Starting phenix.real_space_refine on Wed Nov 15 16:26:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c8d_30305/11_2023/7c8d_30305.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c8d_30305/11_2023/7c8d_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_30305/11_2023/7c8d_30305.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c8d_30305/11_2023/7c8d_30305.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c8d_30305/11_2023/7c8d_30305.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c8d_30305/11_2023/7c8d_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-1.21rc1-5144/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: 3.83, per 1000 atoms: 0.60 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: 2.50 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: 0.58 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: 1.58 Time building geometry restraints manager: 2.66 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: 0.260 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: 1.540 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 22.120 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:11.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.930 ------------------------------------------------------------------------------- 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 *********************** 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 : 0.763 Fit side-chains outliers start: 41 outliers final: 11 residues processed: 160 average time/residue: 1.1244 time to fit residues: 189.7975 Evaluate side-chains 105 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 0.731 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 0.0585 time to fit residues: 1.0371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 506 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.1392 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= 0.179 Angle : 0.530 14.903 8889 Z= 0.275 Chirality : 0.041 0.216 936 Planarity : 0.004 0.037 1146 Dihedral : 4.121 22.336 862 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.72 % Allowed : 24.19 % 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: -1.42 (0.29), residues: 788 helix: -0.31 (0.26), residues: 395 sheet: -0.23 (0.91), residues: 36 loop : -1.70 (0.31), residues: 357 *********************** 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 137 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 105 time to evaluate : 0.758 Fit side-chains outliers start: 32 outliers final: 19 residues processed: 132 average time/residue: 0.9304 time to fit residues: 130.7463 Evaluate side-chains 115 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 96 time to evaluate : 0.724 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 17 residues processed: 2 average time/residue: 0.8354 time to fit residues: 2.8033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.4980 chunk 48 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 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 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 HIS B 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6539 Z= 0.171 Angle : 0.513 14.030 8889 Z= 0.262 Chirality : 0.040 0.158 936 Planarity : 0.004 0.034 1146 Dihedral : 4.047 22.013 862 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 5.46 % Allowed : 25.52 % Favored : 69.03 % 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: -0.85 (0.30), residues: 788 helix: 0.14 (0.27), residues: 395 sheet: -0.10 (0.92), residues: 36 loop : -1.39 (0.32), residues: 357 *********************** 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 140 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 103 time to evaluate : 0.705 Fit side-chains outliers start: 37 outliers final: 24 residues processed: 135 average time/residue: 0.9030 time to fit residues: 130.2430 Evaluate side-chains 124 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 100 time to evaluate : 0.782 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 23 residues processed: 1 average time/residue: 0.0618 time to fit residues: 1.1678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.8980 chunk 7 optimal weight: 0.0030 chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 20 optimal weight: 0.0000 chunk 62 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- 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: 0.7389 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6539 Z= 0.164 Angle : 0.505 14.094 8889 Z= 0.259 Chirality : 0.040 0.167 936 Planarity : 0.003 0.034 1146 Dihedral : 4.014 21.689 862 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 6.19 % Allowed : 24.78 % Favored : 69.03 % 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: -0.59 (0.30), residues: 788 helix: 0.39 (0.27), residues: 395 sheet: -0.08 (0.94), residues: 36 loop : -1.28 (0.32), residues: 357 *********************** 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 139 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 97 time to evaluate : 0.695 Fit side-chains outliers start: 42 outliers final: 23 residues processed: 132 average time/residue: 0.9418 time to fit residues: 132.6756 Evaluate side-chains 115 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 92 time to evaluate : 0.707 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 22 residues processed: 1 average time/residue: 0.0584 time to fit residues: 1.1285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 0.4980 chunk 64 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 67 optimal weight: 0.0570 chunk 19 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.8902 ------------------------------------------------------------------------------- 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: 0.7395 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6539 Z= 0.171 Angle : 0.531 17.092 8889 Z= 0.274 Chirality : 0.040 0.170 936 Planarity : 0.003 0.033 1146 Dihedral : 4.177 24.461 862 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 5.75 % Allowed : 25.07 % Favored : 69.17 % 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: -0.43 (0.30), residues: 788 helix: 0.53 (0.27), residues: 394 sheet: -0.27 (0.93), residues: 36 loop : -1.18 (0.32), residues: 358 *********************** 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 130 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 91 time to evaluate : 0.762 Fit side-chains outliers start: 39 outliers final: 23 residues processed: 125 average time/residue: 0.8463 time to fit residues: 113.5134 Evaluate side-chains 113 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 90 time to evaluate : 0.734 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 22 residues processed: 1 average time/residue: 1.5080 time to fit residues: 2.6171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 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 290 ASN A 345 HIS B 506 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6539 Z= 0.176 Angle : 0.559 17.444 8889 Z= 0.283 Chirality : 0.041 0.173 936 Planarity : 0.003 0.034 1146 Dihedral : 4.202 24.055 862 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 6.34 % Allowed : 24.93 % 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: -0.31 (0.30), residues: 788 helix: 0.63 (0.27), residues: 393 sheet: -0.20 (0.89), residues: 38 loop : -1.12 (0.33), residues: 357 *********************** 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 132 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 89 time to evaluate : 0.791 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 24 residues processed: 125 average time/residue: 0.9502 time to fit residues: 126.5207 Evaluate side-chains 111 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 87 time to evaluate : 0.780 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 23 residues processed: 1 average time/residue: 0.9973 time to fit residues: 2.0070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.0070 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 46 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 overall best weight: 0.7000 ------------------------------------------------------------------------------- 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: 0.7379 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 6539 Z= 0.155 Angle : 0.551 16.675 8889 Z= 0.280 Chirality : 0.040 0.165 936 Planarity : 0.003 0.034 1146 Dihedral : 4.206 23.980 862 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 5.90 % Allowed : 25.22 % 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: -0.17 (0.30), residues: 788 helix: 0.76 (0.27), residues: 394 sheet: -0.22 (0.90), residues: 38 loop : -1.07 (0.33), residues: 356 *********************** 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 128 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 88 time to evaluate : 0.697 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 26 residues processed: 122 average time/residue: 0.9230 time to fit residues: 120.2629 Evaluate side-chains 113 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 87 time to evaluate : 0.743 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 25 residues processed: 1 average time/residue: 0.0635 time to fit residues: 1.1279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 72 optimal weight: 0.0000 chunk 65 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- 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: 0.7411 moved from start: 0.2152 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= 0.197 Angle : 0.654 25.439 8889 Z= 0.330 Chirality : 0.043 0.266 936 Planarity : 0.004 0.033 1146 Dihedral : 4.304 26.118 862 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 5.75 % Allowed : 25.81 % Favored : 68.44 % 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: -0.23 (0.30), residues: 788 helix: 0.70 (0.27), residues: 392 sheet: -0.44 (0.79), residues: 46 loop : -1.05 (0.33), residues: 350 *********************** 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 125 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 86 time to evaluate : 0.786 Fit side-chains revert: symmetry clash outliers start: 39 outliers final: 24 residues processed: 120 average time/residue: 0.8705 time to fit residues: 112.0036 Evaluate side-chains 108 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 84 time to evaluate : 0.812 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 0 time to fit residues: 1.0019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 63 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 46 optimal weight: 0.0030 chunk 74 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- 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: 0.7394 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6539 Z= 0.173 Angle : 0.663 26.545 8889 Z= 0.331 Chirality : 0.043 0.305 936 Planarity : 0.003 0.034 1146 Dihedral : 4.208 25.853 862 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.42 % Allowed : 26.99 % Favored : 68.58 % 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: -0.10 (0.31), residues: 788 helix: 0.78 (0.27), residues: 393 sheet: -0.26 (0.81), residues: 46 loop : -0.98 (0.33), residues: 349 *********************** 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 118 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 88 time to evaluate : 0.802 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 25 residues processed: 116 average time/residue: 0.9778 time to fit residues: 120.8251 Evaluate side-chains 107 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 82 time to evaluate : 0.695 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 25 residues processed: 0 time to fit residues: 0.9420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.7980 chunk 71 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 47 optimal weight: 0.3980 chunk 37 optimal weight: 0.0970 chunk 49 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 9 optimal weight: 0.0770 overall best weight: 0.4536 ------------------------------------------------------------------------------- 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: 0.7356 moved from start: 0.2456 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= 0.140 Angle : 0.631 26.644 8889 Z= 0.316 Chirality : 0.042 0.336 936 Planarity : 0.003 0.036 1146 Dihedral : 3.952 24.879 862 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.28 % Allowed : 28.02 % 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: 0.06 (0.31), residues: 788 helix: 0.92 (0.27), residues: 394 sheet: 0.67 (0.93), residues: 36 loop : -1.01 (0.33), residues: 358 ********************** 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 116 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 87 time to evaluate : 0.785 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 19 residues processed: 115 average time/residue: 0.9754 time to fit residues: 119.5507 Evaluate side-chains 103 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 84 time to evaluate : 0.763 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 19 residues processed: 0 time to fit residues: 1.0414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 63 optimal weight: 0.0030 chunk 7 optimal weight: 4.9990 chunk 11 optimal weight: 0.0870 chunk 54 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 41 optimal weight: 0.0050 overall best weight: 0.3582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.166074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.139082 restraints weight = 8681.198| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.02 r_work: 0.3548 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2608 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= 0.135 Angle : 0.591 19.718 8889 Z= 0.300 Chirality : 0.040 0.189 936 Planarity : 0.003 0.034 1146 Dihedral : 3.989 24.664 862 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.13 % Allowed : 28.47 % Favored : 67.40 % 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: 0.18 (0.31), residues: 788 helix: 1.04 (0.27), residues: 393 sheet: 0.44 (0.97), residues: 36 loop : -0.94 (0.33), residues: 359 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2782.02 seconds wall clock time: 52 minutes 32.03 seconds (3152.03 seconds total)