Starting phenix.real_space_refine on Sun Aug 4 18:45:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c8d_30305/08_2024/7c8d_30305.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c8d_30305/08_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_30305/08_2024/7c8d_30305.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c8d_30305/08_2024/7c8d_30305.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c8d_30305/08_2024/7c8d_30305.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c8d_30305/08_2024/7c8d_30305.cif" } 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 4.14, per 1000 atoms: 0.65 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: 2.53 Conformation dependent library (CDL) restraints added in 1.1 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: 0.72 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: 1.65 Time building geometry restraints manager: 2.78 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 3.040 nonbonded pdb=" OH TYR A 41 " pdb=" OG1 THR B 500 " model vdw 2.188 3.040 nonbonded pdb=" NH1 ARG A 177 " pdb=" O GLU A 495 " model vdw 2.196 3.120 nonbonded pdb=" OH TYR A 183 " pdb=" OD1 ASP A 509 " model vdw 2.217 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.830 Find NCS groups from input model: 0.060 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:11.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.150 ------------------------------------------------------------------------------- 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 : 0.698 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: 1.0375 time to fit residues: 175.0668 Evaluate side-chains 107 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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: 8.9990 chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 0.0970 chunk 20 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 322 ASN A 345 HIS A 416 ASN A 598 GLN B 354 ASN B 360 ASN B 501 ASN B 506 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6539 Z= 0.197 Angle : 0.552 15.200 8889 Z= 0.287 Chirality : 0.042 0.208 936 Planarity : 0.004 0.042 1146 Dihedral : 5.587 57.549 876 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.98 % Allowed : 23.45 % Favored : 72.57 % 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: -1.45 (0.29), residues: 788 helix: -0.35 (0.26), residues: 395 sheet: -0.19 (0.92), residues: 36 loop : -1.71 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 163 HIS 0.003 0.001 HIS A 345 PHE 0.007 0.001 PHE A 315 TYR 0.016 0.001 TYR B 351 ARG 0.003 0.000 ARG A 306 *********************** 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 131 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 104 time to evaluate : 0.736 Fit side-chains REVERT: A 62 MET cc_start: 0.7537 (ttt) cc_final: 0.7286 (ttp) REVERT: A 287 GLN cc_start: 0.6885 (OUTLIER) cc_final: 0.6216 (pp30) REVERT: A 363 LYS cc_start: 0.6844 (mmtp) cc_final: 0.6320 (mttp) REVERT: A 503 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8411 (tt) REVERT: A 579 MET cc_start: 0.8231 (ttm) cc_final: 0.7975 (ttm) REVERT: A 603 PHE cc_start: 0.6502 (t80) cc_final: 0.6202 (t80) REVERT: B 493 GLN cc_start: 0.5801 (tm-30) cc_final: 0.5584 (tm130) outliers start: 27 outliers final: 10 residues processed: 127 average time/residue: 0.9582 time to fit residues: 129.2254 Evaluate side-chains 103 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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 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 B residue 379 CYS Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 444 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 58 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 53 optimal weight: 0.0870 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS B 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6539 Z= 0.169 Angle : 0.522 14.286 8889 Z= 0.267 Chirality : 0.040 0.169 936 Planarity : 0.004 0.035 1146 Dihedral : 5.201 59.169 867 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.42 % Allowed : 23.89 % Favored : 71.68 % 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: -0.86 (0.30), residues: 788 helix: 0.15 (0.27), residues: 394 sheet: -0.10 (0.94), residues: 36 loop : -1.40 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 163 HIS 0.002 0.001 HIS A 241 PHE 0.012 0.001 PHE B 515 TYR 0.014 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 137 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 107 time to evaluate : 0.688 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.7480 (ttt) cc_final: 0.7230 (ttp) REVERT: A 287 GLN cc_start: 0.6884 (OUTLIER) cc_final: 0.6201 (pp30) REVERT: A 306 ARG cc_start: 0.6819 (tpt-90) cc_final: 0.6309 (ttt180) REVERT: A 363 LYS cc_start: 0.6805 (mmtp) cc_final: 0.6266 (mttp) REVERT: A 478 TRP cc_start: 0.7883 (m100) cc_final: 0.7596 (m100) REVERT: A 603 PHE cc_start: 0.6470 (t80) cc_final: 0.6221 (t80) REVERT: B 515 PHE cc_start: 0.5906 (OUTLIER) cc_final: 0.3547 (m-80) outliers start: 30 outliers final: 15 residues processed: 130 average time/residue: 0.9646 time to fit residues: 132.8414 Evaluate side-chains 115 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 98 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 287 GLN Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 334 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 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: 4.9990 chunk 71 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN A 345 HIS A 598 GLN B 493 GLN B 506 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 6539 Z= 0.311 Angle : 0.603 14.396 8889 Z= 0.315 Chirality : 0.044 0.177 936 Planarity : 0.005 0.067 1146 Dihedral : 5.757 57.767 867 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 6.05 % Allowed : 22.42 % Favored : 71.53 % 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: -0.93 (0.30), residues: 788 helix: 0.04 (0.26), residues: 394 sheet: -0.02 (0.98), residues: 36 loop : -1.39 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.013 0.002 PHE A 308 TYR 0.019 0.002 TYR A 516 ARG 0.010 0.001 ARG B 454 *********************** 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 137 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 96 time to evaluate : 0.748 Fit side-chains REVERT: A 208 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7450 (tp30) REVERT: A 249 MET cc_start: 0.6925 (OUTLIER) cc_final: 0.6517 (mtm) REVERT: A 287 GLN cc_start: 0.6917 (OUTLIER) cc_final: 0.6309 (pp30) REVERT: A 306 ARG cc_start: 0.6837 (tpt-90) cc_final: 0.6366 (ttt180) REVERT: A 363 LYS cc_start: 0.6959 (mmtp) cc_final: 0.6318 (mttp) REVERT: B 405 ASP cc_start: 0.8258 (p0) cc_final: 0.8046 (p0) outliers start: 41 outliers final: 21 residues processed: 128 average time/residue: 0.9013 time to fit residues: 123.0495 Evaluate side-chains 121 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 97 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 249 MET 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 334 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 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 469 SER 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: 0.6980 chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 64 optimal weight: 0.0070 chunk 52 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS A 598 GLN B 493 GLN B 506 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6539 Z= 0.167 Angle : 0.532 14.098 8889 Z= 0.272 Chirality : 0.040 0.166 936 Planarity : 0.004 0.043 1146 Dihedral : 5.471 58.379 867 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.87 % Allowed : 23.75 % Favored : 71.39 % 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: -0.60 (0.30), residues: 788 helix: 0.38 (0.27), residues: 393 sheet: 0.17 (0.98), residues: 36 loop : -1.31 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.002 0.001 HIS A 374 PHE 0.017 0.001 PHE B 515 TYR 0.017 0.001 TYR B 351 ARG 0.006 0.000 ARG B 454 *********************** 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 133 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 100 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.7561 (ttt) cc_final: 0.7340 (ttp) REVERT: A 287 GLN cc_start: 0.6926 (OUTLIER) cc_final: 0.6231 (pp30) REVERT: A 306 ARG cc_start: 0.6794 (tpt-90) cc_final: 0.6342 (ttt180) REVERT: A 478 TRP cc_start: 0.7890 (m100) cc_final: 0.7619 (m100) REVERT: B 515 PHE cc_start: 0.5726 (OUTLIER) cc_final: 0.3050 (m-80) outliers start: 33 outliers final: 14 residues processed: 128 average time/residue: 0.9809 time to fit residues: 133.1604 Evaluate side-chains 109 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 93 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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 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 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 A residue 598 GLN Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 399 SER 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: 0.8980 chunk 75 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 0.0770 chunk 6 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 493 GLN B 506 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6539 Z= 0.156 Angle : 0.559 17.213 8889 Z= 0.287 Chirality : 0.040 0.167 936 Planarity : 0.004 0.035 1146 Dihedral : 5.318 58.988 867 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.28 % Allowed : 24.19 % Favored : 71.53 % 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: -0.35 (0.30), residues: 788 helix: 0.60 (0.27), residues: 393 sheet: 0.11 (0.94), residues: 38 loop : -1.20 (0.32), 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 0.017 0.001 PHE B 515 TYR 0.014 0.001 TYR B 351 ARG 0.008 0.000 ARG B 454 *********************** 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 123 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 94 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.7539 (ttt) cc_final: 0.7323 (ttp) REVERT: A 287 GLN cc_start: 0.6882 (OUTLIER) cc_final: 0.6155 (pp30) REVERT: A 478 TRP cc_start: 0.7866 (m100) cc_final: 0.7547 (m100) REVERT: B 515 PHE cc_start: 0.5653 (OUTLIER) cc_final: 0.2939 (m-80) outliers start: 29 outliers final: 15 residues processed: 119 average time/residue: 0.8970 time to fit residues: 114.0875 Evaluate side-chains 113 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 0.795 ------------------------------------------------------------------------------- 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 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 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 A residue 598 GLN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 471 GLU 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: 0.3980 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 506 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6539 Z= 0.251 Angle : 0.606 15.430 8889 Z= 0.316 Chirality : 0.044 0.277 936 Planarity : 0.004 0.051 1146 Dihedral : 5.489 57.587 867 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.98 % Allowed : 25.37 % Favored : 70.65 % 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: -0.55 (0.30), residues: 788 helix: 0.43 (0.27), residues: 393 sheet: -0.43 (0.84), residues: 46 loop : -1.23 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 302 HIS 0.004 0.001 HIS A 241 PHE 0.016 0.001 PHE B 515 TYR 0.017 0.002 TYR A 183 ARG 0.008 0.001 ARG B 454 *********************** 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 125 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 98 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.7586 (ttt) cc_final: 0.7306 (ttp) REVERT: A 287 GLN cc_start: 0.6904 (OUTLIER) cc_final: 0.6183 (pp30) REVERT: A 335 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6587 (tt0) REVERT: A 411 SER cc_start: 0.8074 (OUTLIER) cc_final: 0.7873 (m) REVERT: A 478 TRP cc_start: 0.7844 (m100) cc_final: 0.7515 (m100) REVERT: A 503 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8453 (tt) REVERT: B 457 ARG cc_start: 0.6409 (ttp80) cc_final: 0.6202 (ttp80) REVERT: B 515 PHE cc_start: 0.5911 (OUTLIER) cc_final: 0.3222 (m-80) outliers start: 27 outliers final: 15 residues processed: 121 average time/residue: 0.8997 time to fit residues: 116.1365 Evaluate side-chains 113 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 93 time to evaluate : 0.778 ------------------------------------------------------------------------------- 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 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 335 GLU 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 503 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 598 GLN Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 516 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS A 598 GLN B 506 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2293 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= 0.193 Angle : 0.570 13.873 8889 Z= 0.296 Chirality : 0.042 0.275 936 Planarity : 0.004 0.042 1146 Dihedral : 5.316 57.428 867 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.42 % Allowed : 24.93 % Favored : 70.65 % 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: -0.38 (0.30), residues: 788 helix: 0.57 (0.27), residues: 393 sheet: -0.25 (0.83), residues: 46 loop : -1.18 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 302 HIS 0.003 0.001 HIS A 241 PHE 0.017 0.001 PHE A 308 TYR 0.015 0.002 TYR A 183 ARG 0.007 0.000 ARG B 454 *********************** 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 127 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 97 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 287 GLN cc_start: 0.6891 (OUTLIER) cc_final: 0.6159 (pp30) REVERT: A 478 TRP cc_start: 0.7854 (m100) cc_final: 0.7586 (m100) REVERT: B 515 PHE cc_start: 0.5921 (OUTLIER) cc_final: 0.3215 (m-80) outliers start: 30 outliers final: 17 residues processed: 122 average time/residue: 0.9202 time to fit residues: 120.2515 Evaluate side-chains 108 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 89 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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 142 LEU 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 334 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 A residue 567 THR Chi-restraints excluded: chain A residue 598 GLN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 471 GLU 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: 3.9990 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 46 optimal weight: 0.1980 chunk 74 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS A 598 GLN B 506 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6539 Z= 0.158 Angle : 0.648 26.466 8889 Z= 0.327 Chirality : 0.043 0.331 936 Planarity : 0.004 0.036 1146 Dihedral : 5.069 57.607 867 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.39 % Allowed : 25.81 % Favored : 70.80 % 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: -0.14 (0.31), residues: 788 helix: 0.79 (0.27), residues: 393 sheet: -0.19 (0.82), residues: 46 loop : -1.07 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 302 HIS 0.002 0.001 HIS A 374 PHE 0.019 0.001 PHE A 308 TYR 0.020 0.001 TYR A 183 ARG 0.007 0.000 ARG B 454 *********************** 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 120 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 97 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 287 GLN cc_start: 0.6903 (OUTLIER) cc_final: 0.6167 (pp30) REVERT: A 411 SER cc_start: 0.8052 (OUTLIER) cc_final: 0.7851 (m) REVERT: A 478 TRP cc_start: 0.7817 (m100) cc_final: 0.7526 (m100) REVERT: A 516 TYR cc_start: 0.8501 (t80) cc_final: 0.7773 (t80) REVERT: B 515 PHE cc_start: 0.5864 (OUTLIER) cc_final: 0.3170 (m-80) outliers start: 23 outliers final: 14 residues processed: 115 average time/residue: 0.9098 time to fit residues: 111.3907 Evaluate side-chains 105 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 88 time to evaluate : 0.722 ------------------------------------------------------------------------------- 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 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 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 598 GLN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 471 GLU 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: 6.9990 chunk 71 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 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 345 HIS A 598 GLN B 506 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6539 Z= 0.205 Angle : 0.655 25.176 8889 Z= 0.334 Chirality : 0.044 0.358 936 Planarity : 0.004 0.043 1146 Dihedral : 5.073 57.740 866 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.54 % Allowed : 26.11 % Favored : 70.35 % 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: -0.19 (0.30), residues: 788 helix: 0.73 (0.27), residues: 393 sheet: -0.13 (0.81), residues: 46 loop : -1.07 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 302 HIS 0.003 0.001 HIS A 241 PHE 0.019 0.001 PHE A 308 TYR 0.020 0.002 TYR A 183 ARG 0.007 0.001 ARG B 454 ********************** 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 118 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 94 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7433 (tp30) REVERT: A 287 GLN cc_start: 0.6925 (OUTLIER) cc_final: 0.6165 (pp30) REVERT: A 411 SER cc_start: 0.8067 (OUTLIER) cc_final: 0.7838 (m) REVERT: A 478 TRP cc_start: 0.7821 (m100) cc_final: 0.7506 (m100) REVERT: B 515 PHE cc_start: 0.5973 (OUTLIER) cc_final: 0.3241 (m-80) outliers start: 24 outliers final: 15 residues processed: 111 average time/residue: 0.9707 time to fit residues: 115.0427 Evaluate side-chains 108 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 89 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 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 318 VAL Chi-restraints excluded: chain A residue 334 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 598 GLN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 471 GLU 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.1741 > 50: distance: 26 - 30: 33.815 distance: 30 - 31: 44.134 distance: 31 - 32: 20.508 distance: 31 - 34: 17.988 distance: 32 - 33: 36.892 distance: 32 - 35: 40.468 distance: 35 - 36: 41.374 distance: 36 - 37: 7.559 distance: 37 - 38: 7.591 distance: 37 - 41: 49.813 distance: 39 - 40: 58.009 distance: 41 - 42: 12.867 distance: 42 - 43: 69.528 distance: 42 - 45: 39.739 distance: 43 - 52: 12.152 distance: 46 - 47: 28.622 distance: 46 - 48: 41.650 distance: 47 - 49: 52.481 distance: 48 - 50: 26.279 distance: 49 - 51: 33.718 distance: 50 - 51: 39.093 distance: 52 - 53: 62.074 distance: 54 - 55: 57.426 distance: 54 - 58: 56.927 distance: 58 - 168: 35.082 distance: 60 - 61: 43.787 distance: 61 - 165: 27.321 distance: 65 - 66: 22.462 distance: 66 - 67: 21.912 distance: 66 - 69: 45.707 distance: 67 - 68: 42.616 distance: 67 - 76: 26.535 distance: 69 - 70: 5.436 distance: 70 - 71: 45.415 distance: 70 - 72: 18.881 distance: 71 - 73: 39.313 distance: 72 - 74: 9.494 distance: 73 - 75: 29.562 distance: 74 - 75: 17.935 distance: 76 - 77: 24.507 distance: 76 - 154: 30.693 distance: 77 - 78: 42.183 distance: 77 - 80: 16.821 distance: 78 - 79: 39.549 distance: 78 - 85: 67.301 distance: 79 - 151: 31.025 distance: 80 - 81: 62.485 distance: 81 - 82: 49.452 distance: 82 - 83: 56.712 distance: 83 - 84: 64.266 distance: 86 - 89: 52.922 distance: 87 - 88: 4.313 distance: 87 - 91: 40.280 distance: 89 - 90: 37.395 distance: 90 - 150: 34.576 distance: 91 - 92: 21.226 distance: 91 - 144: 33.511 distance: 92 - 93: 18.147 distance: 92 - 95: 43.536 distance: 93 - 94: 22.812 distance: 93 - 103: 38.805 distance: 94 - 141: 27.121 distance: 95 - 96: 35.145 distance: 96 - 97: 33.370 distance: 96 - 98: 33.996 distance: 97 - 99: 38.698 distance: 98 - 100: 25.445 distance: 99 - 101: 40.944 distance: 100 - 101: 16.103 distance: 101 - 102: 6.132 distance: 103 - 104: 55.942 distance: 104 - 105: 24.002 distance: 105 - 106: 18.709 distance: 105 - 107: 25.186