Starting phenix.real_space_refine (version: dev) on Fri Feb 17 22:16:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ddp_30653/02_2023/7ddp_30653.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ddp_30653/02_2023/7ddp_30653.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ddp_30653/02_2023/7ddp_30653.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ddp_30653/02_2023/7ddp_30653.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ddp_30653/02_2023/7ddp_30653.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ddp_30653/02_2023/7ddp_30653.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A GLU 35": "OE1" <-> "OE2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 115": "NH1" <-> "NH2" Residue "A GLU 145": "OE1" <-> "OE2" Residue "A GLU 150": "OE1" <-> "OE2" Residue "A TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A ARG 192": "NH1" <-> "NH2" Residue "A TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 213": "OD1" <-> "OD2" Residue "A TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 216": "OD1" <-> "OD2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A ASP 225": "OD1" <-> "OD2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A ARG 245": "NH1" <-> "NH2" Residue "A TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 329": "OE1" <-> "OE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 402": "OE1" <-> "OE2" Residue "A ASP 427": "OD1" <-> "OD2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 495": "OE1" <-> "OE2" Residue "A TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 509": "OD1" <-> "OD2" Residue "A TYR 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 518": "NH1" <-> "NH2" Residue "A GLU 536": "OE1" <-> "OE2" Residue "A ASP 597": "OD1" <-> "OD2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ASP 364": "OD1" <-> "OD2" Residue "C TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 389": "OD1" <-> "OD2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 405": "OD1" <-> "OD2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "C ASP 442": "OD1" <-> "OD2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 6477 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4877 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Conformer: "B" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} bond proxies already assigned to first conformer: 4998 Chain: "C" Number of atoms: 1529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1529 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.59, per 1000 atoms: 1.02 Number of scatterers: 6477 At special positions: 0 Unit cell: (102.356, 97.3875, 105.338, 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 37 16.00 O 1231 8.00 N 1065 7.00 C 4143 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=2.04 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 C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 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 Links applied NAG-ASN " NAG A 902 " - " ASN A 546 " " NAG A 903 " - " ASN A 90 " " NAG A 904 " - " ASN A 322 " " NAG A 905 " - " ASN A 53 " " NAG C 601 " - " ASN C 343 " Time building additional restraints: 2.63 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 901 " - 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: 1488 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 5 sheets defined 56.8% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 4.030A pdb=" N GLN A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 81 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 removed outlier: 3.596A pdb=" N GLU A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.529A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.806A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 157 through 194 removed outlier: 4.205A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 219 through 252 removed outlier: 4.122A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.775A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.623A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.708A 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 414 removed outlier: 3.557A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 447 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 512 through 532 removed outlier: 4.283A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 4.098A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.726A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.335A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 388 removed outlier: 3.680A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 506 Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.784A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.523A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 448 through 454 removed outlier: 5.328A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.540A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 310 hydrogen bonds defined for protein. 881 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: 1.80 Time building geometry restraints manager: 2.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2071 1.35 - 1.46: 1708 1.46 - 1.58: 2820 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6657 Sorted by residual: bond pdb=" N TYR C 489 " pdb=" CA TYR C 489 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.21e-02 6.83e+03 9.23e+00 bond pdb=" N PHE C 456 " pdb=" CA PHE C 456 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.23e-02 6.61e+03 6.41e+00 bond pdb=" C GLU A 145 " pdb=" N PRO A 146 " ideal model delta sigma weight residual 1.335 1.348 -0.013 9.40e-03 1.13e+04 1.84e+00 bond pdb=" CA TYR C 489 " pdb=" C TYR C 489 " ideal model delta sigma weight residual 1.521 1.535 -0.014 1.26e-02 6.30e+03 1.31e+00 bond pdb=" CA VAL C 524 " pdb=" CB VAL C 524 " ideal model delta sigma weight residual 1.533 1.546 -0.014 1.26e-02 6.30e+03 1.15e+00 ... (remaining 6652 not shown) Histogram of bond angle deviations from ideal: 99.84 - 106.67: 212 106.67 - 113.50: 3507 113.50 - 120.33: 2542 120.33 - 127.16: 2694 127.16 - 133.99: 95 Bond angle restraints: 9050 Sorted by residual: angle pdb=" N VAL A 318 " pdb=" CA VAL A 318 " pdb=" C VAL A 318 " ideal model delta sigma weight residual 112.80 109.72 3.08 1.15e+00 7.56e-01 7.19e+00 angle pdb=" C LEU A 144 " pdb=" N GLU A 145 " pdb=" CA GLU A 145 " ideal model delta sigma weight residual 120.44 123.89 -3.45 1.30e+00 5.92e-01 7.05e+00 angle pdb=" N CYS C 432 " pdb=" CA CYS C 432 " pdb=" C CYS C 432 " ideal model delta sigma weight residual 108.38 111.77 -3.39 1.35e+00 5.49e-01 6.29e+00 angle pdb=" CA CYS C 432 " pdb=" CB CYS C 432 " pdb=" SG CYS C 432 " ideal model delta sigma weight residual 114.40 119.69 -5.29 2.30e+00 1.89e-01 5.28e+00 angle pdb=" N ILE A 421 " pdb=" CA ILE A 421 " pdb=" C ILE A 421 " ideal model delta sigma weight residual 112.98 110.18 2.80 1.25e+00 6.40e-01 5.03e+00 ... (remaining 9045 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 3536 17.97 - 35.94: 310 35.94 - 53.91: 49 53.91 - 71.88: 12 71.88 - 89.85: 11 Dihedral angle restraints: 3918 sinusoidal: 1596 harmonic: 2322 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 93.00 8.59 84.41 1 1.00e+01 1.00e-02 8.67e+01 dihedral pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " pdb=" SG CYS C 432 " pdb=" CB CYS C 432 " ideal model delta sinusoidal sigma weight residual 93.00 15.94 77.06 1 1.00e+01 1.00e-02 7.45e+01 dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " pdb=" CB CYS C 525 " ideal model delta sinusoidal sigma weight residual 93.00 23.03 69.97 1 1.00e+01 1.00e-02 6.31e+01 ... (remaining 3915 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 588 0.029 - 0.058: 255 0.058 - 0.087: 72 0.087 - 0.115: 46 0.115 - 0.144: 4 Chirality restraints: 965 Sorted by residual: chirality pdb=" CA PHE C 456 " pdb=" N PHE C 456 " pdb=" C PHE C 456 " pdb=" CB PHE C 456 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" CA ILE A 468 " pdb=" N ILE A 468 " pdb=" C ILE A 468 " pdb=" CB ILE A 468 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 chirality pdb=" CA PRO A 253 " pdb=" N PRO A 253 " pdb=" C PRO A 253 " pdb=" CB PRO A 253 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.40e-01 ... (remaining 962 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS C 488 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C CYS C 488 " -0.043 2.00e-02 2.50e+03 pdb=" O CYS C 488 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR C 489 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 499 " 0.024 5.00e-02 4.00e+02 3.62e-02 2.10e+00 pdb=" N PRO A 500 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 500 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 500 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 582 " 0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO A 583 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " 0.020 5.00e-02 4.00e+02 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 103 2.66 - 3.22: 6014 3.22 - 3.78: 10236 3.78 - 4.34: 14322 4.34 - 4.90: 23151 Nonbonded interactions: 53826 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 901 " model vdw 2.100 2.230 nonbonded pdb=" OH TYR A 237 " pdb=" O VAL A 485 " model vdw 2.176 2.440 nonbonded pdb=" OD1 ASP C 442 " pdb=" OH TYR C 451 " model vdw 2.236 2.440 nonbonded pdb=" O SER A 254 " pdb=" OG SER A 254 " model vdw 2.241 2.440 nonbonded pdb=" NH1 ARG A 177 " pdb=" O GLU A 495 " model vdw 2.302 2.520 ... (remaining 53821 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 C 4143 2.51 5 N 1065 2.21 5 O 1231 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.570 Check model and map are aligned: 0.100 Process input model: 27.120 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.060 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 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 0.037 6657 Z= 0.164 Angle : 0.538 7.087 9050 Z= 0.307 Chirality : 0.039 0.144 965 Planarity : 0.003 0.036 1165 Dihedral : 14.117 89.849 2409 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.27), residues: 788 helix: -0.20 (0.24), residues: 395 sheet: -2.05 (0.62), residues: 56 loop : -1.70 (0.29), residues: 337 *********************** 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 128 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 126 time to evaluate : 0.784 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 128 average time/residue: 0.2057 time to fit residues: 34.8518 Evaluate side-chains 98 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 0.759 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0868 time to fit residues: 1.2109 ------------------------------------------------------------------------------- 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: 10.0000 chunk 59 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 70 optimal weight: 7.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 6657 Z= 0.269 Angle : 0.582 7.025 9050 Z= 0.296 Chirality : 0.042 0.138 965 Planarity : 0.004 0.031 1165 Dihedral : 4.298 16.891 890 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer Outliers : 2.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.28), residues: 788 helix: 0.60 (0.25), residues: 402 sheet: -1.71 (0.60), residues: 60 loop : -1.25 (0.31), residues: 326 *********************** 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 115 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 101 time to evaluate : 0.751 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 110 average time/residue: 0.2005 time to fit residues: 29.5699 Evaluate side-chains 97 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 0.778 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0694 time to fit residues: 1.8194 ------------------------------------------------------------------------------- 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: 0.4980 chunk 21 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 19 optimal weight: 0.3980 chunk 70 optimal weight: 7.9990 chunk 76 optimal weight: 0.5980 chunk 63 optimal weight: 0.2980 chunk 24 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 6657 Z= 0.136 Angle : 0.508 7.084 9050 Z= 0.256 Chirality : 0.039 0.136 965 Planarity : 0.003 0.027 1165 Dihedral : 3.913 15.195 890 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.29), residues: 788 helix: 1.28 (0.26), residues: 399 sheet: -1.74 (0.61), residues: 58 loop : -0.83 (0.33), residues: 331 *********************** 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 113 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 101 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 109 average time/residue: 0.2097 time to fit residues: 30.9444 Evaluate side-chains 103 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 0.770 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0634 time to fit residues: 1.9861 ------------------------------------------------------------------------------- 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: 5.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 6657 Z= 0.211 Angle : 0.543 8.875 9050 Z= 0.274 Chirality : 0.041 0.136 965 Planarity : 0.003 0.029 1165 Dihedral : 4.120 15.779 890 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 1.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.30), residues: 788 helix: 1.30 (0.26), residues: 401 sheet: -1.67 (0.64), residues: 58 loop : -0.74 (0.33), residues: 329 *********************** 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 110 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 100 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 107 average time/residue: 0.1797 time to fit residues: 26.0733 Evaluate side-chains 100 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 96 time to evaluate : 0.889 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0687 time to fit residues: 1.4724 ------------------------------------------------------------------------------- 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: 2.9990 chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 64 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 38 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 6657 Z= 0.155 Angle : 0.513 8.940 9050 Z= 0.259 Chirality : 0.039 0.131 965 Planarity : 0.003 0.027 1165 Dihedral : 3.941 15.384 890 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.30), residues: 788 helix: 1.44 (0.26), residues: 402 sheet: -1.63 (0.67), residues: 58 loop : -0.63 (0.34), residues: 328 *********************** 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 101 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 94 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 100 average time/residue: 0.1912 time to fit residues: 26.2131 Evaluate side-chains 97 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 94 time to evaluate : 0.729 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0676 time to fit residues: 1.4689 ------------------------------------------------------------------------------- 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: 4.9990 chunk 18 optimal weight: 0.9980 chunk 75 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 39 optimal weight: 0.7980 chunk 72 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 6657 Z= 0.200 Angle : 0.538 9.062 9050 Z= 0.271 Chirality : 0.040 0.128 965 Planarity : 0.003 0.028 1165 Dihedral : 4.057 15.639 890 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 1.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.30), residues: 788 helix: 1.39 (0.26), residues: 402 sheet: -1.51 (0.69), residues: 58 loop : -0.60 (0.34), residues: 328 *********************** 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 103 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 0.906 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 101 average time/residue: 0.2145 time to fit residues: 29.5301 Evaluate side-chains 98 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 0.900 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0632 time to fit residues: 2.1455 ------------------------------------------------------------------------------- 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: 0.6980 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 0.3980 chunk 75 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 34 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 6657 Z= 0.143 Angle : 0.502 8.763 9050 Z= 0.253 Chirality : 0.040 0.129 965 Planarity : 0.003 0.025 1165 Dihedral : 3.911 15.451 890 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.30), residues: 788 helix: 1.59 (0.26), residues: 403 sheet: -1.34 (0.69), residues: 58 loop : -0.58 (0.34), residues: 327 *********************** 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 104 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 98 time to evaluate : 0.707 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 101 average time/residue: 0.2138 time to fit residues: 28.5523 Evaluate side-chains 93 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 0.774 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0745 time to fit residues: 1.4570 ------------------------------------------------------------------------------- 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: 2.9990 chunk 47 optimal weight: 0.8980 chunk 51 optimal weight: 9.9990 chunk 37 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 68 optimal weight: 9.9990 chunk 72 optimal weight: 0.6980 chunk 65 optimal weight: 10.0000 chunk 70 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 6657 Z= 0.176 Angle : 0.525 8.548 9050 Z= 0.263 Chirality : 0.040 0.129 965 Planarity : 0.003 0.026 1165 Dihedral : 3.989 15.179 890 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.30), residues: 788 helix: 1.57 (0.26), residues: 403 sheet: -1.30 (0.70), residues: 58 loop : -0.53 (0.35), residues: 327 *********************** 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 92 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 0.822 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 91 average time/residue: 0.2121 time to fit residues: 25.6632 Evaluate side-chains 91 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 90 time to evaluate : 0.767 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0650 time to fit residues: 1.1862 ------------------------------------------------------------------------------- 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: 0.6980 chunk 55 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 6657 Z= 0.167 Angle : 0.521 8.500 9050 Z= 0.261 Chirality : 0.040 0.129 965 Planarity : 0.003 0.025 1165 Dihedral : 3.953 15.128 890 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.30), residues: 788 helix: 1.61 (0.26), residues: 403 sheet: -1.35 (0.68), residues: 58 loop : -0.47 (0.35), residues: 327 *********************** 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 90 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.729 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.2158 time to fit residues: 25.9333 Evaluate side-chains 90 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.761 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0548 ------------------------------------------------------------------------------- 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: 20.0000 chunk 71 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 9 optimal weight: 0.0870 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 6657 Z= 0.141 Angle : 0.503 8.458 9050 Z= 0.252 Chirality : 0.039 0.130 965 Planarity : 0.003 0.028 1165 Dihedral : 3.841 14.860 890 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.31), residues: 788 helix: 1.72 (0.26), residues: 403 sheet: -1.26 (0.67), residues: 58 loop : -0.37 (0.36), residues: 327 ********************** 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 94 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 0.799 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 94 average time/residue: 0.2016 time to fit residues: 25.6691 Evaluate side-chains 92 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 90 time to evaluate : 0.797 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0739 time to fit residues: 1.4039 ------------------------------------------------------------------------------- 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: 1.9990 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 0.0010 chunk 63 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 54 optimal weight: 0.0570 chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 41 optimal weight: 0.0570 overall best weight: 0.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.157241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.124548 restraints weight = 12670.603| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.42 r_work: 0.3127 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3734 r_free = 0.3734 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3734 r_free = 0.3734 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 6657 Z= 0.134 Angle : 0.497 8.407 9050 Z= 0.248 Chirality : 0.039 0.130 965 Planarity : 0.003 0.026 1165 Dihedral : 3.778 14.362 890 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.31), residues: 788 helix: 1.80 (0.26), residues: 403 sheet: -1.16 (0.67), residues: 58 loop : -0.34 (0.36), residues: 327 =============================================================================== Job complete usr+sys time: 1656.00 seconds wall clock time: 30 minutes 57.03 seconds (1857.03 seconds total)