Starting phenix.real_space_refine on Fri Mar 15 04:34:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dcp_27327/03_2024/8dcp_27327.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dcp_27327/03_2024/8dcp_27327.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dcp_27327/03_2024/8dcp_27327.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dcp_27327/03_2024/8dcp_27327.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dcp_27327/03_2024/8dcp_27327.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dcp_27327/03_2024/8dcp_27327.pdb" } resolution = 2.41 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 ------------------------------------------------------------------------------- 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= 1.000 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 75 5.16 5 C 6724 2.51 5 N 1835 2.21 5 O 1961 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 35": "OE1" <-> "OE2" Residue "A GLU 85": "OE1" <-> "OE2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 149": "OE1" <-> "OE2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "A TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 259": "OE1" <-> "OE2" Residue "A GLU 417": "OE1" <-> "OE2" Residue "A GLU 493": "OE1" <-> "OE2" Residue "A ASP 538": "OD1" <-> "OD2" Residue "A GLU 542": "OE1" <-> "OE2" Residue "A GLU 596": "OE1" <-> "OE2" Residue "A ASP 626": "OD1" <-> "OD2" Residue "A TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 707": "OE1" <-> "OE2" Residue "A PHE 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 768": "OE1" <-> "OE2" Residue "A ASP 843": "OD1" <-> "OD2" Residue "A ASP 925": "OD1" <-> "OD2" Residue "A ASP 959": "OD1" <-> "OD2" Residue "A PHE 1016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1018": "OD1" <-> "OD2" Residue "A GLU 1032": "OE1" <-> "OE2" Residue "B TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 496": "OE1" <-> "OE2" Residue "B GLU 555": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10595 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8233 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1005, 8222 Classifications: {'peptide': 1005} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 959} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 1005, 8222 Classifications: {'peptide': 1005} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 959} Chain breaks: 4 bond proxies already assigned to first conformer: 8389 Chain: "B" Number of atoms: 2341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2341 Classifications: {'peptide': 276} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 271} Chain breaks: 1 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 704 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 704 " occ=0.50 Time building chain proxies: 9.28, per 1000 atoms: 0.88 Number of scatterers: 10595 At special positions: 0 Unit cell: (89.88, 130.54, 119.84, 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 75 16.00 O 1961 8.00 N 1835 7.00 C 6724 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.03 Conformation dependent library (CDL) restraints added in 3.3 seconds 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2454 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 11 sheets defined 52.1% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 41 through 52 Processing helix chain 'A' and resid 64 through 68 removed outlier: 3.705A pdb=" N SER A 67 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR A 68 " --> pdb=" O GLU A 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 64 through 68' Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.564A pdb=" N LEU A 92 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG A 93 " --> pdb=" O CYS A 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 89 through 93' Processing helix chain 'A' and resid 107 through 122 removed outlier: 3.509A pdb=" N LYS A 111 " --> pdb=" O ASN A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.684A pdb=" N ASP A 129 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 155 removed outlier: 4.309A pdb=" N LEU A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ASN A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL A 146 " --> pdb=" O ASN A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 167 Processing helix chain 'A' and resid 178 through 183 removed outlier: 3.544A pdb=" N ASN A 183 " --> pdb=" O LYS A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 232 removed outlier: 3.866A pdb=" N SER A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 269 Processing helix chain 'A' and resid 270 through 280 Processing helix chain 'A' and resid 290 through 296 Processing helix chain 'A' and resid 305 through 309 removed outlier: 3.538A pdb=" N SER A 308 " --> pdb=" O PRO A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 330 No H-bonds generated for 'chain 'A' and resid 328 through 330' Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 488 through 496 Processing helix chain 'A' and resid 498 through 503 removed outlier: 3.683A pdb=" N ARG A 502 " --> pdb=" O TRP A 498 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 498 through 503' Processing helix chain 'A' and resid 524 through 536 removed outlier: 3.517A pdb=" N GLN A 530 " --> pdb=" O ASN A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 554 Processing helix chain 'A' and resid 557 through 563 Proline residue: A 562 - end of helix Processing helix chain 'A' and resid 564 through 571 Processing helix chain 'A' and resid 576 through 589 removed outlier: 4.045A pdb=" N ASP A 589 " --> pdb=" O CYS A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 599 Processing helix chain 'A' and resid 600 through 603 Processing helix chain 'A' and resid 608 through 623 Processing helix chain 'A' and resid 624 through 631 Processing helix chain 'A' and resid 631 through 638 Processing helix chain 'A' and resid 639 through 642 Processing helix chain 'A' and resid 647 through 660 Processing helix chain 'A' and resid 660 through 674 removed outlier: 3.690A pdb=" N PHE A 666 " --> pdb=" O ARG A 662 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU A 674 " --> pdb=" O HIS A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 695 Processing helix chain 'A' and resid 697 through 722 removed outlier: 4.058A pdb=" N HIS A 701 " --> pdb=" O MET A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 739 Processing helix chain 'A' and resid 741 through 748 Processing helix chain 'A' and resid 765 through 769 Processing helix chain 'A' and resid 789 through 794 removed outlier: 4.330A pdb=" N LEU A 793 " --> pdb=" O MET A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 828 Processing helix chain 'A' and resid 857 through 864 Processing helix chain 'A' and resid 871 through 874 Processing helix chain 'A' and resid 875 through 885 Processing helix chain 'A' and resid 888 through 912 removed outlier: 4.245A pdb=" N ALA A 892 " --> pdb=" O GLU A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 965 removed outlier: 3.541A pdb=" N VAL A 963 " --> pdb=" O ASP A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 993 Processing helix chain 'A' and resid 994 through 1004 removed outlier: 3.787A pdb=" N PHE A 998 " --> pdb=" O HIS A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1026 removed outlier: 3.889A pdb=" N ILE A1019 " --> pdb=" O SER A1015 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N TYR A1021 " --> pdb=" O ASP A1017 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ILE A1022 " --> pdb=" O ASP A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1048 removed outlier: 3.561A pdb=" N ALA A1046 " --> pdb=" O GLN A1042 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 347 Processing helix chain 'B' and resid 400 through 411 removed outlier: 3.815A pdb=" N LEU B 404 " --> pdb=" O SER B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 416 removed outlier: 3.550A pdb=" N GLN B 415 " --> pdb=" O SER B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 509 removed outlier: 3.858A pdb=" N LYS B 506 " --> pdb=" O GLU B 502 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N GLU B 507 " --> pdb=" O ARG B 503 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TYR B 508 " --> pdb=" O TYR B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 514 removed outlier: 3.863A pdb=" N LYS B 513 " --> pdb=" O GLU B 510 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG B 514 " --> pdb=" O LYS B 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 510 through 514' Processing helix chain 'B' and resid 517 through 588 removed outlier: 4.136A pdb=" N ILE B 521 " --> pdb=" O ASN B 517 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN B 527 " --> pdb=" O ARG B 523 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR B 528 " --> pdb=" O ILE B 524 " (cutoff:3.500A) Proline residue: B 568 - end of helix removed outlier: 3.999A pdb=" N GLY B 588 " --> pdb=" O LEU B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 596 removed outlier: 4.054A pdb=" N LEU B 594 " --> pdb=" O ARG B 590 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 35 removed outlier: 3.601A pdb=" N VAL A 22 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N LEU A 99 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLU A 23 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N VAL A 101 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N LEU A 25 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N PHE A 98 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N VAL A 73 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N PHE A 70 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER A 72 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 205 through 212 removed outlier: 4.457A pdb=" N LEU A 252 " --> pdb=" O PHE A 261 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 326 removed outlier: 6.751A pdb=" N LYS A 325 " --> pdb=" O LYS A 485 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 382 through 392 removed outlier: 6.788A pdb=" N TRP A 383 " --> pdb=" O CYS A 340 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N CYS A 340 " --> pdb=" O TRP A 383 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU A 334 " --> pdb=" O TYR A 389 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLU A 474 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ALA A 341 " --> pdb=" O CYS A 472 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N CYS A 472 " --> pdb=" O ALA A 341 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY A 439 " --> pdb=" O PHE A 477 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 365 through 366 Processing sheet with id=AA6, first strand: chain 'A' and resid 371 through 372 removed outlier: 3.794A pdb=" N LYS A 353 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU A 402 " --> pdb=" O ASN A 426 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ASN A 426 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU A 404 " --> pdb=" O TRP A 424 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N TRP A 424 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE A 406 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 751 through 752 Processing sheet with id=AA8, first strand: chain 'A' and resid 770 through 771 removed outlier: 6.924A pdb=" N VAL A 845 " --> pdb=" O ILE A 841 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 854 through 856 Processing sheet with id=AB1, first strand: chain 'B' and resid 377 through 382 removed outlier: 4.434A pdb=" N THR B 354 " --> pdb=" O ARG B 373 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 384 through 386 521 hydrogen bonds defined for protein. 1492 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: 3.46 Time building geometry restraints manager: 4.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3480 1.34 - 1.46: 2355 1.46 - 1.58: 4841 1.58 - 1.70: 0 1.70 - 1.82: 117 Bond restraints: 10793 Sorted by residual: bond pdb=" CG1 ILE A 121 " pdb=" CD1 ILE A 121 " ideal model delta sigma weight residual 1.513 1.445 0.068 3.90e-02 6.57e+02 3.07e+00 bond pdb=" CG1 ILE A 894 " pdb=" CD1 ILE A 894 " ideal model delta sigma weight residual 1.513 1.450 0.063 3.90e-02 6.57e+02 2.58e+00 bond pdb=" CG LYS A 132 " pdb=" CD LYS A 132 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.02e+00 bond pdb=" CB LYS A 132 " pdb=" CG LYS A 132 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.75e+00 bond pdb=" CB MET B 322 " pdb=" CG MET B 322 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.70e+00 ... (remaining 10788 not shown) Histogram of bond angle deviations from ideal: 98.62 - 105.69: 193 105.69 - 112.77: 5614 112.77 - 119.84: 3697 119.84 - 126.91: 4912 126.91 - 133.98: 132 Bond angle restraints: 14548 Sorted by residual: angle pdb=" CB LYS A 132 " pdb=" CG LYS A 132 " pdb=" CD LYS A 132 " ideal model delta sigma weight residual 111.30 121.47 -10.17 2.30e+00 1.89e-01 1.96e+01 angle pdb=" CA MET B 322 " pdb=" CB MET B 322 " pdb=" CG MET B 322 " ideal model delta sigma weight residual 114.10 122.17 -8.07 2.00e+00 2.50e-01 1.63e+01 angle pdb=" CB MET B 563 " pdb=" CG MET B 563 " pdb=" SD MET B 563 " ideal model delta sigma weight residual 112.70 102.26 10.44 3.00e+00 1.11e-01 1.21e+01 angle pdb=" CB MET A 299 " pdb=" CG MET A 299 " pdb=" SD MET A 299 " ideal model delta sigma weight residual 112.70 123.07 -10.37 3.00e+00 1.11e-01 1.20e+01 angle pdb=" CA GLU A 493 " pdb=" CB GLU A 493 " pdb=" CG GLU A 493 " ideal model delta sigma weight residual 114.10 120.77 -6.67 2.00e+00 2.50e-01 1.11e+01 ... (remaining 14543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 5413 17.83 - 35.66: 823 35.66 - 53.48: 284 53.48 - 71.31: 63 71.31 - 89.14: 29 Dihedral angle restraints: 6612 sinusoidal: 2829 harmonic: 3783 Sorted by residual: dihedral pdb=" CA PRO A 200 " pdb=" C PRO A 200 " pdb=" N ASN A 201 " pdb=" CA ASN A 201 " ideal model delta harmonic sigma weight residual 180.00 161.75 18.25 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA HIS A 940 " pdb=" C HIS A 940 " pdb=" N LYS A 941 " pdb=" CA LYS A 941 " ideal model delta harmonic sigma weight residual 180.00 162.02 17.98 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA SER A 199 " pdb=" C SER A 199 " pdb=" N PRO A 200 " pdb=" CA PRO A 200 " ideal model delta harmonic sigma weight residual 180.00 162.14 17.86 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 6609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 971 0.031 - 0.061: 392 0.061 - 0.092: 128 0.092 - 0.123: 71 0.123 - 0.154: 8 Chirality restraints: 1570 Sorted by residual: chirality pdb=" CB ILE A 197 " pdb=" CA ILE A 197 " pdb=" CG1 ILE A 197 " pdb=" CG2 ILE A 197 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CA ILE A 191 " pdb=" N ILE A 191 " pdb=" C ILE A 191 " pdb=" CB ILE A 191 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" CA ILE A 561 " pdb=" N ILE A 561 " pdb=" C ILE A 561 " pdb=" CB ILE A 561 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.52e-01 ... (remaining 1567 not shown) Planarity restraints: 1871 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 282 " 0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO A 283 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 283 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 283 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 420 " 0.024 5.00e-02 4.00e+02 3.65e-02 2.14e+00 pdb=" N PRO A 421 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 421 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 421 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 216 " -0.022 5.00e-02 4.00e+02 3.28e-02 1.73e+00 pdb=" N PRO A 217 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 217 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 217 " -0.018 5.00e-02 4.00e+02 ... (remaining 1868 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2293 2.78 - 3.31: 9871 3.31 - 3.84: 18197 3.84 - 4.37: 20893 4.37 - 4.90: 35063 Nonbonded interactions: 86317 Sorted by model distance: nonbonded pdb=" NZ LYS A 884 " pdb=" OD1 ASP A 925 " model vdw 2.253 2.520 nonbonded pdb=" O GLY B 321 " pdb=" ND2 ASN B 323 " model vdw 2.263 2.520 nonbonded pdb=" N ASN B 319 " pdb=" ND2 ASN B 319 " model vdw 2.293 3.200 nonbonded pdb=" ND2 ASN A 782 " pdb=" OD1 ASN A 796 " model vdw 2.296 2.520 nonbonded pdb=" NH2 ARG A 398 " pdb=" OD1 ASP A 434 " model vdw 2.296 2.520 ... (remaining 86312 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.010 Normalize map: mean=0, sd=1: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.140 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 36.130 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:12.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 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 0.068 10793 Z= 0.201 Angle : 0.641 10.437 14548 Z= 0.317 Chirality : 0.041 0.154 1570 Planarity : 0.004 0.047 1871 Dihedral : 20.067 89.140 4158 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.06 % Allowed : 33.73 % Favored : 63.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.79 (0.24), residues: 1270 helix: 1.62 (0.22), residues: 575 sheet: -0.03 (0.42), residues: 162 loop : -0.47 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 669 HIS 0.004 0.001 HIS A1047 PHE 0.021 0.002 PHE A 744 TYR 0.017 0.001 TYR B 470 ARG 0.011 0.000 ARG B 543 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 239 time to evaluate : 1.268 Fit side-chains REVERT: A 347 ASN cc_start: 0.7096 (t0) cc_final: 0.6637 (t0) REVERT: A 1041 LYS cc_start: 0.7197 (tttm) cc_final: 0.6896 (tppp) REVERT: B 326 MET cc_start: 0.5247 (mpp) cc_final: 0.4113 (ttp) outliers start: 35 outliers final: 30 residues processed: 272 average time/residue: 1.2738 time to fit residues: 370.6222 Evaluate side-chains 259 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 229 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 573 LYS Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain A residue 777 ARG Chi-restraints excluded: chain A residue 782 ASN Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 941 LYS Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 947 TYR Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 578 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS A 826 ASN A 958 GLN ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN B 478 GLN B 552 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.0689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10793 Z= 0.208 Angle : 0.567 8.533 14548 Z= 0.289 Chirality : 0.041 0.152 1570 Planarity : 0.004 0.042 1871 Dihedral : 7.377 57.736 1465 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 6.37 % Allowed : 30.42 % Favored : 63.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.97 (0.24), residues: 1270 helix: 1.80 (0.22), residues: 597 sheet: 0.02 (0.40), residues: 162 loop : -0.49 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 669 HIS 0.003 0.001 HIS A 59 PHE 0.024 0.002 PHE A 744 TYR 0.020 0.001 TYR B 470 ARG 0.009 0.000 ARG B 557 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 250 time to evaluate : 1.323 Fit side-chains REVERT: A 107 ASN cc_start: 0.7700 (t0) cc_final: 0.7444 (t0) REVERT: A 148 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7648 (tppt) REVERT: A 172 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7076 (mt-10) REVERT: A 211 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8168 (pp) REVERT: A 278 MET cc_start: 0.6693 (mmm) cc_final: 0.6354 (mpp) REVERT: A 739 MET cc_start: 0.8103 (mtt) cc_final: 0.7691 (mtm) REVERT: A 772 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.6422 (mtp) REVERT: A 777 ARG cc_start: 0.5993 (OUTLIER) cc_final: 0.4437 (mpt90) REVERT: A 861 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7520 (mt0) REVERT: A 1041 LYS cc_start: 0.7217 (OUTLIER) cc_final: 0.6911 (tppp) REVERT: B 326 MET cc_start: 0.5309 (mpp) cc_final: 0.4039 (ttp) REVERT: B 542 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.5908 (ttm170) outliers start: 74 outliers final: 26 residues processed: 293 average time/residue: 1.2851 time to fit residues: 404.2807 Evaluate side-chains 276 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 242 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 777 ARG Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 947 TYR Chi-restraints excluded: chain A residue 1017 ASP Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1041 LYS Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 542 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 115 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 92 optimal weight: 9.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 822 ASN A 826 ASN A 958 GLN A1047 HIS B 319 ASN ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.0853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10793 Z= 0.247 Angle : 0.592 8.661 14548 Z= 0.300 Chirality : 0.043 0.156 1570 Planarity : 0.004 0.056 1871 Dihedral : 6.625 58.489 1442 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 5.44 % Allowed : 31.44 % Favored : 63.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.95 (0.24), residues: 1270 helix: 1.78 (0.21), residues: 598 sheet: -0.00 (0.39), residues: 162 loop : -0.50 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 574 HIS 0.004 0.001 HIS A 59 PHE 0.017 0.002 PHE A 128 TYR 0.021 0.002 TYR B 470 ARG 0.009 0.000 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 246 time to evaluate : 1.126 Fit side-chains REVERT: A 123 MET cc_start: 0.8148 (ptm) cc_final: 0.7853 (ptt) REVERT: A 172 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7174 (mt-10) REVERT: A 263 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7148 (mm-30) REVERT: A 772 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.6470 (mtp) REVERT: A 777 ARG cc_start: 0.6014 (OUTLIER) cc_final: 0.4427 (mpt90) REVERT: A 843 ASP cc_start: 0.7653 (t70) cc_final: 0.7390 (t70) REVERT: A 861 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7543 (mt0) REVERT: A 1041 LYS cc_start: 0.7265 (OUTLIER) cc_final: 0.6957 (tppp) REVERT: B 326 MET cc_start: 0.5297 (mpp) cc_final: 0.3889 (ttp) REVERT: B 364 MET cc_start: 0.6294 (mpt) cc_final: 0.5468 (mpt) REVERT: B 478 GLN cc_start: 0.7202 (tp40) cc_final: 0.6713 (tp-100) REVERT: B 542 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.5739 (ttm170) outliers start: 63 outliers final: 28 residues processed: 278 average time/residue: 1.3341 time to fit residues: 396.5097 Evaluate side-chains 275 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 240 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 777 ARG Chi-restraints excluded: chain A residue 782 ASN Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 947 TYR Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 1017 ASP Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1041 LYS Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 576 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 8.9990 chunk 86 optimal weight: 0.4980 chunk 59 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 115 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS A 826 ASN A 958 GLN ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 10793 Z= 0.257 Angle : 0.601 11.591 14548 Z= 0.303 Chirality : 0.043 0.178 1570 Planarity : 0.004 0.053 1871 Dihedral : 6.115 59.614 1432 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 5.86 % Allowed : 30.76 % Favored : 63.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.92 (0.24), residues: 1270 helix: 1.76 (0.21), residues: 599 sheet: -0.03 (0.39), residues: 162 loop : -0.52 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 479 HIS 0.004 0.001 HIS A 59 PHE 0.014 0.002 PHE A 128 TYR 0.021 0.002 TYR B 470 ARG 0.010 0.001 ARG B 557 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 243 time to evaluate : 1.217 Fit side-chains REVERT: A 211 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8212 (pp) REVERT: A 263 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.7163 (mm-30) REVERT: A 772 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.6479 (mtp) REVERT: A 777 ARG cc_start: 0.6001 (OUTLIER) cc_final: 0.4759 (mpt90) REVERT: A 861 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7534 (mt0) REVERT: A 1041 LYS cc_start: 0.7255 (OUTLIER) cc_final: 0.6947 (tppp) REVERT: B 326 MET cc_start: 0.5300 (mpp) cc_final: 0.3838 (ttp) REVERT: B 364 MET cc_start: 0.6302 (mpt) cc_final: 0.5522 (mpt) REVERT: B 478 GLN cc_start: 0.7183 (tp40) cc_final: 0.6657 (tp-100) REVERT: B 542 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.5797 (ttm170) REVERT: B 562 ARG cc_start: 0.6882 (mtp-110) cc_final: 0.6596 (mtp180) outliers start: 68 outliers final: 29 residues processed: 281 average time/residue: 1.2894 time to fit residues: 387.7763 Evaluate side-chains 273 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 237 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 777 ARG Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 947 TYR Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 1017 ASP Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1034 GLU Chi-restraints excluded: chain A residue 1041 LYS Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 576 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 91 optimal weight: 0.0670 chunk 50 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 62 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 overall best weight: 4.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS A 822 ASN A 826 ASN A 958 GLN ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN B 552 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 10793 Z= 0.325 Angle : 0.651 10.658 14548 Z= 0.326 Chirality : 0.045 0.177 1570 Planarity : 0.004 0.049 1871 Dihedral : 6.126 59.617 1428 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 6.20 % Allowed : 30.59 % Favored : 63.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.79 (0.24), residues: 1270 helix: 1.64 (0.21), residues: 599 sheet: -0.06 (0.39), residues: 163 loop : -0.58 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 479 HIS 0.006 0.001 HIS A 59 PHE 0.014 0.002 PHE A 980 TYR 0.023 0.002 TYR B 470 ARG 0.010 0.001 ARG B 557 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 241 time to evaluate : 1.291 Fit side-chains REVERT: A 172 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7157 (mt-10) REVERT: A 211 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8225 (pp) REVERT: A 263 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7189 (mm-30) REVERT: A 772 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.6628 (mtp) REVERT: A 777 ARG cc_start: 0.6056 (OUTLIER) cc_final: 0.4467 (mpt90) REVERT: A 861 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7553 (mt0) REVERT: B 326 MET cc_start: 0.5293 (mpp) cc_final: 0.3762 (ttp) REVERT: B 364 MET cc_start: 0.6315 (mpt) cc_final: 0.5544 (mpt) REVERT: B 478 GLN cc_start: 0.7186 (tp40) cc_final: 0.6654 (tp-100) REVERT: B 532 LYS cc_start: 0.5616 (OUTLIER) cc_final: 0.5367 (mmmm) REVERT: B 542 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.5773 (ttm170) REVERT: B 562 ARG cc_start: 0.6879 (mtp-110) cc_final: 0.6589 (mtp180) outliers start: 72 outliers final: 35 residues processed: 281 average time/residue: 1.3521 time to fit residues: 406.7870 Evaluate side-chains 281 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 238 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 777 ARG Chi-restraints excluded: chain A residue 782 ASN Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 947 TYR Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1017 ASP Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1034 GLU Chi-restraints excluded: chain A residue 1041 LYS Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 532 LYS Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 576 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 102 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS A 826 ASN A 958 GLN ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10793 Z= 0.227 Angle : 0.601 10.459 14548 Z= 0.300 Chirality : 0.042 0.196 1570 Planarity : 0.004 0.039 1871 Dihedral : 5.968 58.529 1428 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.67 % Allowed : 31.95 % Favored : 63.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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 (0.24), residues: 1270 helix: 1.76 (0.21), residues: 599 sheet: 0.02 (0.39), residues: 162 loop : -0.53 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 669 HIS 0.005 0.001 HIS A 59 PHE 0.012 0.002 PHE A 667 TYR 0.019 0.001 TYR B 470 ARG 0.010 0.000 ARG B 557 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 246 time to evaluate : 1.322 Fit side-chains REVERT: A 172 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7163 (mt-10) REVERT: A 211 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8219 (pp) REVERT: A 263 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7152 (mm-30) REVERT: A 278 MET cc_start: 0.6681 (mmm) cc_final: 0.6221 (mpp) REVERT: A 459 ILE cc_start: 0.8066 (OUTLIER) cc_final: 0.7852 (tp) REVERT: A 772 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.6483 (mtp) REVERT: A 777 ARG cc_start: 0.6014 (OUTLIER) cc_final: 0.4401 (mpt90) REVERT: A 843 ASP cc_start: 0.7659 (t70) cc_final: 0.7415 (t70) REVERT: A 861 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7531 (mt0) REVERT: A 1041 LYS cc_start: 0.7235 (OUTLIER) cc_final: 0.6934 (tppp) REVERT: B 326 MET cc_start: 0.5280 (mpp) cc_final: 0.3777 (ttp) REVERT: B 363 LYS cc_start: 0.7509 (OUTLIER) cc_final: 0.7238 (mmpt) REVERT: B 364 MET cc_start: 0.6306 (mpt) cc_final: 0.5505 (mpt) REVERT: B 478 GLN cc_start: 0.7139 (tp40) cc_final: 0.6618 (tp-100) REVERT: B 479 MET cc_start: 0.6564 (mtm) cc_final: 0.6343 (mpp) REVERT: B 542 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.5819 (ttm170) outliers start: 54 outliers final: 31 residues processed: 274 average time/residue: 1.3213 time to fit residues: 387.2943 Evaluate side-chains 279 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 238 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 777 ARG Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 947 TYR Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 1017 ASP Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1034 GLU Chi-restraints excluded: chain A residue 1041 LYS Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 542 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 69 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 122 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS A 822 ASN A 826 ASN A 958 GLN ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 10793 Z= 0.366 Angle : 0.691 10.754 14548 Z= 0.345 Chirality : 0.046 0.198 1570 Planarity : 0.005 0.060 1871 Dihedral : 6.176 58.360 1427 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 5.69 % Allowed : 30.93 % Favored : 63.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.68 (0.23), residues: 1270 helix: 1.52 (0.21), residues: 599 sheet: -0.09 (0.39), residues: 163 loop : -0.60 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 479 HIS 0.007 0.001 HIS A 59 PHE 0.015 0.002 PHE A 980 TYR 0.024 0.002 TYR B 470 ARG 0.010 0.001 ARG B 557 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 239 time to evaluate : 1.379 Fit side-chains REVERT: A 148 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7681 (tppt) REVERT: A 172 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7176 (mt-10) REVERT: A 211 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8233 (pp) REVERT: A 250 TYR cc_start: 0.7931 (OUTLIER) cc_final: 0.7361 (m-80) REVERT: A 263 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7150 (mm-30) REVERT: A 772 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.6716 (mtp) REVERT: A 777 ARG cc_start: 0.6095 (OUTLIER) cc_final: 0.4496 (mpt90) REVERT: A 861 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7537 (mt0) REVERT: A 882 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.7657 (mtmm) REVERT: B 364 MET cc_start: 0.6328 (mpt) cc_final: 0.5539 (mpt) REVERT: B 478 GLN cc_start: 0.7197 (tp40) cc_final: 0.6641 (tp-100) REVERT: B 532 LYS cc_start: 0.5649 (OUTLIER) cc_final: 0.5384 (mmmm) REVERT: B 542 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.5768 (ttm170) outliers start: 66 outliers final: 37 residues processed: 277 average time/residue: 1.3728 time to fit residues: 405.3804 Evaluate side-chains 280 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 232 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 777 ARG Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 882 LYS Chi-restraints excluded: chain A residue 947 TYR Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1017 ASP Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1034 GLU Chi-restraints excluded: chain A residue 1041 LYS Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 532 LYS Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 576 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 826 ASN A 958 GLN ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10793 Z= 0.202 Angle : 0.609 10.310 14548 Z= 0.301 Chirality : 0.042 0.174 1570 Planarity : 0.004 0.055 1871 Dihedral : 5.899 58.699 1427 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.16 % Allowed : 32.63 % Favored : 63.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.95 (0.24), residues: 1270 helix: 1.80 (0.21), residues: 599 sheet: 0.00 (0.39), residues: 163 loop : -0.53 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 669 HIS 0.004 0.001 HIS A 59 PHE 0.014 0.001 PHE A 937 TYR 0.016 0.001 TYR A 622 ARG 0.011 0.000 ARG B 557 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 240 time to evaluate : 1.367 Fit side-chains REVERT: A 172 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7179 (mt-10) REVERT: A 211 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8164 (pp) REVERT: A 263 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7134 (mm-30) REVERT: A 278 MET cc_start: 0.6627 (mmm) cc_final: 0.6049 (mpm) REVERT: A 772 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.6460 (mtp) REVERT: A 843 ASP cc_start: 0.7625 (t70) cc_final: 0.7407 (t70) REVERT: A 861 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7517 (mt0) REVERT: A 1041 LYS cc_start: 0.7202 (tttm) cc_final: 0.6906 (tppp) REVERT: B 340 ARG cc_start: 0.7893 (mmm-85) cc_final: 0.7013 (mtm-85) REVERT: B 364 MET cc_start: 0.6315 (OUTLIER) cc_final: 0.5645 (mpt) REVERT: B 478 GLN cc_start: 0.7148 (tp40) cc_final: 0.6654 (tm-30) REVERT: B 542 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.5844 (ttm170) REVERT: B 562 ARG cc_start: 0.6906 (mtp180) cc_final: 0.6487 (mtp-110) outliers start: 48 outliers final: 30 residues processed: 265 average time/residue: 1.3595 time to fit residues: 384.4952 Evaluate side-chains 272 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 235 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 777 ARG Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 947 TYR Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 1017 ASP Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1034 GLU Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 542 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 89 optimal weight: 20.0000 chunk 35 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 113 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS A 826 ASN A 958 GLN ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10793 Z= 0.237 Angle : 0.636 11.305 14548 Z= 0.312 Chirality : 0.043 0.177 1570 Planarity : 0.004 0.042 1871 Dihedral : 5.887 59.106 1426 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.42 % Allowed : 32.63 % Favored : 62.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.92 (0.24), residues: 1270 helix: 1.75 (0.21), residues: 599 sheet: 0.04 (0.39), residues: 162 loop : -0.53 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 669 HIS 0.005 0.001 HIS A 59 PHE 0.012 0.002 PHE A 667 TYR 0.019 0.001 TYR B 470 ARG 0.010 0.000 ARG B 557 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 237 time to evaluate : 1.368 Fit side-chains REVERT: A 148 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7649 (tppt) REVERT: A 172 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7207 (mt-10) REVERT: A 211 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8189 (pp) REVERT: A 263 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.7146 (mm-30) REVERT: A 278 MET cc_start: 0.6704 (mmm) cc_final: 0.6208 (mpp) REVERT: A 697 MET cc_start: 0.6626 (OUTLIER) cc_final: 0.6389 (mtp) REVERT: A 772 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.6554 (mtp) REVERT: A 777 ARG cc_start: 0.6017 (OUTLIER) cc_final: 0.4519 (mpt90) REVERT: A 843 ASP cc_start: 0.7636 (t70) cc_final: 0.7410 (t70) REVERT: A 861 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7529 (mt0) REVERT: A 1041 LYS cc_start: 0.7215 (tttm) cc_final: 0.6923 (tppp) REVERT: B 340 ARG cc_start: 0.7922 (mmm-85) cc_final: 0.7008 (mtm-85) REVERT: B 364 MET cc_start: 0.6313 (OUTLIER) cc_final: 0.5642 (mpt) REVERT: B 478 GLN cc_start: 0.7155 (tp40) cc_final: 0.6627 (tp-100) REVERT: B 479 MET cc_start: 0.6564 (mtm) cc_final: 0.6353 (mpp) REVERT: B 542 ARG cc_start: 0.7313 (OUTLIER) cc_final: 0.5827 (ttm170) REVERT: B 562 ARG cc_start: 0.6903 (mtp180) cc_final: 0.6477 (mtp-110) outliers start: 51 outliers final: 31 residues processed: 264 average time/residue: 1.3748 time to fit residues: 387.7088 Evaluate side-chains 276 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 235 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 777 ARG Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 947 TYR Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 1017 ASP Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1034 GLU Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 542 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 3.9990 chunk 120 optimal weight: 20.0000 chunk 73 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 126 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS A 826 ASN A 931 HIS A 958 GLN ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 10793 Z= 0.331 Angle : 0.703 12.351 14548 Z= 0.346 Chirality : 0.046 0.185 1570 Planarity : 0.004 0.060 1871 Dihedral : 5.957 58.126 1423 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.25 % Allowed : 32.88 % Favored : 62.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.73 (0.23), residues: 1270 helix: 1.57 (0.21), residues: 598 sheet: -0.07 (0.39), residues: 163 loop : -0.59 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 574 HIS 0.007 0.001 HIS A 59 PHE 0.014 0.002 PHE A 980 TYR 0.024 0.002 TYR B 470 ARG 0.011 0.001 ARG B 557 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 235 time to evaluate : 1.387 Fit side-chains REVERT: A 148 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7684 (tppt) REVERT: A 172 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7193 (mt-10) REVERT: A 211 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8214 (pp) REVERT: A 263 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.7143 (mm-30) REVERT: A 697 MET cc_start: 0.6793 (OUTLIER) cc_final: 0.6349 (mpp) REVERT: A 772 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.6702 (mtp) REVERT: A 777 ARG cc_start: 0.6082 (OUTLIER) cc_final: 0.4613 (mpt90) REVERT: A 843 ASP cc_start: 0.7705 (t70) cc_final: 0.7471 (t70) REVERT: A 861 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7532 (mt0) REVERT: A 1041 LYS cc_start: 0.7284 (tttm) cc_final: 0.7016 (tppp) REVERT: B 319 ASN cc_start: 0.1028 (OUTLIER) cc_final: 0.0307 (m110) REVERT: B 340 ARG cc_start: 0.7949 (mmm-85) cc_final: 0.7008 (mtm-85) REVERT: B 364 MET cc_start: 0.6340 (OUTLIER) cc_final: 0.5670 (mpt) REVERT: B 478 GLN cc_start: 0.7179 (tp40) cc_final: 0.6633 (tp-100) REVERT: B 542 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.5772 (ttm170) REVERT: B 562 ARG cc_start: 0.6881 (mtp180) cc_final: 0.6572 (mtp-110) outliers start: 49 outliers final: 32 residues processed: 263 average time/residue: 1.4266 time to fit residues: 400.6578 Evaluate side-chains 280 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 237 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 777 ARG Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 947 TYR Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1017 ASP Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1034 GLU Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 576 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 100 optimal weight: 9.9990 chunk 42 optimal weight: 0.7980 chunk 103 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 18 optimal weight: 0.4980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS A 826 ASN A 931 HIS A 958 GLN ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN B 552 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.186512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.145614 restraints weight = 23098.383| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.60 r_work: 0.3436 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3298 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3298 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10793 Z= 0.204 Angle : 0.643 11.988 14548 Z= 0.315 Chirality : 0.042 0.166 1570 Planarity : 0.004 0.045 1871 Dihedral : 5.774 58.889 1423 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.65 % Allowed : 33.31 % Favored : 63.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.90 (0.24), residues: 1270 helix: 1.75 (0.21), residues: 598 sheet: 0.01 (0.38), residues: 168 loop : -0.55 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 669 HIS 0.005 0.001 HIS A 59 PHE 0.011 0.001 PHE A 667 TYR 0.018 0.001 TYR B 470 ARG 0.011 0.000 ARG B 557 =============================================================================== Job complete usr+sys time: 6035.40 seconds wall clock time: 106 minutes 15.73 seconds (6375.73 seconds total)