Starting phenix.real_space_refine on Tue Feb 13 11:29:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpz_32693/02_2024/7wpz_32693.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpz_32693/02_2024/7wpz_32693.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpz_32693/02_2024/7wpz_32693.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpz_32693/02_2024/7wpz_32693.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpz_32693/02_2024/7wpz_32693.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpz_32693/02_2024/7wpz_32693.pdb" } resolution = 3.8 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 3672 2.51 5 N 1016 2.21 5 O 1037 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 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 161": "NH1" <-> "NH2" Residue "A TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 460": "NH1" <-> "NH2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 559": "OE1" <-> "OE2" Residue "A TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 467": "NH1" <-> "NH2" Residue "B TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 522": "NH1" <-> "NH2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 551": "NH1" <-> "NH2" Residue "B ARG 554": "NH1" <-> "NH2" Residue "B TYR 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 5756 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4361 Classifications: {'peptide': 595} Incomplete info: {'truncation_to_alanine': 186} Link IDs: {'PTRANS': 24, 'TRANS': 570} Unresolved non-hydrogen bonds: 531 Unresolved non-hydrogen angles: 671 Unresolved non-hydrogen dihedrals: 401 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 23, 'GLU:plan': 36} Unresolved non-hydrogen planarities: 284 Chain: "B" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1194 Classifications: {'peptide': 192} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PTRANS': 11, 'TRANS': 180} Chain breaks: 3 Unresolved non-hydrogen bonds: 341 Unresolved non-hydrogen angles: 441 Unresolved non-hydrogen dihedrals: 265 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 8, 'ASP:plan': 7, 'PHE:plan': 5, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 159 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.85, per 1000 atoms: 0.67 Number of scatterers: 5756 At special positions: 0 Unit cell: (88.56, 94.3, 117.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 1037 8.00 N 1016 7.00 C 3672 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 142 " distance=2.20 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.11 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 411 " distance=2.08 Simple disulfide: pdb=" SG CYS B 441 " - pdb=" SG CYS B 583 " distance=2.07 Simple disulfide: pdb=" SG CYS B 506 " - pdb=" SG CYS B 527 " distance=2.02 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 ALPHA1-3 " BMA C 3 " - " MAN C 4 " ALPHA1-6 " BMA C 3 " - " MAN C 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 701 " - " ASN A 329 " " NAG A 702 " - " ASN A 546 " " NAG A 703 " - " ASN A 91 " " NAG B 601 " - " ASN B 489 " " NAG C 1 " - " ASN A 54 " " NAG D 1 " - " ASN A 104 " " NAG E 1 " - " ASN A 280 " " NAG J 1 " - " ASN A 432 " Time building additional restraints: 2.45 Conformation dependent library (CDL) restraints added in 1.2 seconds 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1486 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 6 sheets defined 58.7% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 21 through 53 Processing helix chain 'A' and resid 56 through 82 removed outlier: 4.082A pdb=" N GLN A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN A 64 " --> pdb=" O ALA A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 102 Processing helix chain 'A' and resid 110 through 130 Processing helix chain 'A' and resid 145 through 153 Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.911A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 4.756A 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 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 218 through 252 removed outlier: 3.824A pdb=" N MET A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.994A pdb=" N ASN A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) 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 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.500A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 385 removed outlier: 4.473A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (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 397 through 414 removed outlier: 3.599A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.706A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 485 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 534 removed outlier: 3.531A pdb=" N PHE A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.855A pdb=" N ILE 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 600 Processing helix chain 'A' and resid 610 through 615 removed outlier: 4.072A pdb=" N GLN A 615 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 393 Processing helix chain 'B' and resid 417 through 422 removed outlier: 3.657A pdb=" N VAL B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 438 Processing helix chain 'B' and resid 453 through 460 removed outlier: 4.424A pdb=" N SER B 458 " --> pdb=" O ALA B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 471 Processing helix chain 'B' and resid 524 through 533 Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 134 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.365A 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 347 through 350 Processing sheet with id=AA4, first strand: chain 'B' and resid 404 through 408 removed outlier: 3.561A pdb=" N LYS B 404 " --> pdb=" O TRP B 449 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N HIS B 485 " --> pdb=" O ASP B 425 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 411 through 412 removed outlier: 6.101A pdb=" N CYS B 411 " --> pdb=" O CYS B 583 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 513 through 514 removed outlier: 6.607A pdb=" N SER B 553 " --> pdb=" O THR B 504 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N CYS B 506 " --> pdb=" O ARG B 551 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ARG B 551 " --> pdb=" O CYS B 506 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TYR B 508 " --> pdb=" O PRO B 549 " (cutoff:3.500A) 334 hydrogen bonds defined for protein. 942 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: 1.61 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 1245 1.33 - 1.46: 2088 1.46 - 1.60: 2530 1.60 - 1.73: 1 1.73 - 1.87: 49 Bond restraints: 5913 Sorted by residual: bond pdb=" CA LEU A 491 " pdb=" C LEU A 491 " ideal model delta sigma weight residual 1.522 1.566 -0.044 8.40e-03 1.42e+04 2.71e+01 bond pdb=" CA ASN A 546 " pdb=" C ASN A 546 " ideal model delta sigma weight residual 1.525 1.579 -0.054 1.40e-02 5.10e+03 1.49e+01 bond pdb=" NE ARG B 483 " pdb=" CZ ARG B 483 " ideal model delta sigma weight residual 1.326 1.368 -0.042 1.10e-02 8.26e+03 1.46e+01 bond pdb=" N PRO A 492 " pdb=" CD PRO A 492 " ideal model delta sigma weight residual 1.473 1.420 0.053 1.40e-02 5.10e+03 1.44e+01 bond pdb=" C5 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.42e+01 ... (remaining 5908 not shown) Histogram of bond angle deviations from ideal: 92.58 - 100.92: 7 100.92 - 109.26: 797 109.26 - 117.59: 3539 117.59 - 125.93: 3621 125.93 - 134.27: 121 Bond angle restraints: 8085 Sorted by residual: angle pdb=" N ILE B 494 " pdb=" CA ILE B 494 " pdb=" C ILE B 494 " ideal model delta sigma weight residual 109.34 92.58 16.76 2.08e+00 2.31e-01 6.49e+01 angle pdb=" C GLY A 537 " pdb=" N PRO A 538 " pdb=" CA PRO A 538 " ideal model delta sigma weight residual 119.76 127.80 -8.04 1.03e+00 9.43e-01 6.09e+01 angle pdb=" C GLU A 489 " pdb=" N PRO A 490 " pdb=" CA PRO A 490 " ideal model delta sigma weight residual 119.56 126.92 -7.36 1.02e+00 9.61e-01 5.21e+01 angle pdb=" C GLU A 335 " pdb=" N PRO A 336 " pdb=" CA PRO A 336 " ideal model delta sigma weight residual 119.85 126.95 -7.10 1.01e+00 9.80e-01 4.94e+01 angle pdb=" C GLU B 576 " pdb=" N PRO B 577 " pdb=" CA PRO B 577 " ideal model delta sigma weight residual 119.78 126.84 -7.06 1.03e+00 9.43e-01 4.70e+01 ... (remaining 8080 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.29: 3529 21.29 - 42.59: 71 42.59 - 63.88: 14 63.88 - 85.17: 9 85.17 - 106.47: 4 Dihedral angle restraints: 3627 sinusoidal: 1321 harmonic: 2306 Sorted by residual: dihedral pdb=" N ILE B 494 " pdb=" C ILE B 494 " pdb=" CA ILE B 494 " pdb=" CB ILE B 494 " ideal model delta harmonic sigma weight residual 123.40 106.22 17.18 0 2.50e+00 1.60e-01 4.72e+01 dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual -86.00 -124.14 38.14 1 1.00e+01 1.00e-02 2.05e+01 dihedral pdb=" C ILE B 494 " pdb=" N ILE B 494 " pdb=" CA ILE B 494 " pdb=" CB ILE B 494 " ideal model delta harmonic sigma weight residual -122.00 -110.76 -11.24 0 2.50e+00 1.60e-01 2.02e+01 ... (remaining 3624 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.232: 862 0.232 - 0.463: 37 0.463 - 0.695: 0 0.695 - 0.927: 1 0.927 - 1.159: 1 Chirality restraints: 901 Sorted by residual: chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.45e+02 chirality pdb=" C1 MAN C 4 " pdb=" O3 BMA C 3 " pdb=" C2 MAN C 4 " pdb=" O5 MAN C 4 " both_signs ideal model delta sigma weight residual False 2.40 2.60 -0.20 2.00e-02 2.50e+03 9.87e+01 chirality pdb=" C1 BMA C 3 " pdb=" O4 NAG C 2 " pdb=" C2 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.25e+01 ... (remaining 898 not shown) Planarity restraints: 1055 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 491 " 0.018 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C LEU A 491 " -0.065 2.00e-02 2.50e+03 pdb=" O LEU A 491 " 0.025 2.00e-02 2.50e+03 pdb=" N PRO A 492 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 329 " -0.027 2.00e-02 2.50e+03 2.77e-02 9.58e+00 pdb=" CG ASN A 329 " 0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN A 329 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 329 " 0.043 2.00e-02 2.50e+03 pdb=" C1 NAG A 701 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 91 " -0.022 2.00e-02 2.50e+03 2.68e-02 8.98e+00 pdb=" CG ASN A 91 " -0.000 2.00e-02 2.50e+03 pdb=" OD1 ASN A 91 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 91 " 0.045 2.00e-02 2.50e+03 pdb=" C1 NAG A 703 " -0.032 2.00e-02 2.50e+03 ... (remaining 1052 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.93: 2433 2.93 - 3.42: 5498 3.42 - 3.91: 9550 3.91 - 4.41: 10552 4.41 - 4.90: 16754 Nonbonded interactions: 44787 Sorted by model distance: nonbonded pdb=" N VAL A 108 " pdb=" N LEU A 109 " model vdw 2.431 2.560 nonbonded pdb=" N ALA B 523 " pdb=" O ALA B 523 " model vdw 2.519 2.496 nonbonded pdb=" N LYS B 562 " pdb=" O LYS B 562 " model vdw 2.581 2.496 nonbonded pdb=" O GLN A 239 " pdb=" ND2 ASN A 599 " model vdw 2.581 2.520 nonbonded pdb=" N ARG B 467 " pdb=" N ILE B 468 " model vdw 2.587 2.560 ... (remaining 44782 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'J' } 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 group one per residue 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: 3.650 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 20.150 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 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 : 0.013 0.094 5913 Z= 0.891 Angle : 1.409 16.756 8085 Z= 0.971 Chirality : 0.111 1.159 901 Planarity : 0.006 0.038 1047 Dihedral : 11.149 106.467 2123 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.39 % Allowed : 2.19 % Favored : 97.43 % Rotamer: Outliers : 0.74 % Allowed : 0.99 % Favored : 98.26 % Cbeta Deviations : 0.13 % 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: -0.13 (0.27), residues: 777 helix: -0.10 (0.23), residues: 405 sheet: 0.71 (0.69), residues: 50 loop : 0.05 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.005 TRP A 328 HIS 0.005 0.001 HIS A 345 PHE 0.024 0.004 PHE A 592 TYR 0.035 0.005 TYR A 217 ARG 0.006 0.001 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 120 time to evaluate : 0.643 Fit side-chains revert: symmetry clash REVERT: A 63 MET cc_start: 0.7652 (ttp) cc_final: 0.7421 (ttp) REVERT: A 223 MET cc_start: 0.7557 (mtm) cc_final: 0.7319 (mtt) REVERT: A 510 TYR cc_start: 0.6825 (m-80) cc_final: 0.6512 (m-10) REVERT: B 474 ASN cc_start: 0.7697 (t0) cc_final: 0.7387 (t0) REVERT: B 475 GLN cc_start: 0.8105 (tt0) cc_final: 0.7542 (tt0) outliers start: 3 outliers final: 0 residues processed: 123 average time/residue: 0.2208 time to fit residues: 33.7937 Evaluate side-chains 68 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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: 0.8980 chunk 59 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 31 optimal weight: 7.9990 chunk 61 optimal weight: 20.0000 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 HIS A 330 ASN A 535 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5913 Z= 0.224 Angle : 0.636 11.188 8085 Z= 0.334 Chirality : 0.045 0.179 901 Planarity : 0.005 0.043 1047 Dihedral : 7.249 69.004 1156 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 0.77 % Favored : 99.10 % Rotamer: Outliers : 1.49 % Allowed : 8.68 % Favored : 89.83 % 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: 1.29 (0.29), residues: 777 helix: 1.40 (0.25), residues: 405 sheet: 1.20 (0.64), residues: 54 loop : 0.20 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 163 HIS 0.008 0.001 HIS A 345 PHE 0.022 0.002 PHE A 592 TYR 0.024 0.002 TYR A 315 ARG 0.005 0.001 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7084 (OUTLIER) cc_final: 0.6734 (mmm) REVERT: A 591 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8826 (tt) REVERT: B 474 ASN cc_start: 0.7710 (t0) cc_final: 0.7389 (t0) outliers start: 6 outliers final: 1 residues processed: 81 average time/residue: 0.1615 time to fit residues: 17.8326 Evaluate side-chains 67 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 591 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 5913 Z= 0.336 Angle : 0.677 7.293 8085 Z= 0.359 Chirality : 0.047 0.273 901 Planarity : 0.005 0.051 1047 Dihedral : 8.063 64.439 1156 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.83 % Favored : 97.04 % Rotamer: Outliers : 2.73 % Allowed : 10.17 % Favored : 87.10 % 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: 0.83 (0.29), residues: 777 helix: 1.21 (0.24), residues: 415 sheet: 0.63 (0.65), residues: 60 loop : -0.28 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 302 HIS 0.007 0.002 HIS B 485 PHE 0.031 0.003 PHE A 308 TYR 0.024 0.002 TYR A 385 ARG 0.006 0.001 ARG A 245 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 72 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: A 68 SER cc_start: 0.8878 (OUTLIER) cc_final: 0.8634 (m) REVERT: A 207 TYR cc_start: 0.8491 (m-80) cc_final: 0.7708 (m-80) REVERT: A 512 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.7729 (m-10) REVERT: B 474 ASN cc_start: 0.8001 (t0) cc_final: 0.7654 (t0) outliers start: 11 outliers final: 6 residues processed: 79 average time/residue: 0.1537 time to fit residues: 17.0418 Evaluate side-chains 78 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 459 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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: 0.7749 moved from start: 0.4679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5913 Z= 0.220 Angle : 0.546 6.184 8085 Z= 0.282 Chirality : 0.043 0.172 901 Planarity : 0.004 0.039 1047 Dihedral : 7.255 56.695 1156 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.45 % Favored : 97.43 % Rotamer: Outliers : 1.74 % Allowed : 11.91 % Favored : 86.35 % 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: 1.15 (0.30), residues: 777 helix: 1.59 (0.25), residues: 415 sheet: 0.82 (0.69), residues: 53 loop : -0.32 (0.37), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 163 HIS 0.003 0.001 HIS A 345 PHE 0.018 0.002 PHE A 592 TYR 0.018 0.002 TYR A 385 ARG 0.003 0.001 ARG A 575 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 SER cc_start: 0.8836 (p) cc_final: 0.8604 (m) REVERT: A 207 TYR cc_start: 0.8461 (m-80) cc_final: 0.7690 (m-80) REVERT: A 512 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.7685 (m-80) REVERT: A 591 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8890 (tt) REVERT: B 474 ASN cc_start: 0.7979 (t0) cc_final: 0.7659 (t0) outliers start: 7 outliers final: 3 residues processed: 78 average time/residue: 0.1590 time to fit residues: 17.3800 Evaluate side-chains 77 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 72 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain B residue 459 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 0 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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: 0.7742 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5913 Z= 0.180 Angle : 0.525 10.389 8085 Z= 0.269 Chirality : 0.043 0.341 901 Planarity : 0.004 0.035 1047 Dihedral : 6.705 50.279 1156 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.73 % Allowed : 11.66 % Favored : 85.61 % 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: 1.33 (0.31), residues: 777 helix: 1.87 (0.26), residues: 408 sheet: 0.66 (0.69), residues: 53 loop : -0.36 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 163 HIS 0.002 0.001 HIS A 373 PHE 0.013 0.001 PHE A 592 TYR 0.016 0.001 TYR A 385 ARG 0.003 0.000 ARG A 575 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 74 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 TRP cc_start: 0.8168 (t-100) cc_final: 0.7660 (t-100) REVERT: A 68 SER cc_start: 0.8854 (OUTLIER) cc_final: 0.8580 (m) REVERT: A 207 TYR cc_start: 0.8436 (m-80) cc_final: 0.7694 (m-80) REVERT: A 512 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.7655 (m-80) REVERT: B 474 ASN cc_start: 0.7975 (t0) cc_final: 0.7692 (t0) outliers start: 11 outliers final: 4 residues processed: 81 average time/residue: 0.1736 time to fit residues: 18.8932 Evaluate side-chains 78 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 442 TYR Chi-restraints excluded: chain B residue 459 TYR 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: 1.9990 chunk 75 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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: 0.7759 moved from start: 0.5130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5913 Z= 0.194 Angle : 0.529 11.225 8085 Z= 0.268 Chirality : 0.044 0.356 901 Planarity : 0.004 0.035 1047 Dihedral : 6.437 59.868 1156 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.23 % Allowed : 12.16 % Favored : 85.61 % 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: 1.27 (0.31), residues: 777 helix: 1.84 (0.26), residues: 413 sheet: 0.55 (0.69), residues: 53 loop : -0.43 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 163 HIS 0.002 0.001 HIS A 373 PHE 0.016 0.002 PHE B 543 TYR 0.017 0.001 TYR A 385 ARG 0.007 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 71 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 TRP cc_start: 0.8159 (t-100) cc_final: 0.7684 (t-100) REVERT: A 68 SER cc_start: 0.8824 (OUTLIER) cc_final: 0.8552 (m) REVERT: A 207 TYR cc_start: 0.8460 (m-80) cc_final: 0.7699 (m-80) REVERT: A 474 MET cc_start: 0.7699 (tpp) cc_final: 0.7267 (mmt) REVERT: A 512 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.7587 (m-80) REVERT: B 474 ASN cc_start: 0.8006 (t0) cc_final: 0.7712 (t0) outliers start: 9 outliers final: 7 residues processed: 76 average time/residue: 0.1550 time to fit residues: 16.2627 Evaluate side-chains 80 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 71 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain B residue 442 TYR Chi-restraints excluded: chain B residue 459 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 47 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 44 optimal weight: 0.2980 chunk 22 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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: 0.7728 moved from start: 0.5276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5913 Z= 0.147 Angle : 0.483 8.110 8085 Z= 0.246 Chirality : 0.042 0.291 901 Planarity : 0.004 0.031 1047 Dihedral : 5.666 43.963 1156 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.99 % Allowed : 12.41 % Favored : 85.61 % 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: 1.46 (0.31), residues: 777 helix: 2.05 (0.26), residues: 410 sheet: 0.35 (0.68), residues: 55 loop : -0.35 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 163 HIS 0.002 0.001 HIS A 241 PHE 0.010 0.001 PHE A 523 TYR 0.016 0.001 TYR A 183 ARG 0.004 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 TRP cc_start: 0.8152 (t-100) cc_final: 0.7689 (t-100) REVERT: A 68 SER cc_start: 0.8743 (p) cc_final: 0.8471 (m) REVERT: A 207 TYR cc_start: 0.8430 (m-80) cc_final: 0.7701 (m-80) REVERT: A 512 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.7534 (m-80) REVERT: B 474 ASN cc_start: 0.7990 (t0) cc_final: 0.7699 (t0) outliers start: 8 outliers final: 3 residues processed: 78 average time/residue: 0.1684 time to fit residues: 17.7245 Evaluate side-chains 73 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 69 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 442 TYR Chi-restraints excluded: chain B residue 459 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 chunk 72 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.7734 moved from start: 0.5412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5913 Z= 0.155 Angle : 0.494 10.192 8085 Z= 0.249 Chirality : 0.042 0.312 901 Planarity : 0.004 0.032 1047 Dihedral : 5.230 37.480 1156 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.49 % Allowed : 11.91 % Favored : 86.60 % 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: 1.51 (0.31), residues: 777 helix: 2.09 (0.26), residues: 413 sheet: 0.27 (0.68), residues: 55 loop : -0.34 (0.37), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 163 HIS 0.002 0.001 HIS A 373 PHE 0.013 0.001 PHE B 543 TYR 0.016 0.001 TYR A 385 ARG 0.006 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 TRP cc_start: 0.8182 (t-100) cc_final: 0.7717 (t-100) REVERT: A 68 SER cc_start: 0.8695 (OUTLIER) cc_final: 0.8433 (m) REVERT: A 207 TYR cc_start: 0.8438 (m-80) cc_final: 0.7699 (m-80) REVERT: A 512 PHE cc_start: 0.8112 (OUTLIER) cc_final: 0.7527 (m-80) REVERT: B 474 ASN cc_start: 0.7986 (t0) cc_final: 0.7707 (t0) outliers start: 6 outliers final: 3 residues processed: 76 average time/residue: 0.1688 time to fit residues: 17.3479 Evaluate side-chains 74 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 442 TYR Chi-restraints excluded: chain B residue 459 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 1.9990 chunk 55 optimal weight: 0.0050 chunk 21 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 46 optimal weight: 0.6980 chunk 74 optimal weight: 0.0570 chunk 45 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.5512 ------------------------------------------------------------------------------- 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: 0.7703 moved from start: 0.5484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5913 Z= 0.134 Angle : 0.473 8.431 8085 Z= 0.239 Chirality : 0.041 0.308 901 Planarity : 0.003 0.029 1047 Dihedral : 4.757 33.305 1156 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.49 % Allowed : 12.41 % Favored : 86.10 % 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: 1.57 (0.31), residues: 777 helix: 2.16 (0.26), residues: 412 sheet: 0.28 (0.67), residues: 55 loop : -0.33 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 163 HIS 0.002 0.001 HIS A 373 PHE 0.010 0.001 PHE A 523 TYR 0.015 0.001 TYR A 385 ARG 0.005 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 71 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 TRP cc_start: 0.8182 (t-100) cc_final: 0.7726 (t-100) REVERT: A 512 PHE cc_start: 0.8043 (OUTLIER) cc_final: 0.7503 (m-80) REVERT: B 474 ASN cc_start: 0.7963 (t0) cc_final: 0.7710 (t0) outliers start: 6 outliers final: 4 residues processed: 75 average time/residue: 0.1653 time to fit residues: 16.7202 Evaluate side-chains 76 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 442 TYR Chi-restraints excluded: chain B residue 459 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 61 optimal weight: 20.0000 chunk 6 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 37 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7714 moved from start: 0.5587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5913 Z= 0.143 Angle : 0.477 8.125 8085 Z= 0.240 Chirality : 0.041 0.304 901 Planarity : 0.004 0.031 1047 Dihedral : 4.588 30.766 1156 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.24 % Allowed : 13.15 % Favored : 85.61 % 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: 1.62 (0.31), residues: 777 helix: 2.23 (0.26), residues: 410 sheet: 0.26 (0.67), residues: 55 loop : -0.33 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 163 HIS 0.003 0.001 HIS A 373 PHE 0.009 0.001 PHE A 523 TYR 0.013 0.001 TYR A 183 ARG 0.006 0.000 ARG A 192 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 TRP cc_start: 0.8184 (t-100) cc_final: 0.7723 (t-100) REVERT: A 68 SER cc_start: 0.8665 (OUTLIER) cc_final: 0.8409 (m) REVERT: A 512 PHE cc_start: 0.8065 (OUTLIER) cc_final: 0.7533 (m-80) REVERT: B 474 ASN cc_start: 0.7976 (t0) cc_final: 0.7723 (t0) outliers start: 5 outliers final: 3 residues processed: 74 average time/residue: 0.1836 time to fit residues: 18.1737 Evaluate side-chains 75 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 442 TYR Chi-restraints excluded: chain B residue 459 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 5.9990 chunk 61 optimal weight: 20.0000 chunk 25 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 3 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.106350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.093177 restraints weight = 12663.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.095085 restraints weight = 6752.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.096337 restraints weight = 4245.962| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.5702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5913 Z= 0.191 Angle : 0.510 8.074 8085 Z= 0.258 Chirality : 0.042 0.297 901 Planarity : 0.004 0.033 1047 Dihedral : 4.850 31.398 1156 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.24 % Allowed : 13.40 % Favored : 85.36 % 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: 1.47 (0.31), residues: 777 helix: 2.10 (0.26), residues: 413 sheet: 0.24 (0.68), residues: 55 loop : -0.42 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.005 0.001 HIS A 159 PHE 0.014 0.001 PHE A 592 TYR 0.015 0.001 TYR A 183 ARG 0.006 0.001 ARG A 192 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1366.76 seconds wall clock time: 25 minutes 25.57 seconds (1525.57 seconds total)