Starting phenix.real_space_refine on Thu Feb 15 13:25:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kur_9581/02_2024/6kur_9581_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kur_9581/02_2024/6kur_9581.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kur_9581/02_2024/6kur_9581.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kur_9581/02_2024/6kur_9581.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kur_9581/02_2024/6kur_9581_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kur_9581/02_2024/6kur_9581_neut.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 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: 5 Type Number sf(0) Gaussians P 28 5.49 5 S 109 5.16 5 C 7765 2.51 5 N 2113 2.21 5 O 2369 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 212": "NH1" <-> "NH2" Residue "A ARG 249": "NH1" <-> "NH2" Residue "A ARG 281": "NH1" <-> "NH2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "A ARG 361": "NH1" <-> "NH2" Residue "A ARG 391": "NH1" <-> "NH2" Residue "A ARG 551": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 138": "NH1" <-> "NH2" Residue "B ARG 216": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 428": "NH1" <-> "NH2" Residue "B ARG 435": "NH1" <-> "NH2" Residue "B ARG 557": "NH1" <-> "NH2" Residue "B ARG 573": "NH1" <-> "NH2" Residue "B ARG 578": "NH1" <-> "NH2" Residue "B ARG 629": "NH1" <-> "NH2" Residue "B ARG 676": "NH1" <-> "NH2" Residue "B ARG 741": "NH1" <-> "NH2" Residue "B ARG 750": "NH1" <-> "NH2" Residue "C ARG 65": "NH1" <-> "NH2" Residue "C ARG 133": "NH1" <-> "NH2" Residue "C ARG 150": "NH1" <-> "NH2" Residue "C ARG 223": "NH1" <-> "NH2" Residue "C ARG 235": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12384 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4176 Classifications: {'peptide': 511} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 489} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 5603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 705, 5603 Classifications: {'peptide': 705} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 678} Chain breaks: 4 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2006 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 11, 'TRANS': 237} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "R" Number of atoms: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 268 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 2, 'rna3p_pyr': 8} Link IDs: {'rna2p': 3, 'rna3p': 9} Chain: "V" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 331 Classifications: {'RNA': 15} Modifications used: {'p5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 10, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 11} Time building chain proxies: 7.13, per 1000 atoms: 0.58 Number of scatterers: 12384 At special positions: 0 Unit cell: (110.16, 110.16, 110.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 109 16.00 P 28 15.00 O 2369 8.00 N 2113 7.00 C 7765 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.79 Conformation dependent library (CDL) restraints added in 2.0 seconds 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2774 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 12 sheets defined 47.2% alpha, 7.7% beta 7 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 3.87 Creating SS restraints... Processing helix chain 'A' and resid 191 through 198 removed outlier: 3.700A pdb=" N ASP A 198 " --> pdb=" O ILE A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 217 removed outlier: 3.500A pdb=" N LEU A 211 " --> pdb=" O ASN A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 234 removed outlier: 4.118A pdb=" N SER A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 295 Processing helix chain 'A' and resid 296 through 300 removed outlier: 3.719A pdb=" N PHE A 299 " --> pdb=" O ASN A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 328 Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 381 through 390 removed outlier: 3.645A pdb=" N GLU A 385 " --> pdb=" O TRP A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 432 Processing helix chain 'A' and resid 434 through 457 removed outlier: 3.704A pdb=" N ARG A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 565 Processing helix chain 'A' and resid 571 through 589 Processing helix chain 'A' and resid 620 through 637 removed outlier: 4.119A pdb=" N CYS A 624 " --> pdb=" O LEU A 620 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ARG A 625 " --> pdb=" O LYS A 621 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N MET A 626 " --> pdb=" O ASP A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 661 removed outlier: 3.623A pdb=" N GLU A 643 " --> pdb=" O ASP A 639 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP A 661 " --> pdb=" O GLN A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 678 Processing helix chain 'A' and resid 679 through 681 No H-bonds generated for 'chain 'A' and resid 679 through 681' Processing helix chain 'A' and resid 684 through 702 Processing helix chain 'B' and resid 6 through 11 Processing helix chain 'B' and resid 18 through 22 removed outlier: 3.734A pdb=" N TYR B 22 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 removed outlier: 3.676A pdb=" N SER B 39 " --> pdb=" O SER B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 99 Processing helix chain 'B' and resid 104 through 118 removed outlier: 3.513A pdb=" N LEU B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 127 Processing helix chain 'B' and resid 141 through 157 Processing helix chain 'B' and resid 164 through 177 removed outlier: 3.584A pdb=" N TYR B 168 " --> pdb=" O THR B 164 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 removed outlier: 3.672A pdb=" N CYS B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 268 Processing helix chain 'B' and resid 281 through 292 removed outlier: 3.570A pdb=" N LYS B 285 " --> pdb=" O LYS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.788A pdb=" N TYR B 320 " --> pdb=" O GLN B 316 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR B 328 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 339 removed outlier: 3.666A pdb=" N ASP B 337 " --> pdb=" O ASN B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 347 Processing helix chain 'B' and resid 378 through 382 removed outlier: 3.573A pdb=" N LEU B 381 " --> pdb=" O ARG B 378 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET B 382 " --> pdb=" O LYS B 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 378 through 382' Processing helix chain 'B' and resid 383 through 392 removed outlier: 3.847A pdb=" N THR B 392 " --> pdb=" O ASP B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 397 Processing helix chain 'B' and resid 416 through 425 removed outlier: 3.501A pdb=" N PHE B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 475 Processing helix chain 'B' and resid 509 through 514 removed outlier: 3.568A pdb=" N ALA B 512 " --> pdb=" O GLU B 509 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE B 513 " --> pdb=" O LEU B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 537 Processing helix chain 'B' and resid 541 through 561 Processing helix chain 'B' and resid 573 through 580 removed outlier: 3.691A pdb=" N ILE B 577 " --> pdb=" O ARG B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 590 removed outlier: 3.682A pdb=" N GLY B 589 " --> pdb=" O ASN B 586 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU B 590 " --> pdb=" O LYS B 587 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 586 through 590' Processing helix chain 'B' and resid 591 through 595 Processing helix chain 'B' and resid 601 through 605 removed outlier: 3.721A pdb=" N LEU B 605 " --> pdb=" O ILE B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 614 Processing helix chain 'B' and resid 618 through 626 Processing helix chain 'B' and resid 675 through 696 removed outlier: 3.800A pdb=" N ALA B 679 " --> pdb=" O MET B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 728 removed outlier: 3.654A pdb=" N ASN B 728 " --> pdb=" O THR B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 752 Processing helix chain 'C' and resid 3 through 15 Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 32 through 37 removed outlier: 3.646A pdb=" N LYS C 37 " --> pdb=" O THR C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 56 Processing helix chain 'C' and resid 65 through 72 removed outlier: 3.942A pdb=" N GLU C 70 " --> pdb=" O GLU C 66 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA C 71 " --> pdb=" O ILE C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 108 removed outlier: 3.772A pdb=" N ILE C 102 " --> pdb=" O SER C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 122 removed outlier: 3.612A pdb=" N TYR C 122 " --> pdb=" O ILE C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 134 removed outlier: 3.690A pdb=" N GLU C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 172 removed outlier: 3.616A pdb=" N GLU C 168 " --> pdb=" O LYS C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 197 Processing helix chain 'C' and resid 206 through 215 removed outlier: 3.741A pdb=" N ALA C 215 " --> pdb=" O ALA C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 236 removed outlier: 3.621A pdb=" N ARG C 235 " --> pdb=" O ARG C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 243 removed outlier: 3.875A pdb=" N GLY C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 275 through 276 removed outlier: 3.624A pdb=" N LYS A 275 " --> pdb=" O ASP A 478 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 350 through 352 removed outlier: 5.349A pdb=" N LYS A 350 " --> pdb=" O GLU B 367 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL B 369 " --> pdb=" O LYS A 350 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE A 352 " --> pdb=" O VAL B 369 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 463 through 466 Processing sheet with id=AA4, first strand: chain 'A' and resid 601 through 604 Processing sheet with id=AA5, first strand: chain 'A' and resid 666 through 667 removed outlier: 3.502A pdb=" N PHE A 666 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY B 485 " --> pdb=" O PHE A 666 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 55 through 56 Processing sheet with id=AA7, first strand: chain 'B' and resid 131 through 133 Processing sheet with id=AA8, first strand: chain 'B' and resid 181 through 185 Processing sheet with id=AA9, first strand: chain 'B' and resid 242 through 245 removed outlier: 7.481A pdb=" N ILE B 226 " --> pdb=" O LYS B 352 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 492 through 493 removed outlier: 3.679A pdb=" N PHE B 493 " --> pdb=" O MET B 496 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 663 through 664 removed outlier: 4.745A pdb=" N ARG B 663 " --> pdb=" O MET C 62 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 149 through 153 496 hydrogen bonds defined for protein. 1392 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 19 hydrogen bonds 38 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 3.95 Time building geometry restraints manager: 5.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2031 1.32 - 1.44: 3402 1.44 - 1.57: 7019 1.57 - 1.69: 54 1.69 - 1.82: 181 Bond restraints: 12687 Sorted by residual: bond pdb=" C GLU B 394 " pdb=" N PRO B 395 " ideal model delta sigma weight residual 1.334 1.376 -0.043 8.40e-03 1.42e+04 2.61e+01 bond pdb=" C LEU B 273 " pdb=" N PRO B 274 " ideal model delta sigma weight residual 1.336 1.388 -0.052 1.20e-02 6.94e+03 1.89e+01 bond pdb=" CA ILE B 730 " pdb=" C ILE B 730 " ideal model delta sigma weight residual 1.523 1.468 0.055 1.27e-02 6.20e+03 1.84e+01 bond pdb=" C PHE A 563 " pdb=" O PHE A 563 " ideal model delta sigma weight residual 1.235 1.196 0.039 1.43e-02 4.89e+03 7.32e+00 bond pdb=" N ILE A 571 " pdb=" CA ILE A 571 " ideal model delta sigma weight residual 1.461 1.430 0.031 1.23e-02 6.61e+03 6.55e+00 ... (remaining 12682 not shown) Histogram of bond angle deviations from ideal: 96.83 - 104.27: 315 104.27 - 111.72: 5546 111.72 - 119.16: 4782 119.16 - 126.61: 6287 126.61 - 134.06: 250 Bond angle restraints: 17180 Sorted by residual: angle pdb=" C4' U R 9 " pdb=" C3' U R 9 " pdb=" O3' U R 9 " ideal model delta sigma weight residual 109.40 121.95 -12.55 1.50e+00 4.44e-01 7.00e+01 angle pdb=" N ASN A 560 " pdb=" CA ASN A 560 " pdb=" C ASN A 560 " ideal model delta sigma weight residual 113.55 105.32 8.23 1.26e+00 6.30e-01 4.27e+01 angle pdb=" N PHE A 563 " pdb=" CA PHE A 563 " pdb=" C PHE A 563 " ideal model delta sigma weight residual 112.93 104.68 8.25 1.33e+00 5.65e-01 3.85e+01 angle pdb=" N MET A 574 " pdb=" CA MET A 574 " pdb=" C MET A 574 " ideal model delta sigma weight residual 111.69 105.79 5.90 1.23e+00 6.61e-01 2.30e+01 angle pdb=" O ILE B 730 " pdb=" C ILE B 730 " pdb=" N ILE B 731 " ideal model delta sigma weight residual 122.57 127.66 -5.09 1.25e+00 6.40e-01 1.66e+01 ... (remaining 17175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.18: 7685 35.18 - 70.36: 118 70.36 - 105.53: 12 105.53 - 140.71: 1 140.71 - 175.89: 1 Dihedral angle restraints: 7817 sinusoidal: 3545 harmonic: 4272 Sorted by residual: dihedral pdb=" CA ILE C 186 " pdb=" C ILE C 186 " pdb=" N GLN C 187 " pdb=" CA GLN C 187 " ideal model delta harmonic sigma weight residual -180.00 -151.05 -28.95 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA ASN B 728 " pdb=" C ASN B 728 " pdb=" N GLY B 729 " pdb=" CA GLY B 729 " ideal model delta harmonic sigma weight residual -180.00 -153.89 -26.11 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA ILE A 604 " pdb=" C ILE A 604 " pdb=" N ALA A 605 " pdb=" CA ALA A 605 " ideal model delta harmonic sigma weight residual 180.00 155.17 24.83 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 7814 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1808 0.112 - 0.224: 73 0.224 - 0.336: 4 0.336 - 0.448: 0 0.448 - 0.560: 1 Chirality restraints: 1886 Sorted by residual: chirality pdb=" C3' U R 9 " pdb=" C4' U R 9 " pdb=" O3' U R 9 " pdb=" C2' U R 9 " both_signs ideal model delta sigma weight residual False -2.74 -2.18 -0.56 2.00e-01 2.50e+01 7.84e+00 chirality pdb=" CB ILE B 304 " pdb=" CA ILE B 304 " pdb=" CG1 ILE B 304 " pdb=" CG2 ILE B 304 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CB ILE C 249 " pdb=" CA ILE C 249 " pdb=" CG1 ILE C 249 " pdb=" CG2 ILE C 249 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 1883 not shown) Planarity restraints: 2080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 628 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C ILE A 628 " 0.055 2.00e-02 2.50e+03 pdb=" O ILE A 628 " -0.021 2.00e-02 2.50e+03 pdb=" N VAL A 629 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 425 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.06e+00 pdb=" C GLU A 425 " 0.052 2.00e-02 2.50e+03 pdb=" O GLU A 425 " -0.020 2.00e-02 2.50e+03 pdb=" N GLU A 426 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 424 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.06e+00 pdb=" C CYS A 424 " 0.052 2.00e-02 2.50e+03 pdb=" O CYS A 424 " -0.020 2.00e-02 2.50e+03 pdb=" N GLU A 425 " -0.017 2.00e-02 2.50e+03 ... (remaining 2077 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 316 2.69 - 3.25: 11111 3.25 - 3.80: 17979 3.80 - 4.35: 24423 4.35 - 4.90: 40297 Nonbonded interactions: 94126 Sorted by model distance: nonbonded pdb=" OP2 G V 5 " pdb=" N2 G V 5 " model vdw 2.143 2.520 nonbonded pdb=" OD2 ASP B 523 " pdb=" OH TYR B 560 " model vdw 2.248 2.440 nonbonded pdb=" OE1 GLU A 209 " pdb=" NH2 ARG A 212 " model vdw 2.251 2.520 nonbonded pdb=" O2' U R 8 " pdb=" OP1 U R 9 " model vdw 2.258 2.440 nonbonded pdb=" O LYS A 460 " pdb=" NZ LYS A 486 " model vdw 2.278 2.520 ... (remaining 94121 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 group one per residue 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: 0.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.970 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 36.910 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12687 Z= 0.255 Angle : 0.788 12.553 17180 Z= 0.445 Chirality : 0.052 0.560 1886 Planarity : 0.006 0.062 2080 Dihedral : 12.356 175.889 5043 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.99 % Favored : 92.87 % Rotamer: Outliers : 1.01 % Allowed : 2.41 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.96 (0.16), residues: 1445 helix: -3.55 (0.11), residues: 642 sheet: -1.69 (0.48), residues: 122 loop : -3.30 (0.19), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 386 HIS 0.009 0.002 HIS A 451 PHE 0.023 0.002 PHE B 420 TYR 0.020 0.002 TYR B 38 ARG 0.008 0.001 ARG A 438 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 1301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 491 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 383 ASN cc_start: 0.8232 (t0) cc_final: 0.7712 (t0) REVERT: A 516 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8145 (tm-30) REVERT: A 558 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8492 (tm) REVERT: A 568 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8695 (ptt90) REVERT: A 653 LEU cc_start: 0.9177 (mp) cc_final: 0.8890 (mt) REVERT: A 702 LYS cc_start: 0.8045 (tmtt) cc_final: 0.7689 (tttp) REVERT: B 71 THR cc_start: 0.8139 (p) cc_final: 0.7856 (p) REVERT: B 226 ILE cc_start: 0.9133 (mt) cc_final: 0.8875 (pt) REVERT: B 388 ASP cc_start: 0.7501 (m-30) cc_final: 0.7187 (m-30) REVERT: B 554 GLN cc_start: 0.8937 (tp40) cc_final: 0.8584 (tp-100) REVERT: B 675 MET cc_start: 0.5670 (mmm) cc_final: 0.5241 (mmt) REVERT: B 705 ILE cc_start: 0.8832 (pt) cc_final: 0.8609 (mt) REVERT: B 730 ILE cc_start: 0.7212 (OUTLIER) cc_final: 0.6597 (mm) REVERT: B 736 TYR cc_start: 0.8314 (t80) cc_final: 0.7757 (t80) REVERT: C 180 ASN cc_start: 0.4069 (t0) cc_final: 0.3837 (m-40) REVERT: C 205 VAL cc_start: 0.8948 (t) cc_final: 0.8647 (p) REVERT: C 235 ARG cc_start: 0.7965 (ptm-80) cc_final: 0.7727 (ptm-80) outliers start: 13 outliers final: 4 residues processed: 501 average time/residue: 0.3092 time to fit residues: 206.2050 Evaluate side-chains 297 residues out of total 1301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 290 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 559 LYS Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain C residue 133 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 0.3980 chunk 59 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 133 optimal weight: 0.9980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN A 263 HIS ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 ASN A 640 ASN A 657 GLN ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 GLN B 157 GLN ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 GLN B 436 ASN B 477 ASN B 554 GLN B 563 HIS B 572 HIS C 141 ASN C 163 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12687 Z= 0.254 Angle : 0.625 9.609 17180 Z= 0.324 Chirality : 0.042 0.150 1886 Planarity : 0.005 0.052 2080 Dihedral : 13.645 179.430 2027 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.71 % Favored : 93.22 % Rotamer: Outliers : 3.26 % Allowed : 13.35 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.20), residues: 1445 helix: -1.10 (0.18), residues: 663 sheet: -0.79 (0.51), residues: 126 loop : -3.08 (0.20), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 386 HIS 0.006 0.001 HIS A 451 PHE 0.022 0.002 PHE B 108 TYR 0.013 0.001 TYR B 168 ARG 0.006 0.001 ARG C 50 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 287 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 382 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.8230 (m-80) REVERT: A 383 ASN cc_start: 0.8200 (t0) cc_final: 0.7908 (t0) REVERT: A 387 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.8778 (mm) REVERT: A 442 LYS cc_start: 0.9061 (tttt) cc_final: 0.8572 (ttmm) REVERT: A 453 GLU cc_start: 0.7834 (tp30) cc_final: 0.7529 (tp30) REVERT: A 516 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8190 (tm-30) REVERT: A 568 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.8804 (ptt90) REVERT: B 41 GLU cc_start: 0.7304 (tm-30) cc_final: 0.6791 (tm-30) REVERT: B 210 MET cc_start: 0.5959 (ptt) cc_final: 0.5714 (ptp) REVERT: B 289 SER cc_start: 0.8791 (m) cc_final: 0.8317 (p) REVERT: B 388 ASP cc_start: 0.7789 (m-30) cc_final: 0.7460 (m-30) REVERT: B 423 MET cc_start: 0.8312 (mtm) cc_final: 0.8109 (mtm) REVERT: B 442 LEU cc_start: 0.8811 (tp) cc_final: 0.8421 (mt) REVERT: B 523 ASP cc_start: 0.7777 (m-30) cc_final: 0.7305 (m-30) REVERT: B 528 MET cc_start: 0.8143 (mtp) cc_final: 0.7914 (mtm) REVERT: B 675 MET cc_start: 0.5103 (mmm) cc_final: 0.4530 (mmt) REVERT: B 705 ILE cc_start: 0.8918 (pt) cc_final: 0.8680 (mt) REVERT: C 65 ARG cc_start: 0.6982 (ptp-110) cc_final: 0.6766 (ptp-110) outliers start: 42 outliers final: 25 residues processed: 313 average time/residue: 0.2624 time to fit residues: 115.7977 Evaluate side-chains 265 residues out of total 1301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 237 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 383 ASN Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 199 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 74 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 chunk 119 optimal weight: 9.9990 chunk 132 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 HIS C 141 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12687 Z= 0.179 Angle : 0.557 8.675 17180 Z= 0.285 Chirality : 0.041 0.140 1886 Planarity : 0.004 0.051 2080 Dihedral : 13.349 179.213 2012 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.09 % Favored : 93.84 % Rotamer: Outliers : 3.57 % Allowed : 15.06 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.21), residues: 1445 helix: -0.10 (0.20), residues: 665 sheet: -0.24 (0.58), residues: 100 loop : -2.83 (0.20), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 83 HIS 0.005 0.001 HIS A 451 PHE 0.016 0.001 PHE B 108 TYR 0.011 0.001 TYR A 549 ARG 0.005 0.000 ARG C 235 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 265 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 382 PHE cc_start: 0.8853 (OUTLIER) cc_final: 0.8314 (m-80) REVERT: A 383 ASN cc_start: 0.8266 (t0) cc_final: 0.7948 (t0) REVERT: A 425 GLU cc_start: 0.8225 (tp30) cc_final: 0.7853 (mm-30) REVERT: A 442 LYS cc_start: 0.9037 (tttt) cc_final: 0.8541 (ttmm) REVERT: A 516 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8098 (tm-30) REVERT: A 654 MET cc_start: 0.8786 (tpp) cc_final: 0.8516 (tpp) REVERT: B 1 MET cc_start: 0.7491 (tmm) cc_final: 0.7258 (tmm) REVERT: B 41 GLU cc_start: 0.7228 (tm-30) cc_final: 0.6745 (tm-30) REVERT: B 151 ASP cc_start: 0.7858 (t0) cc_final: 0.7488 (t0) REVERT: B 154 GLN cc_start: 0.8671 (mm-40) cc_final: 0.8131 (mm-40) REVERT: B 210 MET cc_start: 0.5949 (ptt) cc_final: 0.5642 (ptp) REVERT: B 266 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7341 (mm-30) REVERT: B 289 SER cc_start: 0.8773 (m) cc_final: 0.8300 (p) REVERT: B 323 MET cc_start: 0.7533 (ttp) cc_final: 0.7330 (ttp) REVERT: B 388 ASP cc_start: 0.7840 (m-30) cc_final: 0.7630 (m-30) REVERT: B 442 LEU cc_start: 0.8773 (tp) cc_final: 0.8471 (mt) REVERT: B 523 ASP cc_start: 0.7603 (m-30) cc_final: 0.7165 (m-30) REVERT: C 164 LYS cc_start: 0.9045 (tppt) cc_final: 0.8838 (tppt) REVERT: C 176 GLU cc_start: 0.7318 (mp0) cc_final: 0.7102 (pm20) REVERT: C 217 GLN cc_start: 0.7323 (tt0) cc_final: 0.7022 (mt0) outliers start: 46 outliers final: 27 residues processed: 293 average time/residue: 0.2627 time to fit residues: 108.9813 Evaluate side-chains 269 residues out of total 1301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 241 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 383 ASN Chi-restraints excluded: chain B residue 482 LYS Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain B residue 600 ASN Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 199 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 132 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 142 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN A 263 HIS ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 554 GLN B 725 GLN C 141 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 12687 Z= 0.373 Angle : 0.680 13.704 17180 Z= 0.349 Chirality : 0.046 0.191 1886 Planarity : 0.005 0.060 2080 Dihedral : 13.528 178.117 2008 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.10 % Favored : 91.83 % Rotamer: Outliers : 4.74 % Allowed : 16.54 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.21), residues: 1445 helix: 0.27 (0.20), residues: 657 sheet: -0.41 (0.57), residues: 100 loop : -2.80 (0.20), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 38 HIS 0.009 0.002 HIS A 263 PHE 0.022 0.002 PHE B 122 TYR 0.015 0.002 TYR B 350 ARG 0.010 0.001 ARG B 578 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 237 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 MET cc_start: 0.8097 (tmm) cc_final: 0.7580 (tmm) REVERT: A 297 MET cc_start: 0.7023 (mpp) cc_final: 0.6642 (mtm) REVERT: A 305 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8360 (ttmm) REVERT: A 385 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6480 (mp0) REVERT: A 516 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8202 (tm-30) REVERT: A 584 GLU cc_start: 0.8215 (tp30) cc_final: 0.7555 (tp30) REVERT: B 41 GLU cc_start: 0.7579 (tm-30) cc_final: 0.6992 (tm-30) REVERT: B 78 LEU cc_start: 0.8572 (tp) cc_final: 0.8232 (tp) REVERT: B 148 LEU cc_start: 0.9186 (mp) cc_final: 0.8877 (mp) REVERT: B 151 ASP cc_start: 0.7907 (t0) cc_final: 0.7565 (t0) REVERT: B 388 ASP cc_start: 0.7829 (m-30) cc_final: 0.7587 (m-30) REVERT: B 523 ASP cc_start: 0.7950 (m-30) cc_final: 0.7560 (m-30) REVERT: B 578 ARG cc_start: 0.8195 (ttm110) cc_final: 0.7938 (mtp85) REVERT: B 730 ILE cc_start: 0.6171 (OUTLIER) cc_final: 0.5848 (pt) REVERT: C 38 TRP cc_start: 0.8495 (OUTLIER) cc_final: 0.7387 (m100) REVERT: C 163 GLN cc_start: 0.8790 (tp40) cc_final: 0.8341 (tp40) REVERT: C 164 LYS cc_start: 0.9042 (tppt) cc_final: 0.7861 (tppt) outliers start: 61 outliers final: 38 residues processed: 281 average time/residue: 0.2547 time to fit residues: 101.9098 Evaluate side-chains 260 residues out of total 1301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 218 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 383 ASN Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 482 LYS Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 38 TRP Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 199 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 118 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 72 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN C 141 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12687 Z= 0.199 Angle : 0.576 10.903 17180 Z= 0.292 Chirality : 0.041 0.139 1886 Planarity : 0.004 0.060 2080 Dihedral : 13.315 179.248 2008 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.37 % Favored : 93.56 % Rotamer: Outliers : 3.49 % Allowed : 18.56 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.22), residues: 1445 helix: 0.62 (0.20), residues: 659 sheet: -0.49 (0.53), residues: 114 loop : -2.68 (0.21), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 357 HIS 0.004 0.001 HIS A 451 PHE 0.019 0.001 PHE A 292 TYR 0.015 0.001 TYR C 11 ARG 0.006 0.000 ARG B 578 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 241 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.6959 (ttm) REVERT: A 387 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8789 (mm) REVERT: A 427 LEU cc_start: 0.8888 (tt) cc_final: 0.8687 (tt) REVERT: A 516 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8148 (tm-30) REVERT: A 584 GLU cc_start: 0.8186 (tp30) cc_final: 0.7576 (tp30) REVERT: B 41 GLU cc_start: 0.7424 (tm-30) cc_final: 0.6872 (tm-30) REVERT: B 148 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8801 (mp) REVERT: B 151 ASP cc_start: 0.8019 (t0) cc_final: 0.7488 (t0) REVERT: B 248 MET cc_start: 0.7525 (tpp) cc_final: 0.7150 (tpp) REVERT: B 388 ASP cc_start: 0.7724 (m-30) cc_final: 0.7497 (m-30) REVERT: B 412 MET cc_start: 0.7204 (mpp) cc_final: 0.6856 (mpp) REVERT: B 474 MET cc_start: 0.8863 (tpp) cc_final: 0.8483 (mtp) REVERT: B 492 GLU cc_start: 0.7280 (tt0) cc_final: 0.7046 (tt0) REVERT: B 523 ASP cc_start: 0.7819 (m-30) cc_final: 0.7526 (m-30) REVERT: B 578 ARG cc_start: 0.8117 (ttm110) cc_final: 0.7885 (mtp85) REVERT: C 176 GLU cc_start: 0.7706 (mp0) cc_final: 0.7371 (pm20) outliers start: 45 outliers final: 29 residues processed: 272 average time/residue: 0.2598 time to fit residues: 100.7474 Evaluate side-chains 256 residues out of total 1301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 224 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 308 ASN Chi-restraints excluded: chain B residue 383 ASN Chi-restraints excluded: chain B residue 482 LYS Chi-restraints excluded: chain B residue 505 ASN Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain B residue 600 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 199 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 47 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 83 optimal weight: 0.7980 chunk 35 optimal weight: 0.0870 chunk 142 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 137 optimal weight: 7.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 GLN ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.4939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12687 Z= 0.183 Angle : 0.573 9.443 17180 Z= 0.289 Chirality : 0.041 0.144 1886 Planarity : 0.004 0.060 2080 Dihedral : 13.270 179.593 2006 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.92 % Favored : 93.01 % Rotamer: Outliers : 3.65 % Allowed : 18.01 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.22), residues: 1445 helix: 0.72 (0.20), residues: 666 sheet: -0.43 (0.53), residues: 114 loop : -2.57 (0.21), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 357 HIS 0.004 0.001 HIS A 451 PHE 0.019 0.001 PHE A 292 TYR 0.007 0.001 TYR A 633 ARG 0.005 0.000 ARG C 133 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 236 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.7127 (OUTLIER) cc_final: 0.6784 (ttm) REVERT: A 196 MET cc_start: 0.8214 (tmm) cc_final: 0.7825 (tmm) REVERT: A 305 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8526 (ttmm) REVERT: A 385 GLU cc_start: 0.6733 (OUTLIER) cc_final: 0.6269 (mp0) REVERT: A 387 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8789 (mm) REVERT: A 516 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8147 (tm-30) REVERT: B 41 GLU cc_start: 0.7482 (tm-30) cc_final: 0.6976 (tm-30) REVERT: B 148 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8801 (mp) REVERT: B 151 ASP cc_start: 0.7971 (t0) cc_final: 0.7441 (t0) REVERT: B 248 MET cc_start: 0.7701 (tpp) cc_final: 0.7289 (tpp) REVERT: B 388 ASP cc_start: 0.7727 (m-30) cc_final: 0.7519 (m-30) REVERT: B 523 ASP cc_start: 0.7758 (m-30) cc_final: 0.7475 (m-30) REVERT: B 748 ARG cc_start: 0.7954 (mmm160) cc_final: 0.7740 (mmm160) REVERT: C 38 TRP cc_start: 0.8349 (OUTLIER) cc_final: 0.7600 (m100) REVERT: C 164 LYS cc_start: 0.8980 (tppt) cc_final: 0.8137 (tppt) REVERT: C 176 GLU cc_start: 0.7839 (mp0) cc_final: 0.7465 (pm20) REVERT: C 231 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8948 (mm) outliers start: 47 outliers final: 29 residues processed: 264 average time/residue: 0.2511 time to fit residues: 94.6222 Evaluate side-chains 257 residues out of total 1301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 221 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 308 ASN Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 383 ASN Chi-restraints excluded: chain B residue 482 LYS Chi-restraints excluded: chain B residue 505 ASN Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain B residue 600 ASN Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 38 TRP Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 231 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 16 optimal weight: 0.2980 chunk 81 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 chunk 119 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN C 141 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12687 Z= 0.156 Angle : 0.568 8.312 17180 Z= 0.286 Chirality : 0.041 0.138 1886 Planarity : 0.004 0.063 2080 Dihedral : 13.179 178.790 2006 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.88 % Favored : 94.05 % Rotamer: Outliers : 3.34 % Allowed : 18.32 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.22), residues: 1445 helix: 0.92 (0.21), residues: 664 sheet: -0.32 (0.53), residues: 114 loop : -2.44 (0.22), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 357 HIS 0.004 0.001 HIS A 451 PHE 0.023 0.001 PHE B 108 TYR 0.008 0.001 TYR B 560 ARG 0.012 0.000 ARG B 578 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 243 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.7010 (OUTLIER) cc_final: 0.6670 (ttm) REVERT: A 196 MET cc_start: 0.7973 (tmm) cc_final: 0.7517 (tmm) REVERT: A 305 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8532 (ttmm) REVERT: A 339 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8190 (ptt-90) REVERT: A 385 GLU cc_start: 0.6690 (OUTLIER) cc_final: 0.6255 (mp0) REVERT: A 387 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8832 (mm) REVERT: B 41 GLU cc_start: 0.7471 (tm-30) cc_final: 0.6995 (tm-30) REVERT: B 134 TRP cc_start: 0.8108 (p90) cc_final: 0.7842 (p90) REVERT: B 148 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8825 (mp) REVERT: B 151 ASP cc_start: 0.7926 (t0) cc_final: 0.7369 (t0) REVERT: B 222 ARG cc_start: 0.8483 (ttm170) cc_final: 0.7881 (ttt180) REVERT: B 248 MET cc_start: 0.7829 (tpp) cc_final: 0.7342 (tpp) REVERT: B 492 GLU cc_start: 0.7106 (tt0) cc_final: 0.6764 (tt0) REVERT: B 523 ASP cc_start: 0.7815 (m-30) cc_final: 0.7542 (m-30) REVERT: B 578 ARG cc_start: 0.8209 (ttm110) cc_final: 0.7836 (mtp85) REVERT: C 14 LEU cc_start: 0.8134 (mt) cc_final: 0.7789 (mp) REVERT: C 38 TRP cc_start: 0.8263 (OUTLIER) cc_final: 0.7590 (m100) REVERT: C 176 GLU cc_start: 0.7872 (mp0) cc_final: 0.7525 (pm20) REVERT: C 231 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8947 (mm) outliers start: 43 outliers final: 26 residues processed: 268 average time/residue: 0.2516 time to fit residues: 95.9521 Evaluate side-chains 263 residues out of total 1301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 229 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 308 ASN Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 383 ASN Chi-restraints excluded: chain B residue 482 LYS Chi-restraints excluded: chain B residue 600 ASN Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 38 TRP Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 231 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 56 optimal weight: 0.0970 chunk 84 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 111 optimal weight: 0.1980 chunk 128 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12687 Z= 0.193 Angle : 0.590 9.243 17180 Z= 0.295 Chirality : 0.041 0.150 1886 Planarity : 0.004 0.064 2080 Dihedral : 13.200 179.119 2006 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.06 % Favored : 92.87 % Rotamer: Outliers : 3.34 % Allowed : 18.79 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.22), residues: 1445 helix: 0.96 (0.21), residues: 667 sheet: -0.31 (0.52), residues: 120 loop : -2.36 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 178 HIS 0.005 0.001 HIS A 451 PHE 0.019 0.001 PHE B 108 TYR 0.008 0.001 TYR B 692 ARG 0.010 0.000 ARG B 578 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 229 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.7063 (OUTLIER) cc_final: 0.6762 (ttm) REVERT: A 305 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8548 (ttmm) REVERT: A 339 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8178 (ptt-90) REVERT: A 385 GLU cc_start: 0.6626 (OUTLIER) cc_final: 0.6168 (mp0) REVERT: A 387 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8859 (mm) REVERT: B 41 GLU cc_start: 0.7494 (tm-30) cc_final: 0.6999 (tm-30) REVERT: B 148 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8770 (mp) REVERT: B 151 ASP cc_start: 0.7906 (t0) cc_final: 0.7397 (t0) REVERT: B 248 MET cc_start: 0.7878 (tpp) cc_final: 0.7404 (tpp) REVERT: B 523 ASP cc_start: 0.7645 (m-30) cc_final: 0.7244 (m-30) REVERT: B 578 ARG cc_start: 0.8199 (ttm110) cc_final: 0.7886 (mtp85) REVERT: C 14 LEU cc_start: 0.7969 (mt) cc_final: 0.7744 (mp) REVERT: C 38 TRP cc_start: 0.8312 (OUTLIER) cc_final: 0.7652 (m100) REVERT: C 176 GLU cc_start: 0.7603 (mp0) cc_final: 0.7130 (pm20) REVERT: C 231 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8946 (mm) outliers start: 43 outliers final: 27 residues processed: 254 average time/residue: 0.2464 time to fit residues: 90.0340 Evaluate side-chains 257 residues out of total 1301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 222 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 308 ASN Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 383 ASN Chi-restraints excluded: chain B residue 482 LYS Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 38 TRP Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 231 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 6.9990 chunk 132 optimal weight: 0.6980 chunk 135 optimal weight: 5.9990 chunk 79 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 119 optimal weight: 9.9990 chunk 124 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN C 141 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.5308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12687 Z= 0.215 Angle : 0.610 9.855 17180 Z= 0.305 Chirality : 0.042 0.163 1886 Planarity : 0.004 0.061 2080 Dihedral : 13.233 179.048 2006 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.57 % Favored : 93.36 % Rotamer: Outliers : 3.11 % Allowed : 19.33 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.22), residues: 1445 helix: 1.00 (0.21), residues: 661 sheet: -0.30 (0.54), residues: 113 loop : -2.30 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 357 HIS 0.004 0.001 HIS A 451 PHE 0.018 0.001 PHE C 212 TYR 0.018 0.001 TYR C 11 ARG 0.010 0.000 ARG B 578 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 224 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.7154 (OUTLIER) cc_final: 0.6807 (ttm) REVERT: A 196 MET cc_start: 0.8115 (tmm) cc_final: 0.7898 (ttm) REVERT: A 305 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8551 (ttmm) REVERT: A 339 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8408 (ptt-90) REVERT: A 385 GLU cc_start: 0.6667 (OUTLIER) cc_final: 0.6251 (mp0) REVERT: A 387 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8840 (mm) REVERT: B 41 GLU cc_start: 0.7506 (tm-30) cc_final: 0.6986 (tm-30) REVERT: B 148 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8794 (mp) REVERT: B 151 ASP cc_start: 0.7887 (t0) cc_final: 0.7359 (t0) REVERT: B 248 MET cc_start: 0.8010 (tpp) cc_final: 0.7618 (tpp) REVERT: B 523 ASP cc_start: 0.7693 (m-30) cc_final: 0.7385 (m-30) REVERT: B 578 ARG cc_start: 0.8206 (ttm110) cc_final: 0.7878 (mtp85) REVERT: B 710 MET cc_start: 0.7710 (mmt) cc_final: 0.7418 (tpt) REVERT: C 14 LEU cc_start: 0.7871 (mt) cc_final: 0.7641 (mp) REVERT: C 38 TRP cc_start: 0.8288 (OUTLIER) cc_final: 0.7697 (m100) REVERT: C 231 ILE cc_start: 0.9163 (OUTLIER) cc_final: 0.8949 (mm) outliers start: 40 outliers final: 30 residues processed: 247 average time/residue: 0.2489 time to fit residues: 87.3847 Evaluate side-chains 254 residues out of total 1301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 216 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 308 ASN Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 383 ASN Chi-restraints excluded: chain B residue 482 LYS Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 38 TRP Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 231 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 139 optimal weight: 5.9990 chunk 85 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.5463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 12687 Z= 0.268 Angle : 0.648 11.810 17180 Z= 0.324 Chirality : 0.043 0.148 1886 Planarity : 0.004 0.061 2080 Dihedral : 13.390 179.261 2006 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.27 % Favored : 92.66 % Rotamer: Outliers : 3.03 % Allowed : 19.41 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.22), residues: 1445 helix: 0.92 (0.20), residues: 661 sheet: -0.48 (0.53), residues: 113 loop : -2.31 (0.22), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 357 HIS 0.005 0.001 HIS A 451 PHE 0.025 0.002 PHE B 108 TYR 0.009 0.001 TYR A 633 ARG 0.009 0.001 ARG B 578 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 220 time to evaluate : 1.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7858 (pm20) cc_final: 0.7655 (pm20) REVERT: A 196 MET cc_start: 0.8129 (tmm) cc_final: 0.7813 (tmm) REVERT: A 305 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8571 (ttmm) REVERT: A 339 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8372 (ptt-90) REVERT: A 385 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6484 (mp0) REVERT: A 387 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8860 (mm) REVERT: A 627 LEU cc_start: 0.9222 (mt) cc_final: 0.8880 (mp) REVERT: B 41 GLU cc_start: 0.7438 (tm-30) cc_final: 0.6869 (tm-30) REVERT: B 148 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8822 (mp) REVERT: B 151 ASP cc_start: 0.7987 (t0) cc_final: 0.7402 (t0) REVERT: B 248 MET cc_start: 0.8014 (tpp) cc_final: 0.7582 (tpp) REVERT: B 482 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8756 (ptmt) REVERT: B 492 GLU cc_start: 0.7260 (tt0) cc_final: 0.7058 (tt0) REVERT: B 523 ASP cc_start: 0.7786 (m-30) cc_final: 0.7495 (m-30) REVERT: B 578 ARG cc_start: 0.8208 (ttm110) cc_final: 0.7916 (mtp85) REVERT: B 710 MET cc_start: 0.7379 (mmt) cc_final: 0.7039 (tpt) REVERT: C 14 LEU cc_start: 0.8015 (mt) cc_final: 0.7785 (mp) REVERT: C 38 TRP cc_start: 0.8379 (OUTLIER) cc_final: 0.7755 (m100) REVERT: C 231 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8939 (mm) outliers start: 39 outliers final: 27 residues processed: 244 average time/residue: 0.2645 time to fit residues: 91.2524 Evaluate side-chains 247 residues out of total 1301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 212 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 308 ASN Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 383 ASN Chi-restraints excluded: chain B residue 482 LYS Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 38 TRP Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 231 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 32 optimal weight: 0.0000 chunk 116 optimal weight: 9.9990 chunk 48 optimal weight: 0.6980 chunk 119 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN C 141 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.138342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.108470 restraints weight = 19450.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.112000 restraints weight = 10151.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.114331 restraints weight = 6713.621| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.5496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12687 Z= 0.172 Angle : 0.600 11.006 17180 Z= 0.299 Chirality : 0.041 0.142 1886 Planarity : 0.004 0.060 2080 Dihedral : 13.301 178.513 2006 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.95 % Favored : 93.98 % Rotamer: Outliers : 2.95 % Allowed : 19.80 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.23), residues: 1445 helix: 1.10 (0.21), residues: 657 sheet: -0.49 (0.52), residues: 119 loop : -2.20 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 357 HIS 0.004 0.001 HIS A 451 PHE 0.025 0.001 PHE B 108 TYR 0.017 0.001 TYR C 11 ARG 0.009 0.000 ARG B 578 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2754.79 seconds wall clock time: 50 minutes 56.43 seconds (3056.43 seconds total)