7320 (tp30) cc_final: 0.6903 (tp30) outliers start: 23 outliers final: 6 residues processed: 285 average time/residue: 1.1100 time to fit residues: 341.6054 Evaluate side-chains 275 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 268 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 628 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 120 optimal weight: 0.3980 chunk 99 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 38 optimal weight: 0.0270 chunk 89 optimal weight: 0.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN B 430 ASN B 550 GLN ** B 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10528 Z= 0.199 Angle : 0.576 6.783 14312 Z= 0.280 Chirality : 0.044 0.228 1570 Planarity : 0.004 0.046 1806 Dihedral : 10.596 96.882 1598 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.25 % Allowed : 15.65 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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 (0.24), residues: 1228 helix: 0.63 (0.27), residues: 390 sheet: -0.11 (0.47), residues: 132 loop : -0.61 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 396 HIS 0.004 0.001 HIS A 285 PHE 0.012 0.001 PHE B 523 TYR 0.021 0.001 TYR B 107 ARG 0.005 0.000 ARG A 741 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 267 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLU cc_start: 0.7386 (pm20) cc_final: 0.7130 (pm20) REVERT: A 160 THR cc_start: 0.8081 (OUTLIER) cc_final: 0.7764 (m) REVERT: A 270 ARG cc_start: 0.7401 (ptm-80) cc_final: 0.6670 (ptt90) REVERT: A 305 GLN cc_start: 0.7310 (mp10) cc_final: 0.7085 (mp10) REVERT: A 359 MET cc_start: 0.6972 (mpp) cc_final: 0.6700 (mpp) REVERT: A 458 TYR cc_start: 0.7800 (t80) cc_final: 0.7561 (t80) REVERT: A 576 ASP cc_start: 0.5204 (m-30) cc_final: 0.4957 (m-30) REVERT: A 649 LEU cc_start: 0.8463 (tp) cc_final: 0.8198 (tp) REVERT: B 104 ILE cc_start: 0.8423 (tt) cc_final: 0.8188 (pt) REVERT: B 108 ILE cc_start: 0.8233 (mp) cc_final: 0.7831 (mp) REVERT: B 135 MET cc_start: 0.6545 (mmm) cc_final: 0.6226 (mmm) REVERT: B 266 ARG cc_start: 0.7441 (tpp-160) cc_final: 0.7181 (ttm110) REVERT: B 268 ASP cc_start: 0.7232 (m-30) cc_final: 0.6995 (m-30) REVERT: B 281 LEU cc_start: 0.8276 (tt) cc_final: 0.8029 (tt) REVERT: B 316 THR cc_start: 0.8244 (m) cc_final: 0.8029 (t) REVERT: B 348 TYR cc_start: 0.7710 (t80) cc_final: 0.7410 (t80) REVERT: B 364 VAL cc_start: 0.8252 (t) cc_final: 0.7949 (m) REVERT: B 463 TYR cc_start: 0.6436 (t80) cc_final: 0.6115 (t80) REVERT: B 574 ASP cc_start: 0.6270 (t0) cc_final: 0.5982 (t0) REVERT: B 577 MET cc_start: 0.6468 (mtp) cc_final: 0.6071 (mtp) REVERT: B 592 MET cc_start: 0.6395 (mtp) cc_final: 0.6062 (mtp) REVERT: B 672 GLU cc_start: 0.7293 (tp30) cc_final: 0.7035 (tp30) outliers start: 25 outliers final: 11 residues processed: 278 average time/residue: 1.0940 time to fit residues: 328.7738 Evaluate side-chains 275 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 263 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 611 LYS Chi-restraints excluded: chain B residue 628 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 HIS A 485 HIS A 721 GLN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN B 550 GLN B 605 ASN ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 10528 Z= 0.461 Angle : 0.701 10.238 14312 Z= 0.347 Chirality : 0.050 0.266 1570 Planarity : 0.005 0.060 1806 Dihedral : 10.490 92.727 1596 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.06 % Allowed : 17.09 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.24), residues: 1228 helix: 0.12 (0.26), residues: 390 sheet: -0.14 (0.46), residues: 130 loop : -0.91 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 396 HIS 0.008 0.001 HIS B 571 PHE 0.023 0.003 PHE B 306 TYR 0.022 0.003 TYR B 610 ARG 0.005 0.001 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 283 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 GLU cc_start: 0.7435 (pm20) cc_final: 0.7177 (pm20) REVERT: A 160 THR cc_start: 0.8166 (OUTLIER) cc_final: 0.7828 (m) REVERT: A 269 LYS cc_start: 0.7928 (ptpt) cc_final: 0.7608 (ptpp) REVERT: A 270 ARG cc_start: 0.7535 (ptm-80) cc_final: 0.7025 (ptt90) REVERT: A 305 GLN cc_start: 0.7307 (mp10) cc_final: 0.7096 (mp10) REVERT: A 458 TYR cc_start: 0.7845 (t80) cc_final: 0.7625 (t80) REVERT: A 715 MET cc_start: 0.6371 (tpp) cc_final: 0.5959 (tpp) REVERT: B 104 ILE cc_start: 0.8535 (tt) cc_final: 0.8323 (pt) REVERT: B 108 ILE cc_start: 0.8247 (mp) cc_final: 0.7994 (mp) REVERT: B 133 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6880 (tt) REVERT: B 135 MET cc_start: 0.6636 (mmm) cc_final: 0.6137 (mmm) REVERT: B 139 ASP cc_start: 0.7501 (m-30) cc_final: 0.7144 (m-30) REVERT: B 266 ARG cc_start: 0.7475 (tpp-160) cc_final: 0.7227 (ttm110) REVERT: B 268 ASP cc_start: 0.7187 (m-30) cc_final: 0.6963 (m-30) REVERT: B 281 LEU cc_start: 0.8347 (tt) cc_final: 0.8104 (tp) REVERT: B 364 VAL cc_start: 0.8302 (OUTLIER) cc_final: 0.8025 (m) REVERT: B 463 TYR cc_start: 0.6663 (t80) cc_final: 0.6316 (t80) REVERT: B 510 LYS cc_start: 0.7755 (ptmt) cc_final: 0.7374 (ptpt) REVERT: B 574 ASP cc_start: 0.6254 (t0) cc_final: 0.5873 (t0) REVERT: B 577 MET cc_start: 0.6499 (mtp) cc_final: 0.6036 (mtp) REVERT: B 600 TYR cc_start: 0.7403 (p90) cc_final: 0.6958 (p90) REVERT: B 620 VAL cc_start: 0.7313 (t) cc_final: 0.7101 (t) REVERT: B 672 GLU cc_start: 0.7338 (tp30) cc_final: 0.7081 (tp30) outliers start: 34 outliers final: 16 residues processed: 301 average time/residue: 1.1362 time to fit residues: 369.0763 Evaluate side-chains 285 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 266 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 499 LYS Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 628 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 101 optimal weight: 0.5980 chunk 82 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 40 optimal weight: 0.0770 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN A 388 GLN A 397 HIS ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10528 Z= 0.202 Angle : 0.604 8.731 14312 Z= 0.295 Chirality : 0.044 0.232 1570 Planarity : 0.005 0.052 1806 Dihedral : 9.504 96.500 1596 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.34 % Allowed : 19.15 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: -0.54 (0.24), residues: 1228 helix: 0.38 (0.26), residues: 388 sheet: -0.35 (0.46), residues: 135 loop : -0.75 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 396 HIS 0.003 0.001 HIS A 285 PHE 0.013 0.002 PHE A 577 TYR 0.018 0.002 TYR B 610 ARG 0.011 0.001 ARG B 179 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 268 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLU cc_start: 0.7434 (pm20) cc_final: 0.7160 (pm20) REVERT: A 115 LYS cc_start: 0.6658 (mmmt) cc_final: 0.6293 (mmmt) REVERT: A 160 THR cc_start: 0.8080 (OUTLIER) cc_final: 0.7764 (m) REVERT: A 269 LYS cc_start: 0.7956 (ptpt) cc_final: 0.7639 (ptpp) REVERT: A 270 ARG cc_start: 0.7583 (ptm-80) cc_final: 0.6861 (ptt90) REVERT: A 305 GLN cc_start: 0.7289 (mp10) cc_final: 0.7076 (mp10) REVERT: A 458 TYR cc_start: 0.7805 (t80) cc_final: 0.7570 (t80) REVERT: A 715 MET cc_start: 0.6298 (tpp) cc_final: 0.5842 (tpp) REVERT: B 103 LYS cc_start: 0.7744 (mmtt) cc_final: 0.7502 (mmtt) REVERT: B 104 ILE cc_start: 0.8393 (tt) cc_final: 0.8127 (pt) REVERT: B 135 MET cc_start: 0.6578 (mmm) cc_final: 0.6070 (mmm) REVERT: B 139 ASP cc_start: 0.7443 (m-30) cc_final: 0.7050 (m-30) REVERT: B 266 ARG cc_start: 0.7443 (tpp-160) cc_final: 0.7193 (ttm110) REVERT: B 268 ASP cc_start: 0.7170 (m-30) cc_final: 0.6949 (m-30) REVERT: B 281 LEU cc_start: 0.8299 (tt) cc_final: 0.8095 (tp) REVERT: B 316 THR cc_start: 0.8248 (m) cc_final: 0.7984 (t) REVERT: B 364 VAL cc_start: 0.8296 (t) cc_final: 0.8020 (m) REVERT: B 369 LYS cc_start: 0.7715 (ttmm) cc_final: 0.7432 (ttmm) REVERT: B 463 TYR cc_start: 0.6471 (t80) cc_final: 0.6197 (t80) REVERT: B 512 VAL cc_start: 0.7522 (t) cc_final: 0.7251 (p) REVERT: B 518 LYS cc_start: 0.7909 (mtpp) cc_final: 0.7695 (mtmm) REVERT: B 543 MET cc_start: 0.5512 (pmm) cc_final: 0.5292 (pmm) REVERT: B 574 ASP cc_start: 0.6223 (t0) cc_final: 0.5869 (t0) REVERT: B 577 MET cc_start: 0.6485 (mtp) cc_final: 0.6076 (mtp) REVERT: B 672 GLU cc_start: 0.7274 (tp30) cc_final: 0.7060 (tp30) REVERT: B 699 VAL cc_start: 0.7646 (t) cc_final: 0.7219 (t) outliers start: 26 outliers final: 15 residues processed: 282 average time/residue: 1.1245 time to fit residues: 341.4461 Evaluate side-chains 277 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 261 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 499 LYS Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 628 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 29 optimal weight: 0.1980 chunk 119 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN A 388 GLN A 397 HIS ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 GLN B 550 GLN B 605 ASN ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10528 Z= 0.207 Angle : 0.611 10.797 14312 Z= 0.293 Chirality : 0.044 0.237 1570 Planarity : 0.004 0.052 1806 Dihedral : 9.186 97.797 1596 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.06 % Allowed : 19.06 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: -0.49 (0.24), residues: 1228 helix: 0.44 (0.27), residues: 388 sheet: -0.32 (0.46), residues: 135 loop : -0.73 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 502 HIS 0.003 0.001 HIS A 285 PHE 0.015 0.001 PHE A 577 TYR 0.017 0.001 TYR B 610 ARG 0.013 0.001 ARG B 179 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 267 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLU cc_start: 0.7451 (pm20) cc_final: 0.7146 (pm20) REVERT: A 160 THR cc_start: 0.8104 (OUTLIER) cc_final: 0.7804 (m) REVERT: A 269 LYS cc_start: 0.7962 (ptpt) cc_final: 0.7632 (ptpp) REVERT: A 305 GLN cc_start: 0.7283 (mp10) cc_final: 0.7081 (mp10) REVERT: A 458 TYR cc_start: 0.7810 (t80) cc_final: 0.7542 (t80) REVERT: A 649 LEU cc_start: 0.8480 (tp) cc_final: 0.8277 (tp) REVERT: A 715 MET cc_start: 0.6293 (tpp) cc_final: 0.5849 (tpp) REVERT: B 103 LYS cc_start: 0.7719 (mmtt) cc_final: 0.7420 (mmtt) REVERT: B 104 ILE cc_start: 0.8411 (tt) cc_final: 0.8157 (pt) REVERT: B 135 MET cc_start: 0.6589 (mmm) cc_final: 0.6084 (mmm) REVERT: B 139 ASP cc_start: 0.7465 (m-30) cc_final: 0.7103 (m-30) REVERT: B 266 ARG cc_start: 0.7453 (tpp-160) cc_final: 0.7204 (ttm110) REVERT: B 268 ASP cc_start: 0.7167 (m-30) cc_final: 0.6950 (m-30) REVERT: B 281 LEU cc_start: 0.8326 (tp) cc_final: 0.8085 (tp) REVERT: B 298 LYS cc_start: 0.8319 (mtmt) cc_final: 0.7954 (mtpp) REVERT: B 316 THR cc_start: 0.8243 (m) cc_final: 0.7980 (t) REVERT: B 364 VAL cc_start: 0.8282 (t) cc_final: 0.7991 (m) REVERT: B 463 TYR cc_start: 0.6464 (t80) cc_final: 0.6200 (t80) REVERT: B 512 VAL cc_start: 0.7523 (t) cc_final: 0.7254 (p) REVERT: B 574 ASP cc_start: 0.6246 (t0) cc_final: 0.5791 (t0) REVERT: B 577 MET cc_start: 0.6423 (mtp) cc_final: 0.5912 (mtp) REVERT: B 600 TYR cc_start: 0.7360 (p90) cc_final: 0.6859 (p90) REVERT: B 699 VAL cc_start: 0.7684 (t) cc_final: 0.7279 (t) outliers start: 34 outliers final: 22 residues processed: 286 average time/residue: 1.0925 time to fit residues: 337.6007 Evaluate side-chains 289 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 266 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 499 LYS Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 628 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 86 optimal weight: 0.3980 chunk 100 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 GLN ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 GLN ** B 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 10528 Z= 0.376 Angle : 0.673 9.104 14312 Z= 0.331 Chirality : 0.048 0.262 1570 Planarity : 0.005 0.057 1806 Dihedral : 9.429 94.401 1596 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.88 % Allowed : 19.87 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: -0.69 (0.24), residues: 1228 helix: 0.17 (0.26), residues: 387 sheet: -0.43 (0.47), residues: 124 loop : -0.79 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 502 HIS 0.004 0.001 HIS A 448 PHE 0.020 0.002 PHE A 333 TYR 0.020 0.002 TYR A 608 ARG 0.008 0.001 ARG B 471 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 271 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLU cc_start: 0.7470 (pm20) cc_final: 0.7201 (pm20) REVERT: A 160 THR cc_start: 0.8184 (OUTLIER) cc_final: 0.7878 (m) REVERT: A 269 LYS cc_start: 0.7999 (ptpt) cc_final: 0.7651 (ptpp) REVERT: A 305 GLN cc_start: 0.7298 (mp10) cc_final: 0.7097 (mp10) REVERT: A 458 TYR cc_start: 0.7833 (t80) cc_final: 0.7614 (t80) REVERT: A 649 LEU cc_start: 0.8645 (tp) cc_final: 0.8437 (tp) REVERT: A 715 MET cc_start: 0.6260 (tpp) cc_final: 0.5789 (tpp) REVERT: B 104 ILE cc_start: 0.8481 (tt) cc_final: 0.8258 (pt) REVERT: B 135 MET cc_start: 0.6620 (mmm) cc_final: 0.6134 (mmm) REVERT: B 139 ASP cc_start: 0.7499 (m-30) cc_final: 0.7171 (m-30) REVERT: B 266 ARG cc_start: 0.7478 (tpp-160) cc_final: 0.7257 (ttm110) REVERT: B 268 ASP cc_start: 0.7184 (m-30) cc_final: 0.6967 (m-30) REVERT: B 281 LEU cc_start: 0.8333 (tp) cc_final: 0.8118 (tp) REVERT: B 298 LYS cc_start: 0.8321 (mtmt) cc_final: 0.7989 (mtpp) REVERT: B 316 THR cc_start: 0.8276 (m) cc_final: 0.7999 (t) REVERT: B 364 VAL cc_start: 0.8319 (t) cc_final: 0.8062 (m) REVERT: B 463 TYR cc_start: 0.6553 (t80) cc_final: 0.6242 (t80) REVERT: B 512 VAL cc_start: 0.7591 (t) cc_final: 0.7307 (p) REVERT: B 574 ASP cc_start: 0.6276 (t0) cc_final: 0.5835 (t0) REVERT: B 577 MET cc_start: 0.6467 (mtp) cc_final: 0.5988 (mtp) REVERT: B 600 TYR cc_start: 0.7412 (p90) cc_final: 0.6945 (p90) REVERT: B 672 GLU cc_start: 0.7303 (tp30) cc_final: 0.7044 (tp30) REVERT: B 699 VAL cc_start: 0.7843 (t) cc_final: 0.7521 (t) outliers start: 32 outliers final: 21 residues processed: 284 average time/residue: 1.1534 time to fit residues: 353.5492 Evaluate side-chains 282 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 260 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 499 LYS Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 628 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 GLN ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 702 GLN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 GLN ** B 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10528 Z= 0.252 Angle : 0.651 9.703 14312 Z= 0.319 Chirality : 0.045 0.245 1570 Planarity : 0.005 0.055 1806 Dihedral : 9.090 94.964 1596 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.52 % Allowed : 21.04 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.24), residues: 1228 helix: 0.24 (0.26), residues: 387 sheet: -0.42 (0.47), residues: 124 loop : -0.71 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 502 HIS 0.003 0.001 HIS A 448 PHE 0.016 0.002 PHE A 333 TYR 0.016 0.002 TYR B 610 ARG 0.008 0.001 ARG B 179 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 257 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 ILE cc_start: 0.8560 (pt) cc_final: 0.8190 (mm) REVERT: A 269 LYS cc_start: 0.7950 (ptpt) cc_final: 0.7605 (ptpp) REVERT: A 277 SER cc_start: 0.7730 (p) cc_final: 0.7407 (t) REVERT: A 458 TYR cc_start: 0.7811 (t80) cc_final: 0.7577 (t80) REVERT: A 649 LEU cc_start: 0.8556 (tp) cc_final: 0.8353 (tp) REVERT: A 715 MET cc_start: 0.6225 (tpp) cc_final: 0.5748 (tpp) REVERT: B 104 ILE cc_start: 0.8447 (tt) cc_final: 0.8203 (pt) REVERT: B 135 MET cc_start: 0.6619 (mmm) cc_final: 0.6116 (mmm) REVERT: B 139 ASP cc_start: 0.7485 (m-30) cc_final: 0.7157 (m-30) REVERT: B 266 ARG cc_start: 0.7470 (tpp-160) cc_final: 0.7245 (ttm110) REVERT: B 268 ASP cc_start: 0.7184 (m-30) cc_final: 0.6965 (m-30) REVERT: B 281 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8097 (tp) REVERT: B 298 LYS cc_start: 0.8307 (mtmt) cc_final: 0.7925 (mtpp) REVERT: B 316 THR cc_start: 0.8270 (m) cc_final: 0.7997 (t) REVERT: B 364 VAL cc_start: 0.8319 (t) cc_final: 0.8056 (m) REVERT: B 463 TYR cc_start: 0.6492 (t80) cc_final: 0.6210 (t80) REVERT: B 512 VAL cc_start: 0.7561 (t) cc_final: 0.7284 (p) REVERT: B 574 ASP cc_start: 0.6278 (t0) cc_final: 0.5853 (t0) REVERT: B 577 MET cc_start: 0.6407 (mtp) cc_final: 0.5861 (mtp) REVERT: B 600 TYR cc_start: 0.7392 (p90) cc_final: 0.6903 (p90) REVERT: B 672 GLU cc_start: 0.7275 (tp30) cc_final: 0.7028 (tp30) REVERT: B 699 VAL cc_start: 0.7716 (t) cc_final: 0.7322 (t) outliers start: 28 outliers final: 20 residues processed: 267 average time/residue: 1.1397 time to fit residues: 328.0501 Evaluate side-chains 276 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 255 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 499 LYS Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 628 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 86 optimal weight: 0.4980 chunk 33 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 72 optimal weight: 7.9990 chunk 116 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 702 GLN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 ASN ** B 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10528 Z= 0.217 Angle : 0.641 10.825 14312 Z= 0.314 Chirality : 0.045 0.238 1570 Planarity : 0.005 0.054 1806 Dihedral : 8.786 94.437 1596 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.34 % Allowed : 21.67 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.54 (0.24), residues: 1228 helix: 0.30 (0.26), residues: 387 sheet: -0.35 (0.48), residues: 124 loop : -0.70 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 502 HIS 0.003 0.001 HIS A 448 PHE 0.023 0.002 PHE A 333 TYR 0.017 0.001 TYR A 468 ARG 0.009 0.001 ARG B 179 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 260 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 ILE cc_start: 0.8503 (pt) cc_final: 0.8159 (mm) REVERT: A 269 LYS cc_start: 0.7966 (ptpt) cc_final: 0.7617 (ptpp) REVERT: A 277 SER cc_start: 0.7728 (p) cc_final: 0.7417 (t) REVERT: A 458 TYR cc_start: 0.7801 (t80) cc_final: 0.7563 (t80) REVERT: A 715 MET cc_start: 0.6219 (tpp) cc_final: 0.5748 (tpp) REVERT: B 104 ILE cc_start: 0.8425 (tt) cc_final: 0.8174 (pt) REVERT: B 135 MET cc_start: 0.6608 (mmm) cc_final: 0.6117 (mmm) REVERT: B 139 ASP cc_start: 0.7468 (m-30) cc_final: 0.7132 (m-30) REVERT: B 266 ARG cc_start: 0.7469 (tpp-160) cc_final: 0.7246 (ttm110) REVERT: B 268 ASP cc_start: 0.7179 (m-30) cc_final: 0.6961 (m-30) REVERT: B 298 LYS cc_start: 0.8266 (mtmt) cc_final: 0.7892 (mtpp) REVERT: B 316 THR cc_start: 0.8267 (m) cc_final: 0.7991 (t) REVERT: B 364 VAL cc_start: 0.8294 (t) cc_final: 0.8027 (m) REVERT: B 369 LYS cc_start: 0.7683 (ttmm) cc_final: 0.7469 (ttmm) REVERT: B 427 GLU cc_start: 0.7580 (mp0) cc_final: 0.7170 (mp0) REVERT: B 463 TYR cc_start: 0.6472 (t80) cc_final: 0.6210 (t80) REVERT: B 512 VAL cc_start: 0.7528 (t) cc_final: 0.7262 (p) REVERT: B 574 ASP cc_start: 0.6278 (t0) cc_final: 0.5825 (t0) REVERT: B 577 MET cc_start: 0.6372 (mtp) cc_final: 0.5827 (mtp) REVERT: B 699 VAL cc_start: 0.7664 (t) cc_final: 0.7293 (t) outliers start: 26 outliers final: 17 residues processed: 273 average time/residue: 1.1294 time to fit residues: 332.6039 Evaluate side-chains 272 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 255 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 499 LYS Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 628 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 81 optimal weight: 0.4980 chunk 122 optimal weight: 0.3980 chunk 112 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 605 ASN ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10528 Z= 0.229 Angle : 0.655 11.581 14312 Z= 0.322 Chirality : 0.045 0.237 1570 Planarity : 0.005 0.125 1806 Dihedral : 8.674 94.032 1596 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.71 % Allowed : 22.48 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.52 (0.24), residues: 1228 helix: 0.27 (0.26), residues: 388 sheet: -0.31 (0.48), residues: 124 loop : -0.66 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 502 HIS 0.007 0.001 HIS A 241 PHE 0.018 0.001 PHE A 333 TYR 0.017 0.001 TYR A 468 ARG 0.015 0.001 ARG A 243 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 258 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 ILE cc_start: 0.8490 (pt) cc_final: 0.8158 (mm) REVERT: A 269 LYS cc_start: 0.7967 (ptpt) cc_final: 0.7614 (ptpp) REVERT: A 277 SER cc_start: 0.7749 (p) cc_final: 0.7424 (t) REVERT: A 458 TYR cc_start: 0.7806 (t80) cc_final: 0.7556 (t80) REVERT: A 715 MET cc_start: 0.6220 (tpp) cc_final: 0.5755 (tpp) REVERT: B 104 ILE cc_start: 0.8428 (tt) cc_final: 0.8176 (pt) REVERT: B 135 MET cc_start: 0.6612 (mmm) cc_final: 0.6314 (mmm) REVERT: B 266 ARG cc_start: 0.7464 (tpp-160) cc_final: 0.7238 (ttm110) REVERT: B 268 ASP cc_start: 0.7175 (m-30) cc_final: 0.6957 (m-30) REVERT: B 298 LYS cc_start: 0.8215 (mtmt) cc_final: 0.7873 (mtpp) REVERT: B 316 THR cc_start: 0.8267 (m) cc_final: 0.7989 (t) REVERT: B 349 ILE cc_start: 0.7035 (pp) cc_final: 0.6772 (pp) REVERT: B 364 VAL cc_start: 0.8294 (t) cc_final: 0.8028 (m) REVERT: B 369 LYS cc_start: 0.7677 (ttmm) cc_final: 0.7460 (ttmm) REVERT: B 427 GLU cc_start: 0.7466 (mp0) cc_final: 0.6978 (mp0) REVERT: B 463 TYR cc_start: 0.6469 (t80) cc_final: 0.6206 (t80) REVERT: B 512 VAL cc_start: 0.7526 (t) cc_final: 0.7254 (p) REVERT: B 574 ASP cc_start: 0.6275 (t0) cc_final: 0.5830 (t0) REVERT: B 577 MET cc_start: 0.6353 (mtp) cc_final: 0.5817 (mtp) REVERT: B 600 TYR cc_start: 0.7404 (p90) cc_final: 0.6951 (p90) REVERT: B 687 MET cc_start: 0.6694 (tpp) cc_final: 0.5739 (tpp) REVERT: B 699 VAL cc_start: 0.7597 (t) cc_final: 0.7222 (t) outliers start: 19 outliers final: 18 residues processed: 266 average time/residue: 1.0508 time to fit residues: 302.3722 Evaluate side-chains 273 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 255 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 499 LYS Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 628 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 702 GLN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.154889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.136854 restraints weight = 13777.683| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.08 r_work: 0.3785 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10528 Z= 0.251 Angle : 0.662 9.215 14312 Z= 0.325 Chirality : 0.046 0.291 1570 Planarity : 0.005 0.104 1806 Dihedral : 8.632 93.488 1596 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.80 % Allowed : 22.48 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.52 (0.24), residues: 1228 helix: 0.33 (0.27), residues: 383 sheet: -0.28 (0.48), residues: 124 loop : -0.69 (0.24), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 437 HIS 0.005 0.001 HIS A 241 PHE 0.024 0.002 PHE A 333 TYR 0.017 0.002 TYR A 468 ARG 0.013 0.001 ARG A 243 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5442.91 seconds wall clock time: 95 minutes 59.96 seconds (5759.96 seconds total)