Starting phenix.real_space_refine on Wed May 15 02:16:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4y_42977/05_2024/8v4y_42977_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4y_42977/05_2024/8v4y_42977.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4y_42977/05_2024/8v4y_42977.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4y_42977/05_2024/8v4y_42977.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4y_42977/05_2024/8v4y_42977_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4y_42977/05_2024/8v4y_42977_updated.pdb" } resolution = 2.8 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= 0.006 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 32 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians P 296 5.49 5 Mg 1 5.21 5 S 34 5.16 5 Be 1 3.05 5 C 9094 2.51 5 N 2943 2.21 5 O 3504 1.98 5 F 3 1.80 5 H 13550 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 74": "OE1" <-> "OE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C ASP 90": "OD1" <-> "OD2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "D PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "W GLU 279": "OE1" <-> "OE2" Residue "W PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W GLU 316": "OE1" <-> "OE2" Residue "W PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W ASP 442": "OD1" <-> "OD2" Residue "W TYR 518": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W ASP 530": "OD1" <-> "OD2" Residue "W TYR 577": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W ASP 578": "OD1" <-> "OD2" Residue "W GLU 619": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 29426 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1604 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "B" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1468 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "C" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1730 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1542 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1604 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 1371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1371 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1752 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1542 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "I" Number of atoms: 4680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 4680 Classifications: {'DNA': 147} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 4646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 4646 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "W" Number of atoms: 7455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 7455 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 18, 'TRANS': 430} Chain breaks: 1 Chain: "W" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 12.76, per 1000 atoms: 0.43 Number of scatterers: 29426 At special positions: 0 Unit cell: (148.19, 128.714, 116.858, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) S 34 16.00 P 296 15.00 Mg 1 11.99 F 3 9.00 O 3504 8.00 N 2943 7.00 C 9094 6.00 Be 1 4.00 H 13550 1.00 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: 25.41 Conformation dependent library (CDL) restraints added in 2.0 seconds 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2298 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 2 sheets defined 57.0% alpha, 3.5% beta 38 base pairs and 190 stacking pairs defined. Time for finding SS restraints: 16.11 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 removed outlier: 3.581A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 78 removed outlier: 3.868A pdb=" N LEU A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 112 removed outlier: 3.748A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 130 Processing helix chain 'B' and resid 16 through 18 No H-bonds generated for 'chain 'B' and resid 16 through 18' Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 31 through 40 removed outlier: 3.666A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 75 removed outlier: 3.859A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 27 through 35 Processing helix chain 'C' and resid 47 through 72 removed outlier: 3.868A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 removed outlier: 3.654A pdb=" N GLN C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'C' and resid 113 through 115 No H-bonds generated for 'chain 'C' and resid 113 through 115' Processing helix chain 'D' and resid 35 through 45 removed outlier: 3.732A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 80 removed outlier: 3.634A pdb=" N ALA D 78 " --> pdb=" O ALA D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 101 through 119 removed outlier: 3.518A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.599A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 77 removed outlier: 4.194A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 113 Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 40 Processing helix chain 'F' and resid 48 through 75 removed outlier: 3.924A pdb=" N TYR F 51 " --> pdb=" O GLY F 48 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU F 52 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG F 55 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU F 58 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU F 63 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE F 66 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG F 67 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU F 74 " --> pdb=" O THR F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 92 Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 47 through 72 removed outlier: 3.612A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 88 Processing helix chain 'G' and resid 93 through 96 No H-bonds generated for 'chain 'G' and resid 93 through 96' Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 35 through 45 removed outlier: 3.789A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 80 Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 101 through 121 Processing helix chain 'W' and resid 182 through 197 Processing helix chain 'W' and resid 211 through 224 Processing helix chain 'W' and resid 238 through 251 removed outlier: 3.645A pdb=" N LEU W 241 " --> pdb=" O LYS W 238 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N HIS W 242 " --> pdb=" O SER W 239 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TRP W 244 " --> pdb=" O LEU W 241 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N MET W 245 " --> pdb=" O HIS W 242 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TRP W 251 " --> pdb=" O PHE W 248 " (cutoff:3.500A) Processing helix chain 'W' and resid 264 through 273 Processing helix chain 'W' and resid 287 through 292 Processing helix chain 'W' and resid 294 through 299 removed outlier: 4.157A pdb=" N LYS W 299 " --> pdb=" O SER W 295 " (cutoff:3.500A) Processing helix chain 'W' and resid 310 through 313 Processing helix chain 'W' and resid 319 through 326 removed outlier: 3.575A pdb=" N ARG W 325 " --> pdb=" O SER W 321 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU W 326 " --> pdb=" O GLU W 322 " (cutoff:3.500A) Processing helix chain 'W' and resid 344 through 354 removed outlier: 4.375A pdb=" N LEU W 350 " --> pdb=" O GLU W 346 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE W 353 " --> pdb=" O SER W 349 " (cutoff:3.500A) Processing helix chain 'W' and resid 362 through 368 removed outlier: 5.177A pdb=" N SER W 367 " --> pdb=" O ASP W 363 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TRP W 368 " --> pdb=" O ASP W 364 " (cutoff:3.500A) Processing helix chain 'W' and resid 386 through 389 No H-bonds generated for 'chain 'W' and resid 386 through 389' Processing helix chain 'W' and resid 397 through 400 No H-bonds generated for 'chain 'W' and resid 397 through 400' Processing helix chain 'W' and resid 418 through 429 Processing helix chain 'W' and resid 439 through 441 No H-bonds generated for 'chain 'W' and resid 439 through 441' Processing helix chain 'W' and resid 449 through 458 Processing helix chain 'W' and resid 460 through 462 No H-bonds generated for 'chain 'W' and resid 460 through 462' Processing helix chain 'W' and resid 476 through 480 Processing helix chain 'W' and resid 483 through 496 removed outlier: 3.613A pdb=" N ASP W 489 " --> pdb=" O MET W 485 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LYS W 490 " --> pdb=" O VAL W 486 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N LEU W 491 " --> pdb=" O VAL W 487 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N LEU W 492 " --> pdb=" O LEU W 488 " (cutoff:3.500A) Proline residue: W 493 - end of helix Processing helix chain 'W' and resid 509 through 522 Processing helix chain 'W' and resid 535 through 546 removed outlier: 3.744A pdb=" N GLN W 539 " --> pdb=" O HIS W 535 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP W 540 " --> pdb=" O ASP W 536 " (cutoff:3.500A) Processing helix chain 'W' and resid 559 through 562 No H-bonds generated for 'chain 'W' and resid 559 through 562' Processing helix chain 'W' and resid 583 through 592 Processing helix chain 'W' and resid 614 through 628 removed outlier: 4.169A pdb=" N LEU W 627 " --> pdb=" O MET W 623 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP W 628 " --> pdb=" O LYS W 624 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'W' and resid 332 through 335 removed outlier: 6.338A pdb=" N LEU W 305 " --> pdb=" O LEU W 333 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N LEU W 335 " --> pdb=" O LEU W 305 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE W 307 " --> pdb=" O LEU W 335 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'W' and resid 408 through 414 448 hydrogen bonds defined for protein. 1269 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 84 hydrogen bonds 168 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 190 stacking parallelities Total time for adding SS restraints: 12.01 Time building geometry restraints manager: 25.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 13544 1.02 - 1.22: 290 1.22 - 1.42: 6691 1.42 - 1.62: 9728 1.62 - 1.82: 65 Bond restraints: 30318 Sorted by residual: bond pdb=" BE BEF W1103 " pdb=" F1 BEF W1103 " ideal model delta sigma weight residual 1.476 1.761 -0.285 2.00e-02 2.50e+03 2.03e+02 bond pdb=" BE BEF W1103 " pdb=" F2 BEF W1103 " ideal model delta sigma weight residual 1.476 1.760 -0.284 2.00e-02 2.50e+03 2.02e+02 bond pdb=" BE BEF W1103 " pdb=" F3 BEF W1103 " ideal model delta sigma weight residual 1.476 1.759 -0.283 2.00e-02 2.50e+03 2.01e+02 bond pdb=" ND2 ASN W 567 " pdb="HD22 ASN W 567 " ideal model delta sigma weight residual 0.860 0.982 -0.122 2.00e-02 2.50e+03 3.70e+01 bond pdb=" ND2 ASN W 436 " pdb="HD21 ASN W 436 " ideal model delta sigma weight residual 0.860 0.981 -0.121 2.00e-02 2.50e+03 3.67e+01 ... (remaining 30313 not shown) Histogram of bond angle deviations from ideal: 95.72 - 103.81: 562 103.81 - 111.89: 32957 111.89 - 119.97: 11987 119.97 - 128.06: 8980 128.06 - 136.14: 456 Bond angle restraints: 54942 Sorted by residual: angle pdb=" N VAL W 502 " pdb=" CA VAL W 502 " pdb=" C VAL W 502 " ideal model delta sigma weight residual 108.48 122.01 -13.53 1.44e+00 4.82e-01 8.83e+01 angle pdb=" N TRP W 177 " pdb=" CA TRP W 177 " pdb=" C TRP W 177 " ideal model delta sigma weight residual 111.71 121.63 -9.92 1.15e+00 7.56e-01 7.44e+01 angle pdb=" N GLY D 101 " pdb=" CA GLY D 101 " pdb=" C GLY D 101 " ideal model delta sigma weight residual 112.73 122.47 -9.74 1.20e+00 6.94e-01 6.59e+01 angle pdb=" N ARG E 83 " pdb=" CA ARG E 83 " pdb=" C ARG E 83 " ideal model delta sigma weight residual 109.95 98.74 11.21 1.44e+00 4.82e-01 6.06e+01 angle pdb=" N GLY W 201 " pdb=" CA GLY W 201 " pdb=" C GLY W 201 " ideal model delta sigma weight residual 112.61 124.64 -12.03 1.60e+00 3.91e-01 5.65e+01 ... (remaining 54937 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.81: 11691 29.81 - 59.62: 1199 59.62 - 89.44: 44 89.44 - 119.25: 1 119.25 - 149.06: 1 Dihedral angle restraints: 12936 sinusoidal: 8882 harmonic: 4054 Sorted by residual: dihedral pdb=" O1B ADP W1101 " pdb=" O3A ADP W1101 " pdb=" PB ADP W1101 " pdb=" PA ADP W1101 " ideal model delta sinusoidal sigma weight residual -60.00 -164.12 104.11 1 2.00e+01 2.50e-03 2.99e+01 dihedral pdb=" CA THR W 609 " pdb=" C THR W 609 " pdb=" N ASP W 610 " pdb=" CA ASP W 610 " ideal model delta harmonic sigma weight residual -180.00 -155.56 -24.44 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA PRO H 100 " pdb=" C PRO H 100 " pdb=" N GLY H 101 " pdb=" CA GLY H 101 " ideal model delta harmonic sigma weight residual -180.00 -158.71 -21.29 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 12933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 2320 0.103 - 0.205: 318 0.205 - 0.308: 59 0.308 - 0.411: 5 0.411 - 0.514: 2 Chirality restraints: 2704 Sorted by residual: chirality pdb=" CA ARG E 40 " pdb=" N ARG E 40 " pdb=" C ARG E 40 " pdb=" CB ARG E 40 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.59e+00 chirality pdb=" CA LYS D 82 " pdb=" N LYS D 82 " pdb=" C LYS D 82 " pdb=" CB LYS D 82 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" CA ASP W 281 " pdb=" N ASP W 281 " pdb=" C ASP W 281 " pdb=" CB ASP W 281 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.02e+00 ... (remaining 2701 not shown) Planarity restraints: 3394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 38 " -0.087 2.00e-02 2.50e+03 4.88e-01 3.58e+03 pdb=" CG ASN C 38 " 0.002 2.00e-02 2.50e+03 pdb=" OD1 ASN C 38 " 0.085 2.00e-02 2.50e+03 pdb=" ND2 ASN C 38 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN C 38 " -0.842 2.00e-02 2.50e+03 pdb="HD22 ASN C 38 " 0.841 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN W 342 " 0.292 2.00e-02 2.50e+03 4.39e-01 2.89e+03 pdb=" CG ASN W 342 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN W 342 " -0.287 2.00e-02 2.50e+03 pdb=" ND2 ASN W 342 " 0.003 2.00e-02 2.50e+03 pdb="HD21 ASN W 342 " 0.709 2.00e-02 2.50e+03 pdb="HD22 ASN W 342 " -0.695 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN W 360 " -0.301 2.00e-02 2.50e+03 4.29e-01 2.76e+03 pdb=" CG ASN W 360 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN W 360 " 0.291 2.00e-02 2.50e+03 pdb=" ND2 ASN W 360 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN W 360 " -0.692 2.00e-02 2.50e+03 pdb="HD22 ASN W 360 " 0.670 2.00e-02 2.50e+03 ... (remaining 3391 not shown) Histogram of nonbonded interaction distances: 1.01 - 1.73: 14 1.73 - 2.44: 13135 2.44 - 3.16: 83242 3.16 - 3.88: 111146 3.88 - 4.60: 180937 Nonbonded interactions: 388474 Sorted by model distance: nonbonded pdb=" HB THR W 474 " pdb=" HE1 HIS W 477 " model vdw 1.007 2.270 nonbonded pdb=" HH TYR W 461 " pdb=" HD2 HIS W 477 " model vdw 1.154 2.100 nonbonded pdb="HH22 ARG A 72 " pdb=" OP1 DC J 51 " model vdw 1.161 1.850 nonbonded pdb="HH12 ARG C 11 " pdb=" H1' DT I 178 " model vdw 1.192 2.270 nonbonded pdb=" HB THR W 474 " pdb=" CE1 HIS W 477 " model vdw 1.283 2.970 ... (remaining 388469 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 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 20 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 11 through 118) } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.410 Extract box with map and model: 13.020 Check model and map are aligned: 0.190 Set scattering table: 0.220 Process input model: 104.100 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.100 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:12.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 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 : 0.011 0.285 16768 Z= 0.695 Angle : 1.331 13.529 23904 Z= 0.893 Chirality : 0.077 0.514 2704 Planarity : 0.011 0.111 1995 Dihedral : 20.030 149.062 7056 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.67 % Favored : 96.16 % Rotamer: Outliers : 0.67 % Allowed : 2.85 % Favored : 96.48 % 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: -1.09 (0.22), residues: 1199 helix: -0.52 (0.17), residues: 721 sheet: 0.43 (0.57), residues: 73 loop : -1.05 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.008 TRP W 348 HIS 0.011 0.003 HIS H 106 PHE 0.043 0.008 PHE W 297 TYR 0.116 0.011 TYR G 57 ARG 0.009 0.001 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 226 time to evaluate : 2.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 95 LYS cc_start: 0.8842 (ttmt) cc_final: 0.8637 (tmtt) REVERT: E 79 LYS cc_start: 0.8754 (tttt) cc_final: 0.8507 (tttp) REVERT: E 105 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7521 (mt-10) REVERT: E 115 LYS cc_start: 0.8840 (mttt) cc_final: 0.8520 (mtmp) REVERT: F 68 ASP cc_start: 0.8292 (m-30) cc_final: 0.8015 (m-30) REVERT: H 117 LYS cc_start: 0.9076 (tttt) cc_final: 0.8866 (tttm) outliers start: 7 outliers final: 2 residues processed: 233 average time/residue: 4.5295 time to fit residues: 1121.6325 Evaluate side-chains 136 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 134 time to evaluate : 2.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain W residue 432 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 112 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 93 GLN H 46 HIS W 342 ASN W 477 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16768 Z= 0.212 Angle : 0.636 5.804 23904 Z= 0.377 Chirality : 0.041 0.146 2704 Planarity : 0.005 0.054 1995 Dihedral : 22.949 165.354 4579 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.25 % Favored : 97.66 % Rotamer: Outliers : 1.33 % Allowed : 13.04 % Favored : 85.63 % 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: 0.72 (0.23), residues: 1199 helix: 1.34 (0.19), residues: 714 sheet: 0.84 (0.58), residues: 72 loop : -1.10 (0.27), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP W 348 HIS 0.015 0.001 HIS W 477 PHE 0.009 0.001 PHE E 78 TYR 0.012 0.001 TYR W 195 ARG 0.006 0.001 ARG E 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 143 time to evaluate : 1.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 95 LYS cc_start: 0.8739 (ttmt) cc_final: 0.8488 (tmtt) REVERT: D 65 ASP cc_start: 0.7945 (t0) cc_final: 0.7653 (t0) REVERT: E 79 LYS cc_start: 0.8660 (tttt) cc_final: 0.8399 (tttp) REVERT: E 115 LYS cc_start: 0.8842 (mttt) cc_final: 0.8497 (mtmp) REVERT: W 444 MET cc_start: 0.8045 (ttp) cc_final: 0.7819 (ttm) outliers start: 14 outliers final: 3 residues processed: 148 average time/residue: 3.4423 time to fit residues: 551.0435 Evaluate side-chains 134 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 131 time to evaluate : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain W residue 429 MET Chi-restraints excluded: chain W residue 432 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 341 GLN W 598 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 16768 Z= 0.333 Angle : 0.675 6.288 23904 Z= 0.398 Chirality : 0.044 0.165 2704 Planarity : 0.005 0.043 1995 Dihedral : 25.121 168.245 4578 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.59 % Favored : 96.25 % Rotamer: Outliers : 2.19 % Allowed : 12.46 % Favored : 85.35 % 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: 1.07 (0.24), residues: 1199 helix: 1.73 (0.20), residues: 713 sheet: 0.67 (0.60), residues: 74 loop : -1.12 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP W 280 HIS 0.008 0.001 HIS W 477 PHE 0.013 0.001 PHE E 84 TYR 0.012 0.002 TYR E 54 ARG 0.009 0.001 ARG E 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 136 time to evaluate : 1.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8220 (mttp) cc_final: 0.7972 (mttp) REVERT: C 41 GLU cc_start: 0.7929 (tt0) cc_final: 0.7707 (tt0) REVERT: C 95 LYS cc_start: 0.8769 (ttmt) cc_final: 0.8494 (tmtm) REVERT: D 65 ASP cc_start: 0.8050 (t0) cc_final: 0.7665 (t0) REVERT: E 79 LYS cc_start: 0.8760 (tttt) cc_final: 0.8514 (tttp) REVERT: E 94 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7068 (mp0) REVERT: E 115 LYS cc_start: 0.8792 (mttt) cc_final: 0.8438 (mtmp) REVERT: F 91 LYS cc_start: 0.8472 (tttp) cc_final: 0.8187 (ttpp) REVERT: G 74 LYS cc_start: 0.8669 (mtpt) cc_final: 0.8326 (mmmt) REVERT: W 620 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.7005 (mmm160) outliers start: 23 outliers final: 9 residues processed: 149 average time/residue: 4.0176 time to fit residues: 648.4024 Evaluate side-chains 136 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 125 time to evaluate : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain W residue 263 ASP Chi-restraints excluded: chain W residue 367 SER Chi-restraints excluded: chain W residue 429 MET Chi-restraints excluded: chain W residue 519 CYS Chi-restraints excluded: chain W residue 620 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 16768 Z= 0.289 Angle : 0.605 6.119 23904 Z= 0.361 Chirality : 0.043 0.156 2704 Planarity : 0.004 0.046 1995 Dihedral : 25.306 160.316 4576 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.67 % Favored : 96.16 % Rotamer: Outliers : 1.43 % Allowed : 13.70 % Favored : 84.87 % 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: 1.24 (0.25), residues: 1199 helix: 1.89 (0.20), residues: 714 sheet: 0.78 (0.61), residues: 74 loop : -1.13 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP W 348 HIS 0.003 0.001 HIS E 113 PHE 0.009 0.001 PHE B 61 TYR 0.008 0.001 TYR A 54 ARG 0.010 0.001 ARG E 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 131 time to evaluate : 1.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8219 (mttp) cc_final: 0.7988 (mttp) REVERT: C 41 GLU cc_start: 0.7934 (tt0) cc_final: 0.7709 (tt0) REVERT: C 95 LYS cc_start: 0.8743 (ttmt) cc_final: 0.8454 (tptt) REVERT: D 65 ASP cc_start: 0.7992 (t0) cc_final: 0.7585 (t0) REVERT: E 42 ARG cc_start: 0.7826 (mtp85) cc_final: 0.7598 (mtp180) REVERT: E 79 LYS cc_start: 0.8660 (tttt) cc_final: 0.8419 (tttp) REVERT: E 94 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7056 (mp0) REVERT: E 115 LYS cc_start: 0.8790 (mttt) cc_final: 0.8439 (mtmp) REVERT: F 91 LYS cc_start: 0.8469 (tttp) cc_final: 0.8194 (ttpp) REVERT: G 74 LYS cc_start: 0.8828 (mtpt) cc_final: 0.8507 (mmmt) REVERT: W 284 VAL cc_start: 0.8926 (t) cc_final: 0.8666 (m) REVERT: W 620 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.6907 (mmm160) outliers start: 15 outliers final: 7 residues processed: 137 average time/residue: 3.7965 time to fit residues: 558.6589 Evaluate side-chains 136 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 127 time to evaluate : 2.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain W residue 263 ASP Chi-restraints excluded: chain W residue 429 MET Chi-restraints excluded: chain W residue 620 ARG Chi-restraints excluded: chain W residue 622 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16768 Z= 0.299 Angle : 0.603 6.345 23904 Z= 0.358 Chirality : 0.043 0.151 2704 Planarity : 0.005 0.044 1995 Dihedral : 25.846 158.622 4576 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.17 % Favored : 95.66 % Rotamer: Outliers : 1.62 % Allowed : 13.89 % Favored : 84.49 % 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: 1.28 (0.25), residues: 1199 helix: 1.95 (0.20), residues: 714 sheet: 0.63 (0.61), residues: 75 loop : -1.14 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP W 348 HIS 0.003 0.001 HIS E 113 PHE 0.009 0.001 PHE B 61 TYR 0.016 0.001 TYR W 195 ARG 0.007 0.001 ARG E 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 133 time to evaluate : 1.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8230 (mttp) cc_final: 0.7996 (mttp) REVERT: C 41 GLU cc_start: 0.7926 (tt0) cc_final: 0.7704 (tt0) REVERT: C 95 LYS cc_start: 0.8780 (ttmt) cc_final: 0.8500 (tptt) REVERT: C 114 VAL cc_start: 0.8504 (t) cc_final: 0.8258 (p) REVERT: D 65 ASP cc_start: 0.7996 (t0) cc_final: 0.7601 (t0) REVERT: E 42 ARG cc_start: 0.7832 (mtp85) cc_final: 0.7594 (mtp180) REVERT: E 79 LYS cc_start: 0.8705 (tttt) cc_final: 0.8470 (tttp) REVERT: E 94 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7062 (mp0) REVERT: E 115 LYS cc_start: 0.8776 (mttt) cc_final: 0.8440 (mtmp) REVERT: E 120 MET cc_start: 0.8087 (mtm) cc_final: 0.7728 (mtp) REVERT: F 91 LYS cc_start: 0.8487 (tttp) cc_final: 0.8202 (ttpp) REVERT: G 74 LYS cc_start: 0.8871 (mtpt) cc_final: 0.8524 (mmmt) REVERT: W 284 VAL cc_start: 0.8922 (t) cc_final: 0.8709 (m) REVERT: W 620 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.6924 (mmm160) outliers start: 17 outliers final: 8 residues processed: 143 average time/residue: 3.8854 time to fit residues: 596.6687 Evaluate side-chains 133 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 123 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain W residue 263 ASP Chi-restraints excluded: chain W residue 367 SER Chi-restraints excluded: chain W residue 429 MET Chi-restraints excluded: chain W residue 620 ARG Chi-restraints excluded: chain W residue 622 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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: 0.7264 moved from start: 0.5273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16768 Z= 0.271 Angle : 0.583 6.020 23904 Z= 0.347 Chirality : 0.042 0.148 2704 Planarity : 0.004 0.045 1995 Dihedral : 26.042 160.179 4576 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.00 % Favored : 96.83 % Rotamer: Outliers : 1.05 % Allowed : 14.65 % Favored : 84.30 % 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: 1.37 (0.25), residues: 1199 helix: 2.05 (0.20), residues: 714 sheet: 0.62 (0.61), residues: 75 loop : -1.14 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP W 348 HIS 0.003 0.001 HIS W 477 PHE 0.013 0.001 PHE W 391 TYR 0.008 0.001 TYR B 51 ARG 0.004 0.000 ARG E 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 130 time to evaluate : 2.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8251 (mttp) cc_final: 0.8021 (mttp) REVERT: C 41 GLU cc_start: 0.7935 (tt0) cc_final: 0.7724 (tt0) REVERT: C 95 LYS cc_start: 0.8779 (ttmt) cc_final: 0.8503 (tptt) REVERT: C 114 VAL cc_start: 0.8537 (t) cc_final: 0.8259 (p) REVERT: D 65 ASP cc_start: 0.7971 (t0) cc_final: 0.7576 (t0) REVERT: E 42 ARG cc_start: 0.7779 (mtp85) cc_final: 0.7521 (mtp180) REVERT: E 53 ARG cc_start: 0.7128 (ttp80) cc_final: 0.6883 (ttm170) REVERT: E 79 LYS cc_start: 0.8662 (tttt) cc_final: 0.8429 (tttp) REVERT: E 94 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7800 (mm-30) REVERT: E 115 LYS cc_start: 0.8785 (mttt) cc_final: 0.8454 (mtmp) REVERT: E 120 MET cc_start: 0.8108 (mtm) cc_final: 0.7723 (mtp) REVERT: F 91 LYS cc_start: 0.8475 (tttp) cc_final: 0.8205 (ttpp) REVERT: G 74 LYS cc_start: 0.8887 (mtpt) cc_final: 0.8531 (mmmt) REVERT: W 284 VAL cc_start: 0.8932 (t) cc_final: 0.8709 (m) REVERT: W 620 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.6888 (mmm160) outliers start: 11 outliers final: 6 residues processed: 136 average time/residue: 4.0787 time to fit residues: 600.9640 Evaluate side-chains 132 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 124 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain W residue 263 ASP Chi-restraints excluded: chain W residue 367 SER Chi-restraints excluded: chain W residue 429 MET Chi-restraints excluded: chain W residue 620 ARG Chi-restraints excluded: chain W residue 622 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.5429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 16768 Z= 0.385 Angle : 0.609 6.067 23904 Z= 0.361 Chirality : 0.045 0.172 2704 Planarity : 0.005 0.044 1995 Dihedral : 26.324 160.660 4576 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.42 % Favored : 95.41 % Rotamer: Outliers : 1.52 % Allowed : 14.08 % Favored : 84.40 % 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: 1.19 (0.25), residues: 1199 helix: 1.91 (0.20), residues: 713 sheet: 0.48 (0.60), residues: 75 loop : -1.21 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP W 348 HIS 0.005 0.001 HIS W 477 PHE 0.011 0.001 PHE B 61 TYR 0.010 0.001 TYR E 41 ARG 0.003 0.000 ARG A 131 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 1.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8266 (mttp) cc_final: 0.8034 (mttp) REVERT: C 41 GLU cc_start: 0.7922 (tt0) cc_final: 0.7716 (tt0) REVERT: C 95 LYS cc_start: 0.8783 (ttmt) cc_final: 0.8512 (tptp) REVERT: C 114 VAL cc_start: 0.8536 (t) cc_final: 0.8267 (p) REVERT: D 65 ASP cc_start: 0.8003 (t0) cc_final: 0.7603 (t0) REVERT: E 42 ARG cc_start: 0.7870 (mtp85) cc_final: 0.7614 (mtp180) REVERT: E 53 ARG cc_start: 0.7143 (ttp80) cc_final: 0.6920 (ttm170) REVERT: E 79 LYS cc_start: 0.8690 (tttt) cc_final: 0.8450 (tttp) REVERT: E 94 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7109 (mp0) REVERT: E 115 LYS cc_start: 0.8778 (mttt) cc_final: 0.8432 (mtmp) REVERT: E 120 MET cc_start: 0.8151 (mtm) cc_final: 0.7780 (mtp) REVERT: F 91 LYS cc_start: 0.8480 (tttp) cc_final: 0.8203 (ttpp) REVERT: G 74 LYS cc_start: 0.8901 (mtpt) cc_final: 0.8514 (mmmt) REVERT: W 284 VAL cc_start: 0.8951 (t) cc_final: 0.8714 (m) REVERT: W 620 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.6866 (mmm160) outliers start: 16 outliers final: 12 residues processed: 133 average time/residue: 3.8497 time to fit residues: 550.2209 Evaluate side-chains 138 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 124 time to evaluate : 1.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain W residue 263 ASP Chi-restraints excluded: chain W residue 367 SER Chi-restraints excluded: chain W residue 388 LEU Chi-restraints excluded: chain W residue 429 MET Chi-restraints excluded: chain W residue 620 ARG Chi-restraints excluded: chain W residue 622 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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: 0.7279 moved from start: 0.5514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16768 Z= 0.252 Angle : 0.581 7.265 23904 Z= 0.345 Chirality : 0.041 0.143 2704 Planarity : 0.004 0.047 1995 Dihedral : 26.375 161.616 4576 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.50 % Favored : 96.33 % Rotamer: Outliers : 1.24 % Allowed : 14.46 % Favored : 84.30 % 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: 1.35 (0.25), residues: 1199 helix: 2.06 (0.20), residues: 713 sheet: 0.38 (0.60), residues: 77 loop : -1.14 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP W 348 HIS 0.004 0.001 HIS W 477 PHE 0.008 0.001 PHE B 61 TYR 0.008 0.001 TYR W 195 ARG 0.003 0.000 ARG E 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 131 time to evaluate : 2.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8082 (pm20) cc_final: 0.7792 (pm20) REVERT: A 64 LYS cc_start: 0.8257 (mttp) cc_final: 0.8025 (mttp) REVERT: C 41 GLU cc_start: 0.7933 (tt0) cc_final: 0.7719 (tt0) REVERT: C 95 LYS cc_start: 0.8774 (ttmt) cc_final: 0.8500 (tptp) REVERT: C 114 VAL cc_start: 0.8542 (t) cc_final: 0.8278 (p) REVERT: D 65 ASP cc_start: 0.7962 (t0) cc_final: 0.7528 (t0) REVERT: E 53 ARG cc_start: 0.7109 (ttp80) cc_final: 0.6815 (ttm170) REVERT: E 79 LYS cc_start: 0.8651 (tttt) cc_final: 0.8425 (tttp) REVERT: E 115 LYS cc_start: 0.8810 (mttt) cc_final: 0.8474 (mtmp) REVERT: E 120 MET cc_start: 0.8123 (mtm) cc_final: 0.7750 (mtp) REVERT: F 91 LYS cc_start: 0.8478 (tttp) cc_final: 0.8204 (ttpp) REVERT: G 74 LYS cc_start: 0.8896 (mtpt) cc_final: 0.8522 (mmmt) REVERT: W 284 VAL cc_start: 0.8955 (t) cc_final: 0.8729 (m) REVERT: W 620 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.6848 (mmm160) outliers start: 13 outliers final: 10 residues processed: 138 average time/residue: 3.8797 time to fit residues: 576.1835 Evaluate side-chains 138 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 127 time to evaluate : 2.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain W residue 263 ASP Chi-restraints excluded: chain W residue 367 SER Chi-restraints excluded: chain W residue 388 LEU Chi-restraints excluded: chain W residue 429 MET Chi-restraints excluded: chain W residue 620 ARG Chi-restraints excluded: chain W residue 622 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 122 optimal weight: 0.3980 chunk 128 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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: 0.7274 moved from start: 0.5605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16768 Z= 0.241 Angle : 0.571 6.269 23904 Z= 0.339 Chirality : 0.040 0.145 2704 Planarity : 0.004 0.045 1995 Dihedral : 26.413 161.881 4576 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.00 % Favored : 95.83 % Rotamer: Outliers : 1.05 % Allowed : 14.37 % Favored : 84.59 % 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 (0.25), residues: 1199 helix: 2.13 (0.20), residues: 714 sheet: 0.60 (0.61), residues: 75 loop : -1.10 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP W 348 HIS 0.003 0.001 HIS W 477 PHE 0.008 0.001 PHE B 61 TYR 0.007 0.001 TYR W 195 ARG 0.003 0.000 ARG E 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 131 time to evaluate : 2.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8079 (pm20) cc_final: 0.7788 (pm20) REVERT: A 64 LYS cc_start: 0.8251 (mttp) cc_final: 0.8022 (mttp) REVERT: C 41 GLU cc_start: 0.7923 (tt0) cc_final: 0.7714 (tt0) REVERT: C 95 LYS cc_start: 0.8749 (ttmt) cc_final: 0.8473 (tptp) REVERT: C 114 VAL cc_start: 0.8549 (t) cc_final: 0.8286 (p) REVERT: D 65 ASP cc_start: 0.7992 (t0) cc_final: 0.7583 (t0) REVERT: E 79 LYS cc_start: 0.8614 (tttt) cc_final: 0.8391 (tttp) REVERT: E 115 LYS cc_start: 0.8790 (mttt) cc_final: 0.8474 (mtmp) REVERT: E 120 MET cc_start: 0.8120 (mtm) cc_final: 0.7755 (mtp) REVERT: F 91 LYS cc_start: 0.8498 (tttp) cc_final: 0.8210 (ttpp) REVERT: G 74 LYS cc_start: 0.8881 (mtpt) cc_final: 0.8518 (mmmt) REVERT: W 284 VAL cc_start: 0.8963 (t) cc_final: 0.8750 (m) REVERT: W 620 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.6797 (mmm160) outliers start: 11 outliers final: 9 residues processed: 138 average time/residue: 3.7927 time to fit residues: 568.3140 Evaluate side-chains 137 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 127 time to evaluate : 2.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain W residue 263 ASP Chi-restraints excluded: chain W residue 367 SER Chi-restraints excluded: chain W residue 388 LEU Chi-restraints excluded: chain W residue 429 MET Chi-restraints excluded: chain W residue 620 ARG Chi-restraints excluded: chain W residue 622 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 0.3980 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- 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: 0.7283 moved from start: 0.5650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16768 Z= 0.265 Angle : 0.583 9.141 23904 Z= 0.343 Chirality : 0.041 0.147 2704 Planarity : 0.004 0.046 1995 Dihedral : 26.481 162.043 4576 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.92 % Favored : 95.91 % Rotamer: Outliers : 1.14 % Allowed : 14.56 % Favored : 84.30 % 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: 1.40 (0.25), residues: 1199 helix: 2.11 (0.20), residues: 713 sheet: 0.23 (0.59), residues: 77 loop : -1.11 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP W 348 HIS 0.004 0.001 HIS W 477 PHE 0.009 0.001 PHE B 61 TYR 0.007 0.001 TYR W 183 ARG 0.003 0.000 ARG A 131 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 128 time to evaluate : 1.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8088 (pm20) cc_final: 0.7800 (pm20) REVERT: A 64 LYS cc_start: 0.8256 (mttp) cc_final: 0.8030 (mttp) REVERT: C 41 GLU cc_start: 0.7929 (tt0) cc_final: 0.7725 (tt0) REVERT: C 95 LYS cc_start: 0.8775 (ttmt) cc_final: 0.8503 (tptp) REVERT: C 114 VAL cc_start: 0.8564 (t) cc_final: 0.8308 (p) REVERT: D 65 ASP cc_start: 0.7959 (t0) cc_final: 0.7554 (t0) REVERT: E 79 LYS cc_start: 0.8609 (tttt) cc_final: 0.8388 (tttp) REVERT: E 115 LYS cc_start: 0.8794 (mttt) cc_final: 0.8473 (mtmp) REVERT: E 120 MET cc_start: 0.8135 (mtm) cc_final: 0.7773 (mtp) REVERT: F 91 LYS cc_start: 0.8499 (tttp) cc_final: 0.8214 (ttpp) REVERT: G 74 LYS cc_start: 0.8897 (mtpt) cc_final: 0.8528 (mmmt) REVERT: W 284 VAL cc_start: 0.8969 (t) cc_final: 0.8758 (m) REVERT: W 620 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.6802 (mmm160) outliers start: 12 outliers final: 9 residues processed: 136 average time/residue: 3.9008 time to fit residues: 570.4583 Evaluate side-chains 135 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 125 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain W residue 263 ASP Chi-restraints excluded: chain W residue 367 SER Chi-restraints excluded: chain W residue 388 LEU Chi-restraints excluded: chain W residue 429 MET Chi-restraints excluded: chain W residue 620 ARG Chi-restraints excluded: chain W residue 622 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.084183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.064018 restraints weight = 88029.086| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.44 r_work: 0.2921 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.5728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16768 Z= 0.222 Angle : 0.575 9.061 23904 Z= 0.338 Chirality : 0.040 0.145 2704 Planarity : 0.004 0.046 1995 Dihedral : 26.504 162.412 4576 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.09 % Favored : 95.75 % Rotamer: Outliers : 0.95 % Allowed : 15.03 % Favored : 84.02 % 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: 1.52 (0.25), residues: 1199 helix: 2.17 (0.20), residues: 716 sheet: 0.32 (0.59), residues: 77 loop : -1.03 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP W 348 HIS 0.003 0.001 HIS W 477 PHE 0.008 0.001 PHE B 61 TYR 0.007 0.001 TYR B 51 ARG 0.002 0.000 ARG A 131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12218.95 seconds wall clock time: 215 minutes 34.20 seconds (12934.20 seconds total)