Starting phenix.real_space_refine on Fri Mar 15 06:37:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8b_24314/03_2024/7r8b_24314_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8b_24314/03_2024/7r8b_24314.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8b_24314/03_2024/7r8b_24314.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8b_24314/03_2024/7r8b_24314.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8b_24314/03_2024/7r8b_24314_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8b_24314/03_2024/7r8b_24314_updated.pdb" } resolution = 3.1 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= 0.004 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 67 5.16 5 C 7027 2.51 5 N 1838 2.21 5 O 1936 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 112": "OE1" <-> "OE2" Residue "A GLU 123": "OE1" <-> "OE2" Residue "A ASP 127": "OD1" <-> "OD2" Residue "A GLU 146": "OE1" <-> "OE2" Residue "A ASP 182": "OD1" <-> "OD2" Residue "A TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 299": "OD1" <-> "OD2" Residue "A ASP 308": "OD1" <-> "OD2" Residue "A GLU 313": "OE1" <-> "OE2" Residue "A GLU 317": "OE1" <-> "OE2" Residue "A GLU 343": "OE1" <-> "OE2" Residue "A ASP 360": "OD1" <-> "OD2" Residue "A ASP 455": "OD1" <-> "OD2" Residue "A TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 579": "OE1" <-> "OE2" Residue "A PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 646": "OD1" <-> "OD2" Residue "B ASP 25": "OD1" <-> "OD2" Residue "B PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 51": "OD1" <-> "OD2" Residue "B PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 189": "OE1" <-> "OE2" Residue "B TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 257": "NH1" <-> "NH2" Residue "B ASP 323": "OD1" <-> "OD2" Residue "B ASP 328": "OD1" <-> "OD2" Residue "B GLU 333": "OE1" <-> "OE2" Residue "B ARG 339": "NH1" <-> "NH2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B GLU 351": "OE1" <-> "OE2" Residue "B ASP 410": "OD1" <-> "OD2" Residue "B ASP 413": "OD1" <-> "OD2" Residue "B TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 466": "OD1" <-> "OD2" Residue "B TYR 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 627": "OD1" <-> "OD2" Residue "B GLU 634": "OE1" <-> "OE2" Residue "B TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 38": "NH1" <-> "NH2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "C PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C GLU 73": "OE1" <-> "OE2" Residue "C ASP 76": "OD1" <-> "OD2" Residue "C TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 108": "NH1" <-> "NH2" Residue "C ASP 111": "OD1" <-> "OD2" Residue "C PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 61": "OD1" <-> "OD2" Residue "D TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 75": "OD1" <-> "OD2" Residue "D PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 101": "OE1" <-> "OE2" 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: 10868 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4626 Classifications: {'peptide': 588} Link IDs: {'PTRANS': 22, 'TRANS': 565} Chain breaks: 3 Chain: "B" Number of atoms: 4482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4482 Classifications: {'peptide': 564} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 539} Chain breaks: 3 Chain: "C" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 901 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "D" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 803 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 100} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.22, per 1000 atoms: 0.48 Number of scatterers: 10868 At special positions: 0 Unit cell: (114.121, 105.791, 122.451, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 67 16.00 O 1936 8.00 N 1838 7.00 C 7027 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 587 " - pdb=" SG CYS A 600 " distance=2.03 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 117 " distance=2.03 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 108 " 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 Time building additional restraints: 4.17 Conformation dependent library (CDL) restraints added in 2.1 seconds 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2540 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 8 sheets defined 47.8% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.42 Creating SS restraints... Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 92 through 100 Processing helix chain 'A' and resid 144 through 155 Processing helix chain 'A' and resid 161 through 174 Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 195 through 209 removed outlier: 4.573A pdb=" N GLN A 209 " --> pdb=" O ALA A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 239 Processing helix chain 'A' and resid 277 through 286 Processing helix chain 'A' and resid 297 through 304 Processing helix chain 'A' and resid 312 through 331 Processing helix chain 'A' and resid 333 through 346 Processing helix chain 'A' and resid 364 through 380 Processing helix chain 'A' and resid 383 through 404 removed outlier: 5.299A pdb=" N ASN A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N LEU A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHE A 403 " --> pdb=" O PHE A 399 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 453 Proline residue: A 431 - end of helix Proline residue: A 443 - end of helix Processing helix chain 'A' and resid 460 through 490 Proline residue: A 473 - end of helix removed outlier: 4.877A pdb=" N TRP A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR A 489 " --> pdb=" O VAL A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 523 Proline residue: A 509 - end of helix Processing helix chain 'A' and resid 527 through 544 Processing helix chain 'A' and resid 557 through 565 removed outlier: 3.771A pdb=" N TYR A 564 " --> pdb=" O LYS A 560 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 579 Processing helix chain 'A' and resid 606 through 612 Processing helix chain 'A' and resid 614 through 647 removed outlier: 4.428A pdb=" N THR A 617 " --> pdb=" O PRO A 614 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER A 618 " --> pdb=" O GLY A 615 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE A 620 " --> pdb=" O THR A 617 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N THR A 621 " --> pdb=" O SER A 618 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET A 622 " --> pdb=" O ARG A 619 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE A 630 " --> pdb=" O LEU A 627 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A 631 " --> pdb=" O TYR A 628 " (cutoff:3.500A) Proline residue: A 632 - end of helix removed outlier: 3.604A pdb=" N ASP A 646 " --> pdb=" O LYS A 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 119 Processing helix chain 'B' and resid 141 through 147 Processing helix chain 'B' and resid 163 through 174 Processing helix chain 'B' and resid 181 through 194 Processing helix chain 'B' and resid 198 through 200 No H-bonds generated for 'chain 'B' and resid 198 through 200' Processing helix chain 'B' and resid 215 through 227 Processing helix chain 'B' and resid 245 through 260 Processing helix chain 'B' and resid 274 through 279 removed outlier: 3.600A pdb=" N ARG B 278 " --> pdb=" O SER B 274 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 274 through 279' Processing helix chain 'B' and resid 300 through 307 removed outlier: 3.560A pdb=" N ALA B 306 " --> pdb=" O GLN B 302 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 307 " --> pdb=" O TYR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 324 Processing helix chain 'B' and resid 335 through 352 removed outlier: 4.051A pdb=" N LYS B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 412 removed outlier: 4.041A pdb=" N ARG B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 434 Processing helix chain 'B' and resid 445 through 457 Processing helix chain 'B' and resid 459 through 472 Processing helix chain 'B' and resid 475 through 484 Processing helix chain 'B' and resid 491 through 516 Proline residue: B 502 - end of helix Proline residue: B 514 - end of helix Processing helix chain 'B' and resid 526 through 552 Processing helix chain 'B' and resid 556 through 572 Processing helix chain 'B' and resid 586 through 593 Processing helix chain 'B' and resid 595 through 607 Processing helix chain 'B' and resid 627 through 632 Processing helix chain 'B' and resid 640 through 664 Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'D' and resid 100 through 102 No H-bonds generated for 'chain 'D' and resid 100 through 102' Processing sheet with id= A, first strand: chain 'A' and resid 74 through 77 removed outlier: 4.773A pdb=" N VAL A 113 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 270 through 275 removed outlier: 6.581A pdb=" N ILE A 265 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N CYS A 274 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILE A 263 " --> pdb=" O CYS A 274 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL A 245 " --> pdb=" O GLN A 80 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 93 through 96 Processing sheet with id= D, first strand: chain 'B' and resid 290 through 296 removed outlier: 6.731A pdb=" N LEU B 285 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU B 294 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL B 283 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL B 265 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ILE B 103 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ILE B 267 " --> pdb=" O ILE B 103 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N GLY B 105 " --> pdb=" O ILE B 267 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 22 through 26 Processing sheet with id= F, first strand: chain 'C' and resid 116 through 118 removed outlier: 5.865A pdb=" N ARG C 57 " --> pdb=" O TRP C 66 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N TRP C 66 " --> pdb=" O ARG C 57 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 24 through 27 Processing sheet with id= H, first strand: chain 'D' and resid 30 through 32 removed outlier: 6.013A pdb=" N LYS D 123 " --> pdb=" O LEU D 31 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLN D 57 " --> pdb=" O ARG D 66 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ARG D 66 " --> pdb=" O GLN D 57 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LYS D 59 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ILE D 64 " --> pdb=" O LYS D 59 " (cutoff:3.500A) 543 hydrogen bonds defined for protein. 1518 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.43 Time building geometry restraints manager: 4.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3453 1.34 - 1.46: 2633 1.46 - 1.58: 4913 1.58 - 1.70: 0 1.70 - 1.82: 107 Bond restraints: 11106 Sorted by residual: bond pdb=" C PHE A 442 " pdb=" N PRO A 443 " ideal model delta sigma weight residual 1.334 1.366 -0.032 1.51e-02 4.39e+03 4.49e+00 bond pdb=" CA LYS B 126 " pdb=" CB LYS B 126 " ideal model delta sigma weight residual 1.526 1.545 -0.020 1.68e-02 3.54e+03 1.37e+00 bond pdb=" C ILE B 459 " pdb=" N PRO B 460 " ideal model delta sigma weight residual 1.335 1.349 -0.014 1.28e-02 6.10e+03 1.25e+00 bond pdb=" C3 CLR A 701 " pdb=" O1 CLR A 701 " ideal model delta sigma weight residual 1.413 1.391 0.022 2.00e-02 2.50e+03 1.24e+00 bond pdb=" CA THR A 430 " pdb=" C THR A 430 " ideal model delta sigma weight residual 1.520 1.533 -0.013 1.23e-02 6.61e+03 1.08e+00 ... (remaining 11101 not shown) Histogram of bond angle deviations from ideal: 100.27 - 107.01: 305 107.01 - 113.75: 6069 113.75 - 120.49: 4474 120.49 - 127.23: 4094 127.23 - 133.97: 99 Bond angle restraints: 15041 Sorted by residual: angle pdb=" C PRO A 556 " pdb=" N ILE A 557 " pdb=" CA ILE A 557 " ideal model delta sigma weight residual 120.33 123.55 -3.22 8.00e-01 1.56e+00 1.62e+01 angle pdb=" C VAL A 404 " pdb=" N LEU A 405 " pdb=" CA LEU A 405 " ideal model delta sigma weight residual 121.54 128.47 -6.93 1.91e+00 2.74e-01 1.32e+01 angle pdb=" C ALA D 70 " pdb=" N ALA D 71 " pdb=" CA ALA D 71 " ideal model delta sigma weight residual 121.54 128.02 -6.48 1.91e+00 2.74e-01 1.15e+01 angle pdb=" N VAL B 205 " pdb=" CA VAL B 205 " pdb=" C VAL B 205 " ideal model delta sigma weight residual 111.91 109.05 2.86 8.90e-01 1.26e+00 1.04e+01 angle pdb=" N ILE B 292 " pdb=" CA ILE B 292 " pdb=" C ILE B 292 " ideal model delta sigma weight residual 111.90 109.40 2.50 8.10e-01 1.52e+00 9.53e+00 ... (remaining 15036 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 6087 17.40 - 34.81: 494 34.81 - 52.21: 95 52.21 - 69.61: 29 69.61 - 87.02: 7 Dihedral angle restraints: 6712 sinusoidal: 2754 harmonic: 3958 Sorted by residual: dihedral pdb=" CB ARG A 198 " pdb=" CG ARG A 198 " pdb=" CD ARG A 198 " pdb=" NE ARG A 198 " ideal model delta sinusoidal sigma weight residual 60.00 119.50 -59.50 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N ARG A 122 " pdb=" CA ARG A 122 " pdb=" CB ARG A 122 " pdb=" CG ARG A 122 " ideal model delta sinusoidal sigma weight residual -60.00 -118.56 58.56 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CB MET B 558 " pdb=" CG MET B 558 " pdb=" SD MET B 558 " pdb=" CE MET B 558 " ideal model delta sinusoidal sigma weight residual -60.00 -2.80 -57.20 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 6709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1597 0.072 - 0.143: 112 0.143 - 0.215: 2 0.215 - 0.286: 3 0.286 - 0.358: 2 Chirality restraints: 1716 Sorted by residual: chirality pdb=" C14 CLR B 801 " pdb=" C13 CLR B 801 " pdb=" C15 CLR B 801 " pdb=" C8 CLR B 801 " both_signs ideal model delta sigma weight residual False -2.32 -2.68 0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" C14 CLR A 701 " pdb=" C13 CLR A 701 " pdb=" C15 CLR A 701 " pdb=" C8 CLR A 701 " both_signs ideal model delta sigma weight residual False -2.32 -2.64 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" C9 CLR B 801 " pdb=" C10 CLR B 801 " pdb=" C11 CLR B 801 " pdb=" C8 CLR B 801 " both_signs ideal model delta sigma weight residual False -2.45 -2.69 0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 1713 not shown) Planarity restraints: 1884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 490 " 0.023 5.00e-02 4.00e+02 3.46e-02 1.91e+00 pdb=" N PRO B 491 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 491 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 491 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 276 " 0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO A 277 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 277 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 277 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 126 " -0.006 2.00e-02 2.50e+03 1.13e-02 1.28e+00 pdb=" C LYS B 126 " 0.020 2.00e-02 2.50e+03 pdb=" O LYS B 126 " -0.007 2.00e-02 2.50e+03 pdb=" N ILE B 127 " -0.007 2.00e-02 2.50e+03 ... (remaining 1881 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 157 2.66 - 3.22: 9906 3.22 - 3.78: 16859 3.78 - 4.34: 23085 4.34 - 4.90: 38684 Nonbonded interactions: 88691 Sorted by model distance: nonbonded pdb=" OG SER D 27 " pdb=" OG1 THR D 42 " model vdw 2.103 2.440 nonbonded pdb=" O VAL A 542 " pdb=" OG SER A 546 " model vdw 2.204 2.440 nonbonded pdb=" OG SER D 83 " pdb=" OG1 THR D 94 " model vdw 2.258 2.440 nonbonded pdb=" O ASN A 410 " pdb=" OG1 THR A 586 " model vdw 2.267 2.440 nonbonded pdb=" NE ARG A 550 " pdb=" O LEU B 434 " model vdw 2.290 2.520 ... (remaining 88686 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: 1.090 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: 5.920 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 31.010 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 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 : 0.002 0.032 11106 Z= 0.131 Angle : 0.553 7.058 15041 Z= 0.314 Chirality : 0.040 0.358 1716 Planarity : 0.003 0.035 1884 Dihedral : 13.495 87.019 4163 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.94 % Allowed : 18.92 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: -1.73 (0.21), residues: 1351 helix: 0.06 (0.18), residues: 702 sheet: -1.48 (0.35), residues: 182 loop : -2.85 (0.25), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 584 HIS 0.003 0.000 HIS B 531 PHE 0.006 0.001 PHE A 502 TYR 0.007 0.001 TYR C 115 ARG 0.003 0.000 ARG B 329 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 210 time to evaluate : 1.332 Fit side-chains REVERT: A 118 ARG cc_start: 0.7989 (mpt180) cc_final: 0.7713 (mmt90) REVERT: A 134 GLN cc_start: 0.7281 (tt0) cc_final: 0.6876 (tm-30) REVERT: A 313 GLU cc_start: 0.7240 (tm-30) cc_final: 0.6878 (tm-30) REVERT: A 437 ASN cc_start: 0.7595 (m-40) cc_final: 0.7357 (m110) REVERT: A 523 ILE cc_start: 0.7575 (tp) cc_final: 0.7314 (tp) REVERT: A 553 GLN cc_start: 0.8461 (mm-40) cc_final: 0.8218 (mm110) REVERT: B 446 MET cc_start: 0.7227 (mmt) cc_final: 0.7018 (mmt) REVERT: C 86 LYS cc_start: 0.8507 (tttp) cc_final: 0.8245 (ttmt) REVERT: C 101 TYR cc_start: 0.8674 (m-80) cc_final: 0.8163 (m-80) REVERT: D 90 ASP cc_start: 0.7779 (m-30) cc_final: 0.7572 (m-30) REVERT: D 99 GLU cc_start: 0.8270 (mp0) cc_final: 0.7320 (mp0) outliers start: 23 outliers final: 11 residues processed: 227 average time/residue: 0.2728 time to fit residues: 84.0744 Evaluate side-chains 154 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 143 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 112 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 179 HIS A 206 GLN A 230 GLN A 347 HIS A 454 GLN A 462 GLN ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 ASN A 597 ASN A 604 GLN A 607 GLN B 43 GLN B 99 GLN B 153 GLN B 250 ASN B 262 ASN B 271 GLN B 438 HIS B 526 GLN ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN C 75 ASN D 57 GLN D 58 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11106 Z= 0.234 Angle : 0.554 9.842 15041 Z= 0.276 Chirality : 0.041 0.230 1716 Planarity : 0.004 0.034 1884 Dihedral : 5.235 47.406 1646 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.55 % Allowed : 18.58 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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 (0.23), residues: 1351 helix: 1.06 (0.20), residues: 703 sheet: -0.98 (0.36), residues: 188 loop : -2.34 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 584 HIS 0.005 0.001 HIS B 531 PHE 0.015 0.001 PHE B 595 TYR 0.018 0.001 TYR D 111 ARG 0.004 0.000 ARG D 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 145 time to evaluate : 1.343 Fit side-chains REVERT: A 310 GLN cc_start: 0.7487 (pt0) cc_final: 0.7265 (pt0) REVERT: A 313 GLU cc_start: 0.7081 (tm-30) cc_final: 0.6675 (tm-30) REVERT: A 523 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7622 (tp) REVERT: A 553 GLN cc_start: 0.8563 (mm-40) cc_final: 0.8355 (mm-40) REVERT: B 50 ARG cc_start: 0.7240 (ttp-170) cc_final: 0.6889 (ttm110) REVERT: B 319 ASP cc_start: 0.7560 (m-30) cc_final: 0.7276 (m-30) REVERT: C 86 LYS cc_start: 0.8568 (tttp) cc_final: 0.8305 (ttmt) REVERT: C 101 TYR cc_start: 0.8785 (m-80) cc_final: 0.8271 (m-80) REVERT: D 75 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7465 (m-30) REVERT: D 99 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7222 (mp0) outliers start: 42 outliers final: 27 residues processed: 174 average time/residue: 0.2429 time to fit residues: 59.1325 Evaluate side-chains 167 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 137 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 75 ASP Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 113 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 ASN A 597 ASN B 135 ASN B 150 HIS B 172 GLN B 199 GLN ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 11106 Z= 0.385 Angle : 0.603 8.762 15041 Z= 0.304 Chirality : 0.044 0.191 1716 Planarity : 0.004 0.034 1884 Dihedral : 5.142 45.203 1639 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 5.41 % Allowed : 17.31 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: -0.38 (0.23), residues: 1351 helix: 1.05 (0.20), residues: 696 sheet: -0.70 (0.37), residues: 188 loop : -2.06 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 584 HIS 0.003 0.001 HIS B 531 PHE 0.018 0.002 PHE A 642 TYR 0.018 0.002 TYR D 111 ARG 0.005 0.001 ARG A 321 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 136 time to evaluate : 1.160 Fit side-chains revert: symmetry clash REVERT: A 118 ARG cc_start: 0.7796 (mmt90) cc_final: 0.7573 (mmt90) REVERT: A 313 GLU cc_start: 0.7270 (tm-30) cc_final: 0.6908 (tm-30) REVERT: A 480 MET cc_start: 0.8214 (tpp) cc_final: 0.7968 (mmm) REVERT: A 553 GLN cc_start: 0.8612 (mm-40) cc_final: 0.8400 (mm-40) REVERT: B 513 MET cc_start: 0.8261 (mtt) cc_final: 0.7989 (mtt) REVERT: C 86 LYS cc_start: 0.8587 (tttp) cc_final: 0.8188 (ttpt) REVERT: C 101 TYR cc_start: 0.8852 (m-80) cc_final: 0.8284 (m-80) REVERT: D 99 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7301 (mp0) outliers start: 64 outliers final: 47 residues processed: 187 average time/residue: 0.2374 time to fit residues: 62.2638 Evaluate side-chains 179 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 131 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 117 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 63 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 116 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 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 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 ASN B 172 GLN ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11106 Z= 0.175 Angle : 0.523 10.916 15041 Z= 0.262 Chirality : 0.040 0.158 1716 Planarity : 0.003 0.036 1884 Dihedral : 5.018 48.341 1639 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.38 % Allowed : 19.00 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.23), residues: 1351 helix: 1.39 (0.20), residues: 695 sheet: -0.49 (0.37), residues: 188 loop : -1.85 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 461 HIS 0.005 0.001 HIS B 531 PHE 0.027 0.001 PHE C 89 TYR 0.013 0.001 TYR D 111 ARG 0.003 0.000 ARG B 26 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 134 time to evaluate : 1.225 Fit side-chains revert: symmetry clash REVERT: A 118 ARG cc_start: 0.7746 (mmt90) cc_final: 0.7509 (mmt90) REVERT: A 134 GLN cc_start: 0.7709 (tt0) cc_final: 0.7231 (pt0) REVERT: A 313 GLU cc_start: 0.7212 (tm-30) cc_final: 0.6834 (tm-30) REVERT: A 464 MET cc_start: 0.8006 (tmm) cc_final: 0.7599 (tmm) REVERT: A 553 GLN cc_start: 0.8586 (mm-40) cc_final: 0.8381 (mm-40) REVERT: B 406 GLN cc_start: 0.8139 (tt0) cc_final: 0.7928 (tt0) REVERT: C 86 LYS cc_start: 0.8568 (tttp) cc_final: 0.8162 (ttmt) REVERT: C 101 TYR cc_start: 0.8798 (m-80) cc_final: 0.8176 (m-80) REVERT: D 99 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7253 (mp0) outliers start: 40 outliers final: 31 residues processed: 162 average time/residue: 0.2523 time to fit residues: 56.7067 Evaluate side-chains 159 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 127 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 117 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 ASN ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11106 Z= 0.353 Angle : 0.592 11.589 15041 Z= 0.296 Chirality : 0.043 0.190 1716 Planarity : 0.004 0.032 1884 Dihedral : 5.095 47.642 1637 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 5.15 % Allowed : 17.31 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.03 (0.23), residues: 1351 helix: 1.28 (0.20), residues: 696 sheet: -0.37 (0.38), residues: 188 loop : -1.76 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 584 HIS 0.004 0.001 HIS B 531 PHE 0.041 0.002 PHE C 89 TYR 0.015 0.001 TYR D 111 ARG 0.004 0.000 ARG A 321 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 129 time to evaluate : 1.349 Fit side-chains revert: symmetry clash REVERT: A 118 ARG cc_start: 0.7776 (mmt90) cc_final: 0.7491 (mmt90) REVERT: A 134 GLN cc_start: 0.7781 (tt0) cc_final: 0.7193 (pt0) REVERT: A 313 GLU cc_start: 0.7307 (tm-30) cc_final: 0.6977 (tm-30) REVERT: A 553 GLN cc_start: 0.8628 (mm-40) cc_final: 0.8401 (mm-40) REVERT: B 208 MET cc_start: 0.6766 (pp-130) cc_final: 0.6391 (ppp) REVERT: B 406 GLN cc_start: 0.8275 (tt0) cc_final: 0.7994 (tt0) REVERT: C 86 LYS cc_start: 0.8571 (tttp) cc_final: 0.8204 (ttmt) REVERT: D 25 THR cc_start: 0.9068 (OUTLIER) cc_final: 0.8756 (p) REVERT: D 31 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7898 (tt) REVERT: D 99 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7301 (mp0) outliers start: 61 outliers final: 50 residues processed: 178 average time/residue: 0.2404 time to fit residues: 60.0252 Evaluate side-chains 178 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 125 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 117 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 76 optimal weight: 0.0050 chunk 32 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 ASN ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 11106 Z= 0.332 Angle : 0.588 12.814 15041 Z= 0.292 Chirality : 0.043 0.186 1716 Planarity : 0.004 0.032 1884 Dihedral : 5.120 49.154 1637 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.73 % Allowed : 18.24 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.23), residues: 1351 helix: 1.30 (0.20), residues: 696 sheet: -0.26 (0.37), residues: 188 loop : -1.73 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 584 HIS 0.004 0.001 HIS B 531 PHE 0.016 0.001 PHE A 642 TYR 0.014 0.001 TYR D 111 ARG 0.003 0.000 ARG A 321 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 124 time to evaluate : 1.296 Fit side-chains revert: symmetry clash REVERT: A 118 ARG cc_start: 0.7768 (mmt90) cc_final: 0.7474 (mmt90) REVERT: A 134 GLN cc_start: 0.7769 (tt0) cc_final: 0.7198 (pt0) REVERT: A 313 GLU cc_start: 0.7318 (tm-30) cc_final: 0.7007 (tm-30) REVERT: A 480 MET cc_start: 0.8262 (tpp) cc_final: 0.8047 (mmm) REVERT: A 553 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8391 (mm-40) REVERT: B 208 MET cc_start: 0.6740 (pp-130) cc_final: 0.6363 (ppp) REVERT: B 406 GLN cc_start: 0.8294 (tt0) cc_final: 0.8010 (tt0) REVERT: C 86 LYS cc_start: 0.8564 (tttp) cc_final: 0.8235 (ttmt) REVERT: D 25 THR cc_start: 0.9068 (OUTLIER) cc_final: 0.8779 (p) REVERT: D 31 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7894 (tt) REVERT: D 99 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7339 (mp0) outliers start: 56 outliers final: 50 residues processed: 168 average time/residue: 0.2484 time to fit residues: 58.4125 Evaluate side-chains 176 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 123 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 117 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 130 optimal weight: 0.0970 chunk 81 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 ASN ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11106 Z= 0.215 Angle : 0.547 12.581 15041 Z= 0.271 Chirality : 0.040 0.183 1716 Planarity : 0.003 0.033 1884 Dihedral : 5.043 52.518 1637 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 4.31 % Allowed : 18.75 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.29 (0.23), residues: 1351 helix: 1.49 (0.20), residues: 696 sheet: -0.24 (0.37), residues: 188 loop : -1.63 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 461 HIS 0.005 0.001 HIS B 531 PHE 0.013 0.001 PHE A 642 TYR 0.012 0.001 TYR D 111 ARG 0.004 0.000 ARG B 26 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 126 time to evaluate : 1.322 Fit side-chains revert: symmetry clash REVERT: A 118 ARG cc_start: 0.7680 (mmt90) cc_final: 0.7388 (mmt90) REVERT: A 134 GLN cc_start: 0.7739 (tt0) cc_final: 0.7301 (pt0) REVERT: A 313 GLU cc_start: 0.7295 (tm-30) cc_final: 0.6957 (tm-30) REVERT: A 553 GLN cc_start: 0.8593 (mm-40) cc_final: 0.8362 (mm-40) REVERT: B 208 MET cc_start: 0.6737 (pp-130) cc_final: 0.6503 (ppp) REVERT: B 406 GLN cc_start: 0.8220 (tt0) cc_final: 0.7953 (tt0) REVERT: C 86 LYS cc_start: 0.8507 (tttp) cc_final: 0.8193 (ttmt) REVERT: D 25 THR cc_start: 0.9039 (OUTLIER) cc_final: 0.8742 (p) REVERT: D 99 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7307 (mp0) outliers start: 51 outliers final: 48 residues processed: 167 average time/residue: 0.2576 time to fit residues: 59.2941 Evaluate side-chains 174 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 124 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 117 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 25 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 ASN ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 11106 Z= 0.296 Angle : 0.582 13.363 15041 Z= 0.286 Chirality : 0.042 0.180 1716 Planarity : 0.004 0.033 1884 Dihedral : 5.072 53.042 1637 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 5.32 % Allowed : 17.82 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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 (0.23), residues: 1351 helix: 1.43 (0.20), residues: 696 sheet: -0.21 (0.37), residues: 188 loop : -1.61 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 461 HIS 0.005 0.001 HIS B 531 PHE 0.015 0.001 PHE A 642 TYR 0.014 0.001 TYR D 111 ARG 0.004 0.000 ARG B 26 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 120 time to evaluate : 1.257 Fit side-chains revert: symmetry clash REVERT: A 118 ARG cc_start: 0.7698 (mmt90) cc_final: 0.7383 (mmt90) REVERT: A 134 GLN cc_start: 0.7782 (tt0) cc_final: 0.7218 (pt0) REVERT: A 313 GLU cc_start: 0.7286 (tm-30) cc_final: 0.6942 (tm-30) REVERT: A 553 GLN cc_start: 0.8601 (mm-40) cc_final: 0.8364 (mm-40) REVERT: B 208 MET cc_start: 0.6732 (pp-130) cc_final: 0.6495 (ppp) REVERT: B 406 GLN cc_start: 0.8267 (tt0) cc_final: 0.7986 (tt0) REVERT: C 86 LYS cc_start: 0.8539 (tttp) cc_final: 0.8217 (ttmt) REVERT: D 25 THR cc_start: 0.9046 (OUTLIER) cc_final: 0.8770 (p) REVERT: D 31 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7892 (tt) REVERT: D 99 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7318 (mp0) outliers start: 63 outliers final: 52 residues processed: 173 average time/residue: 0.2457 time to fit residues: 59.3568 Evaluate side-chains 173 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 118 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 126 GLN Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 117 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 1.9990 chunk 121 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 72 optimal weight: 0.0050 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11106 Z= 0.210 Angle : 0.544 13.492 15041 Z= 0.270 Chirality : 0.040 0.163 1716 Planarity : 0.003 0.033 1884 Dihedral : 5.015 56.053 1637 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.81 % Allowed : 17.99 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.43 (0.24), residues: 1351 helix: 1.57 (0.20), residues: 696 sheet: -0.12 (0.37), residues: 188 loop : -1.55 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 461 HIS 0.005 0.001 HIS B 531 PHE 0.020 0.001 PHE C 89 TYR 0.012 0.001 TYR B 571 ARG 0.004 0.000 ARG B 26 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 125 time to evaluate : 1.184 Fit side-chains revert: symmetry clash REVERT: A 118 ARG cc_start: 0.7697 (mmt90) cc_final: 0.7402 (mmt90) REVERT: A 134 GLN cc_start: 0.7748 (tt0) cc_final: 0.7298 (pt0) REVERT: A 313 GLU cc_start: 0.7258 (tm-30) cc_final: 0.6888 (tm-30) REVERT: A 553 GLN cc_start: 0.8579 (mm-40) cc_final: 0.8344 (mm-40) REVERT: B 208 MET cc_start: 0.6739 (pp-130) cc_final: 0.6487 (ppp) REVERT: B 406 GLN cc_start: 0.8253 (tt0) cc_final: 0.7986 (tt0) REVERT: C 86 LYS cc_start: 0.8497 (tttp) cc_final: 0.8168 (ttmt) REVERT: C 104 MET cc_start: 0.8771 (mmm) cc_final: 0.8119 (mmm) REVERT: D 25 THR cc_start: 0.9050 (OUTLIER) cc_final: 0.8780 (p) REVERT: D 31 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7916 (tt) REVERT: D 99 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7283 (mp0) outliers start: 57 outliers final: 50 residues processed: 174 average time/residue: 0.2468 time to fit residues: 59.4431 Evaluate side-chains 178 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 125 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 126 GLN Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 117 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11106 Z= 0.190 Angle : 0.542 14.127 15041 Z= 0.267 Chirality : 0.040 0.214 1716 Planarity : 0.003 0.033 1884 Dihedral : 4.971 59.026 1637 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.48 % Allowed : 18.58 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.55 (0.24), residues: 1351 helix: 1.67 (0.20), residues: 697 sheet: -0.08 (0.37), residues: 188 loop : -1.50 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 461 HIS 0.005 0.001 HIS B 531 PHE 0.020 0.001 PHE C 89 TYR 0.012 0.001 TYR B 571 ARG 0.004 0.000 ARG B 26 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 127 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.7663 (mmt90) cc_final: 0.7377 (mmt90) REVERT: A 134 GLN cc_start: 0.7717 (tt0) cc_final: 0.7286 (pt0) REVERT: A 313 GLU cc_start: 0.7226 (tm-30) cc_final: 0.6838 (tm-30) REVERT: A 553 GLN cc_start: 0.8572 (mm-40) cc_final: 0.8334 (mm-40) REVERT: B 208 MET cc_start: 0.6712 (pp-130) cc_final: 0.6457 (ppp) REVERT: B 406 GLN cc_start: 0.8229 (tt0) cc_final: 0.7981 (tt0) REVERT: C 86 LYS cc_start: 0.8444 (tttp) cc_final: 0.8077 (ttmt) REVERT: D 25 THR cc_start: 0.9055 (OUTLIER) cc_final: 0.8766 (p) REVERT: D 31 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7918 (tt) REVERT: D 37 GLU cc_start: 0.8548 (pm20) cc_final: 0.8262 (pm20) REVERT: D 99 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7278 (mp0) outliers start: 53 outliers final: 49 residues processed: 171 average time/residue: 0.2585 time to fit residues: 61.9619 Evaluate side-chains 175 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 123 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 126 GLN Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 117 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 0.0970 chunk 32 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 107 optimal weight: 0.4980 chunk 44 optimal weight: 3.9990 chunk 110 optimal weight: 0.0770 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 0.4980 chunk 94 optimal weight: 2.9990 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.111727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.085102 restraints weight = 15439.872| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.20 r_work: 0.2800 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11106 Z= 0.129 Angle : 0.512 14.023 15041 Z= 0.252 Chirality : 0.039 0.215 1716 Planarity : 0.003 0.032 1884 Dihedral : 4.800 54.729 1637 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.12 % Allowed : 19.93 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.81 (0.24), residues: 1351 helix: 1.90 (0.20), residues: 699 sheet: 0.02 (0.37), residues: 187 loop : -1.40 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 461 HIS 0.004 0.001 HIS B 531 PHE 0.020 0.001 PHE C 89 TYR 0.015 0.001 TYR B 571 ARG 0.004 0.000 ARG B 26 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2562.15 seconds wall clock time: 46 minutes 32.62 seconds (2792.62 seconds total)