Starting phenix.real_space_refine on Thu Feb 15 13:52:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c8d_30305/02_2024/7c8d_30305.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c8d_30305/02_2024/7c8d_30305.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c8d_30305/02_2024/7c8d_30305.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c8d_30305/02_2024/7c8d_30305.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c8d_30305/02_2024/7c8d_30305.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c8d_30305/02_2024/7c8d_30305.pdb" } resolution = 3.0 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= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6104 atoms to isotropic. 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 Zn 1 6.06 5 S 36 5.16 5 C 4074 2.51 5 N 1058 2.21 5 O 1190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 23": "OE1" <-> "OE2" Residue "A PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 30": "OE1" <-> "OE2" Residue "A GLU 37": "OE1" <-> "OE2" Residue "A GLU 38": "OE1" <-> "OE2" Residue "A ASP 56": "OD1" <-> "OD2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A GLU 74": "OE1" <-> "OE2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A ARG 115": "NH1" <-> "NH2" Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 153": "OE1" <-> "OE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "A GLU 171": "OE1" <-> "OE2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 192": "NH1" <-> "NH2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 245": "NH1" <-> "NH2" Residue "A TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 305": "NH1" <-> "NH2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 350": "OD1" <-> "OD2" Residue "A PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 375": "OE1" <-> "OE2" Residue "A TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 431": "OD1" <-> "OD2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A ASP 494": "OD1" <-> "OD2" Residue "A TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 509": "OD1" <-> "OD2" Residue "A PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 518": "NH1" <-> "NH2" Residue "A GLU 536": "OE1" <-> "OE2" Residue "A GLU 571": "OE1" <-> "OE2" Residue "A GLU 576": "OE1" <-> "OE2" Residue "A TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 389": "OD1" <-> "OD2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 398": "OD1" <-> "OD2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B ARG 408": "NH1" <-> "NH2" Residue "B ASP 420": "OD1" <-> "OD2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 516": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6359 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4815 Classifications: {'peptide': 597} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 568} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 54 Chain: "B" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.22, per 1000 atoms: 0.66 Number of scatterers: 6359 At special positions: 0 Unit cell: (96.3937, 93.4125, 107.325, 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) Zn 1 29.99 S 36 16.00 O 1190 8.00 N 1058 7.00 C 4074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.05 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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: 2.52 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 374 " 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1490 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 7 sheets defined 53.3% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.692A pdb=" N THR A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N HIS A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLU A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 81 removed outlier: 3.551A pdb=" N LYS A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 83 No H-bonds generated for 'chain 'A' and resid 82 through 83' Processing helix chain 'A' and resid 84 through 88 Processing helix chain 'A' and resid 90 through 102 removed outlier: 4.278A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 128 removed outlier: 3.575A pdb=" N ASN A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER A 128 " --> pdb=" O SER A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 157 through 171 removed outlier: 3.665A pdb=" N ALA A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 194 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 220 through 252 removed outlier: 3.512A pdb=" N LYS A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 4.212A pdb=" N ASP A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 282 Proline residue: A 280 - end of helix Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.704A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 331 removed outlier: 3.577A pdb=" N SER A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 385 removed outlier: 3.750A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 400 through 413 removed outlier: 3.605A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 419 Processing helix chain 'A' and resid 433 through 447 removed outlier: 3.549A pdb=" N PHE A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.814A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.503A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 564 removed outlier: 4.435A pdb=" N LYS A 564 " --> pdb=" O GLY A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.843A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.512A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.212A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.112A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 348 through 350 Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.784A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AA6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA7, first strand: chain 'B' and resid 473 through 474 290 hydrogen bonds defined for protein. 822 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: 1.71 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2037 1.35 - 1.48: 1777 1.48 - 1.61: 2669 1.61 - 1.73: 0 1.73 - 1.86: 56 Bond restraints: 6539 Sorted by residual: bond pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " ideal model delta sigma weight residual 1.808 1.862 -0.054 3.30e-02 9.18e+02 2.71e+00 bond pdb=" N VAL A 364 " pdb=" CA VAL A 364 " ideal model delta sigma weight residual 1.460 1.472 -0.012 1.23e-02 6.61e+03 9.96e-01 bond pdb=" N HIS A 345 " pdb=" CA HIS A 345 " ideal model delta sigma weight residual 1.458 1.445 0.013 1.48e-02 4.57e+03 7.81e-01 bond pdb=" CA ASP B 364 " pdb=" C ASP B 364 " ideal model delta sigma weight residual 1.530 1.521 0.009 1.08e-02 8.57e+03 7.57e-01 bond pdb=" CA TYR A 83 " pdb=" CB TYR A 83 " ideal model delta sigma weight residual 1.528 1.542 -0.014 1.68e-02 3.54e+03 6.57e-01 ... (remaining 6534 not shown) Histogram of bond angle deviations from ideal: 100.18 - 106.96: 221 106.96 - 113.74: 3480 113.74 - 120.52: 2712 120.52 - 127.30: 2380 127.30 - 134.08: 96 Bond angle restraints: 8889 Sorted by residual: angle pdb=" C PRO A 135 " pdb=" N ASN A 136 " pdb=" CA ASN A 136 " ideal model delta sigma weight residual 121.54 126.34 -4.80 1.91e+00 2.74e-01 6.31e+00 angle pdb=" N ASP A 499 " pdb=" CA ASP A 499 " pdb=" C ASP A 499 " ideal model delta sigma weight residual 109.81 114.93 -5.12 2.21e+00 2.05e-01 5.36e+00 angle pdb=" CA CYS B 432 " pdb=" CB CYS B 432 " pdb=" SG CYS B 432 " ideal model delta sigma weight residual 114.40 119.57 -5.17 2.30e+00 1.89e-01 5.06e+00 angle pdb=" CA LEU B 335 " pdb=" CB LEU B 335 " pdb=" CG LEU B 335 " ideal model delta sigma weight residual 116.30 124.10 -7.80 3.50e+00 8.16e-02 4.97e+00 angle pdb=" N CYS B 432 " pdb=" CA CYS B 432 " pdb=" C CYS B 432 " ideal model delta sigma weight residual 108.60 111.76 -3.16 1.46e+00 4.69e-01 4.69e+00 ... (remaining 8884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 3364 17.84 - 35.68: 356 35.68 - 53.52: 102 53.52 - 71.36: 20 71.36 - 89.20: 21 Dihedral angle restraints: 3863 sinusoidal: 1540 harmonic: 2323 Sorted by residual: dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual -86.00 -33.10 -52.90 1 1.00e+01 1.00e-02 3.81e+01 dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual -86.00 -37.81 -48.19 1 1.00e+01 1.00e-02 3.20e+01 dihedral pdb=" CA THR B 500 " pdb=" C THR B 500 " pdb=" N ASN B 501 " pdb=" CA ASN B 501 " ideal model delta harmonic sigma weight residual 180.00 157.46 22.54 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 3860 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 551 0.031 - 0.061: 280 0.061 - 0.092: 65 0.092 - 0.122: 38 0.122 - 0.153: 2 Chirality restraints: 936 Sorted by residual: chirality pdb=" CA ILE B 434 " pdb=" N ILE B 434 " pdb=" C ILE B 434 " pdb=" CB ILE B 434 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.83e-01 chirality pdb=" CA VAL A 283 " pdb=" N VAL A 283 " pdb=" C VAL A 283 " pdb=" CB VAL A 283 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.17e-01 chirality pdb=" CA ASN B 501 " pdb=" N ASN B 501 " pdb=" C ASN B 501 " pdb=" CB ASN B 501 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.66e-01 ... (remaining 933 not shown) Planarity restraints: 1146 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 383 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO B 384 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 384 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 384 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 234 " 0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRO A 235 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 235 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 235 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 489 " 0.019 5.00e-02 4.00e+02 2.92e-02 1.37e+00 pdb=" N PRO A 490 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 490 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 490 " 0.016 5.00e-02 4.00e+02 ... (remaining 1143 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 68 2.58 - 3.16: 5111 3.16 - 3.74: 10330 3.74 - 4.32: 14653 4.32 - 4.90: 23826 Nonbonded interactions: 53988 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 801 " model vdw 1.998 2.230 nonbonded pdb=" OH TYR A 237 " pdb=" O VAL A 485 " model vdw 2.158 2.440 nonbonded pdb=" OH TYR A 41 " pdb=" OG1 THR B 500 " model vdw 2.188 2.440 nonbonded pdb=" NH1 ARG A 177 " pdb=" O GLU A 495 " model vdw 2.196 2.520 nonbonded pdb=" OH TYR A 183 " pdb=" OD1 ASP A 509 " model vdw 2.217 2.440 ... (remaining 53983 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 1.560 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 22.680 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:11.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6539 Z= 0.188 Angle : 0.531 7.804 8889 Z= 0.301 Chirality : 0.040 0.153 936 Planarity : 0.004 0.036 1146 Dihedral : 17.372 89.203 2352 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 6.05 % Allowed : 20.21 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -2.80 (0.26), residues: 788 helix: -1.60 (0.23), residues: 390 sheet: -0.38 (0.88), residues: 36 loop : -2.25 (0.29), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 163 HIS 0.003 0.001 HIS A 34 PHE 0.010 0.001 PHE A 308 TYR 0.010 0.001 TYR A 385 ARG 0.002 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 125 time to evaluate : 0.670 Fit side-chains REVERT: A 62 MET cc_start: 0.7469 (ttt) cc_final: 0.7189 (ttp) REVERT: A 363 LYS cc_start: 0.6862 (mmtp) cc_final: 0.6277 (mttp) REVERT: A 510 TYR cc_start: 0.8058 (m-80) cc_final: 0.7855 (m-80) REVERT: A 579 MET cc_start: 0.8197 (ttm) cc_final: 0.7966 (ttm) outliers start: 41 outliers final: 11 residues processed: 160 average time/residue: 1.1024 time to fit residues: 185.8877 Evaluate side-chains 107 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 9.9990 chunk 59 optimal weight: 0.9990 chunk 32 optimal weight: 0.1980 chunk 20 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 290 ASN A 345 HIS A 416 ASN A 598 GLN B 354 ASN B 360 ASN B 506 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6539 Z= 0.196 Angle : 0.542 15.480 8889 Z= 0.281 Chirality : 0.041 0.215 936 Planarity : 0.004 0.037 1146 Dihedral : 5.497 53.766 876 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.13 % Allowed : 24.78 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -1.47 (0.29), residues: 788 helix: -0.37 (0.26), residues: 396 sheet: -0.22 (0.91), residues: 36 loop : -1.70 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 163 HIS 0.003 0.001 HIS A 345 PHE 0.008 0.001 PHE A 308 TYR 0.016 0.001 TYR B 351 ARG 0.004 0.000 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 108 time to evaluate : 0.756 Fit side-chains REVERT: A 62 MET cc_start: 0.7547 (ttt) cc_final: 0.7296 (ttp) REVERT: A 287 GLN cc_start: 0.6884 (OUTLIER) cc_final: 0.6217 (pp30) REVERT: A 363 LYS cc_start: 0.6820 (mmtp) cc_final: 0.6268 (mttp) REVERT: A 465 LYS cc_start: 0.8094 (mttt) cc_final: 0.7753 (mtpt) REVERT: A 503 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8411 (tt) REVERT: A 579 MET cc_start: 0.8266 (ttm) cc_final: 0.8004 (ttm) REVERT: A 603 PHE cc_start: 0.6314 (t80) cc_final: 0.5901 (t80) outliers start: 28 outliers final: 13 residues processed: 131 average time/residue: 0.9632 time to fit residues: 133.7714 Evaluate side-chains 111 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 96 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 481 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 58 optimal weight: 0.0980 chunk 48 optimal weight: 0.0040 chunk 19 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS B 501 ASN B 506 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 6539 Z= 0.149 Angle : 0.501 14.173 8889 Z= 0.255 Chirality : 0.040 0.169 936 Planarity : 0.003 0.035 1146 Dihedral : 4.985 54.391 867 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.57 % Allowed : 25.52 % Favored : 69.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 (0.30), residues: 788 helix: 0.20 (0.27), residues: 395 sheet: -0.10 (0.93), residues: 36 loop : -1.40 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 163 HIS 0.002 0.001 HIS A 374 PHE 0.013 0.001 PHE B 515 TYR 0.013 0.001 TYR A 516 ARG 0.005 0.000 ARG A 531 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 108 time to evaluate : 0.738 Fit side-chains REVERT: A 62 MET cc_start: 0.7486 (ttt) cc_final: 0.7253 (ttp) REVERT: A 287 GLN cc_start: 0.6886 (OUTLIER) cc_final: 0.6223 (pp30) REVERT: A 306 ARG cc_start: 0.6829 (tpt-90) cc_final: 0.6324 (ttt180) REVERT: A 363 LYS cc_start: 0.6785 (mmtp) cc_final: 0.6217 (mttp) REVERT: A 478 TRP cc_start: 0.7914 (m100) cc_final: 0.7656 (m100) REVERT: A 603 PHE cc_start: 0.6262 (t80) cc_final: 0.5918 (t80) REVERT: B 406 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7874 (mt-10) REVERT: B 515 PHE cc_start: 0.5954 (OUTLIER) cc_final: 0.3515 (m-80) outliers start: 31 outliers final: 17 residues processed: 132 average time/residue: 0.9662 time to fit residues: 135.4354 Evaluate side-chains 124 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 105 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 33 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN A 345 HIS B 506 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6539 Z= 0.259 Angle : 0.559 14.310 8889 Z= 0.290 Chirality : 0.043 0.175 936 Planarity : 0.004 0.034 1146 Dihedral : 5.428 56.797 867 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 6.19 % Allowed : 25.07 % Favored : 68.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.80 (0.30), residues: 788 helix: 0.15 (0.26), residues: 394 sheet: -0.03 (0.95), residues: 36 loop : -1.32 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 163 HIS 0.004 0.001 HIS A 241 PHE 0.011 0.001 PHE A 308 TYR 0.020 0.002 TYR A 516 ARG 0.005 0.001 ARG A 531 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 98 time to evaluate : 0.971 Fit side-chains REVERT: A 208 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7577 (tp30) REVERT: A 287 GLN cc_start: 0.6882 (OUTLIER) cc_final: 0.6216 (pp30) REVERT: A 306 ARG cc_start: 0.6833 (tpt-90) cc_final: 0.6378 (ttt180) REVERT: A 363 LYS cc_start: 0.6891 (mmtp) cc_final: 0.6236 (mttp) REVERT: A 478 TRP cc_start: 0.7924 (m100) cc_final: 0.7632 (m100) REVERT: B 515 PHE cc_start: 0.6045 (OUTLIER) cc_final: 0.3447 (m-80) outliers start: 42 outliers final: 22 residues processed: 134 average time/residue: 0.9727 time to fit residues: 138.4385 Evaluate side-chains 120 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 95 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 64 optimal weight: 8.9990 chunk 52 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN A 345 HIS A 598 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6539 Z= 0.197 Angle : 0.528 14.138 8889 Z= 0.273 Chirality : 0.041 0.170 936 Planarity : 0.004 0.035 1146 Dihedral : 5.353 57.120 867 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 6.49 % Allowed : 24.63 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.61 (0.30), residues: 788 helix: 0.36 (0.27), residues: 393 sheet: 0.17 (0.97), residues: 36 loop : -1.30 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 163 HIS 0.003 0.001 HIS A 241 PHE 0.012 0.001 PHE B 515 TYR 0.015 0.001 TYR B 351 ARG 0.006 0.000 ARG A 531 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 101 time to evaluate : 2.174 Fit side-chains REVERT: A 62 MET cc_start: 0.7555 (ttt) cc_final: 0.7327 (ttp) REVERT: A 208 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7530 (tp30) REVERT: A 287 GLN cc_start: 0.6893 (OUTLIER) cc_final: 0.6185 (pp30) REVERT: A 306 ARG cc_start: 0.6819 (tpt-90) cc_final: 0.6379 (ttt180) REVERT: A 478 TRP cc_start: 0.7900 (m100) cc_final: 0.7605 (m100) REVERT: B 515 PHE cc_start: 0.5925 (OUTLIER) cc_final: 0.3475 (m-80) outliers start: 44 outliers final: 25 residues processed: 137 average time/residue: 0.9523 time to fit residues: 138.4903 Evaluate side-chains 126 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 98 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 598 GLN Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 75 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 0.4980 chunk 72 optimal weight: 0.3980 chunk 8 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN A 345 HIS ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 6539 Z= 0.157 Angle : 0.546 17.169 8889 Z= 0.278 Chirality : 0.040 0.173 936 Planarity : 0.004 0.036 1146 Dihedral : 5.164 57.608 867 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 6.19 % Allowed : 24.34 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.34 (0.30), residues: 788 helix: 0.59 (0.27), residues: 394 sheet: 0.15 (0.93), residues: 38 loop : -1.18 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 163 HIS 0.002 0.001 HIS A 374 PHE 0.013 0.001 PHE B 515 TYR 0.015 0.001 TYR A 516 ARG 0.006 0.000 ARG A 531 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 97 time to evaluate : 0.775 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.7535 (ttt) cc_final: 0.7315 (ttp) REVERT: A 208 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7500 (tp30) REVERT: A 287 GLN cc_start: 0.6883 (OUTLIER) cc_final: 0.6165 (pp30) REVERT: A 335 GLU cc_start: 0.6959 (OUTLIER) cc_final: 0.6704 (tt0) REVERT: A 478 TRP cc_start: 0.7868 (m100) cc_final: 0.7623 (m100) REVERT: A 603 PHE cc_start: 0.6315 (t80) cc_final: 0.6023 (t80) REVERT: B 515 PHE cc_start: 0.5974 (OUTLIER) cc_final: 0.3548 (m-80) outliers start: 42 outliers final: 21 residues processed: 132 average time/residue: 0.9178 time to fit residues: 129.2810 Evaluate side-chains 122 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 97 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.0980 chunk 42 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 47 optimal weight: 0.0170 chunk 45 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN A 345 HIS ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 6539 Z= 0.140 Angle : 0.541 16.611 8889 Z= 0.275 Chirality : 0.040 0.169 936 Planarity : 0.004 0.036 1146 Dihedral : 5.063 57.097 867 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.87 % Allowed : 26.40 % Favored : 68.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.31), residues: 788 helix: 0.82 (0.27), residues: 393 sheet: -0.05 (0.90), residues: 38 loop : -1.10 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 302 HIS 0.003 0.000 HIS A 374 PHE 0.013 0.001 PHE B 515 TYR 0.015 0.001 TYR A 516 ARG 0.007 0.000 ARG A 531 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 97 time to evaluate : 0.738 Fit side-chains REVERT: A 208 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7550 (tp30) REVERT: A 287 GLN cc_start: 0.6853 (OUTLIER) cc_final: 0.6139 (pp30) REVERT: A 478 TRP cc_start: 0.7840 (m100) cc_final: 0.7589 (m100) REVERT: A 603 PHE cc_start: 0.6313 (t80) cc_final: 0.6064 (t80) REVERT: B 406 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7598 (mt-10) REVERT: B 421 TYR cc_start: 0.7869 (m-10) cc_final: 0.7560 (m-10) REVERT: B 515 PHE cc_start: 0.5763 (OUTLIER) cc_final: 0.3355 (m-80) outliers start: 33 outliers final: 18 residues processed: 126 average time/residue: 0.9991 time to fit residues: 133.4379 Evaluate side-chains 113 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 7 optimal weight: 0.3980 chunk 59 optimal weight: 0.0870 chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 70 optimal weight: 0.0040 chunk 42 optimal weight: 1.9990 overall best weight: 0.6772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN A 345 HIS ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6539 Z= 0.155 Angle : 0.633 24.880 8889 Z= 0.319 Chirality : 0.042 0.258 936 Planarity : 0.003 0.037 1146 Dihedral : 4.554 56.770 864 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.87 % Allowed : 27.43 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 (0.31), residues: 788 helix: 0.87 (0.27), residues: 394 sheet: 0.28 (0.93), residues: 36 loop : -1.04 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 302 HIS 0.002 0.001 HIS A 241 PHE 0.013 0.001 PHE B 515 TYR 0.016 0.001 TYR A 516 ARG 0.003 0.000 ARG A 531 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 93 time to evaluate : 0.744 Fit side-chains revert: symmetry clash REVERT: A 208 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7534 (tp30) REVERT: A 343 VAL cc_start: 0.5430 (OUTLIER) cc_final: 0.5019 (m) REVERT: A 478 TRP cc_start: 0.7791 (m100) cc_final: 0.7511 (m100) REVERT: B 421 TYR cc_start: 0.7855 (m-10) cc_final: 0.7406 (m-10) REVERT: B 515 PHE cc_start: 0.5659 (OUTLIER) cc_final: 0.3135 (m-80) outliers start: 33 outliers final: 20 residues processed: 120 average time/residue: 0.9477 time to fit residues: 120.8912 Evaluate side-chains 112 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 89 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 516 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6539 Z= 0.165 Angle : 0.659 27.209 8889 Z= 0.328 Chirality : 0.042 0.320 936 Planarity : 0.004 0.038 1146 Dihedral : 4.534 56.594 864 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.87 % Allowed : 27.14 % Favored : 67.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.02 (0.31), residues: 788 helix: 0.86 (0.27), residues: 396 sheet: 0.48 (0.94), residues: 36 loop : -0.97 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 302 HIS 0.002 0.001 HIS A 241 PHE 0.012 0.001 PHE B 515 TYR 0.016 0.001 TYR A 516 ARG 0.006 0.000 ARG A 531 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 92 time to evaluate : 0.841 Fit side-chains revert: symmetry clash REVERT: A 208 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7513 (tp30) REVERT: A 343 VAL cc_start: 0.5546 (OUTLIER) cc_final: 0.5130 (m) REVERT: A 478 TRP cc_start: 0.7774 (m100) cc_final: 0.7475 (m100) REVERT: A 503 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8390 (tt) REVERT: A 598 GLN cc_start: 0.6765 (OUTLIER) cc_final: 0.5968 (tm-30) REVERT: B 421 TYR cc_start: 0.7890 (m-10) cc_final: 0.7398 (m-10) REVERT: B 515 PHE cc_start: 0.5728 (OUTLIER) cc_final: 0.3208 (m-80) outliers start: 33 outliers final: 18 residues processed: 122 average time/residue: 0.9967 time to fit residues: 128.9819 Evaluate side-chains 111 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 88 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 598 GLN Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 516 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 61 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6539 Z= 0.318 Angle : 0.730 27.606 8889 Z= 0.369 Chirality : 0.047 0.332 936 Planarity : 0.004 0.040 1146 Dihedral : 5.169 58.608 864 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 4.87 % Allowed : 27.43 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.44 (0.30), residues: 788 helix: 0.45 (0.27), residues: 393 sheet: -0.20 (0.80), residues: 46 loop : -1.12 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 302 HIS 0.005 0.001 HIS A 241 PHE 0.012 0.002 PHE B 515 TYR 0.025 0.002 TYR A 516 ARG 0.005 0.001 ARG A 531 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 91 time to evaluate : 0.730 Fit side-chains revert: symmetry clash REVERT: A 208 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7532 (tp30) REVERT: A 306 ARG cc_start: 0.6802 (tpt-90) cc_final: 0.6374 (ttt180) REVERT: A 478 TRP cc_start: 0.7871 (m100) cc_final: 0.7502 (m100) outliers start: 33 outliers final: 20 residues processed: 118 average time/residue: 0.9299 time to fit residues: 116.7593 Evaluate side-chains 109 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 88 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 516 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 0.0970 chunk 41 optimal weight: 0.0870 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN A 345 HIS B 501 ASN B 506 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.162796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.135095 restraints weight = 8670.167| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.05 r_work: 0.3511 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6539 Z= 0.154 Angle : 0.634 25.929 8889 Z= 0.319 Chirality : 0.042 0.343 936 Planarity : 0.004 0.039 1146 Dihedral : 4.643 57.266 864 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.10 % Allowed : 29.06 % Favored : 67.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.04 (0.31), residues: 788 helix: 0.80 (0.27), residues: 394 sheet: 0.02 (0.81), residues: 46 loop : -0.96 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 302 HIS 0.002 0.001 HIS A 374 PHE 0.016 0.001 PHE B 515 TYR 0.019 0.001 TYR A 50 ARG 0.005 0.000 ARG A 531 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2810.96 seconds wall clock time: 50 minutes 41.45 seconds (3041.45 seconds total)