Starting phenix.real_space_refine on Sat Aug 10 10:58:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4y_42977/08_2024/8v4y_42977.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4y_42977/08_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_42977/08_2024/8v4y_42977.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4y_42977/08_2024/8v4y_42977.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4y_42977/08_2024/8v4y_42977.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4y_42977/08_2024/8v4y_42977.cif" } 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-5409/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: 13.60, per 1000 atoms: 0.46 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: 22.80 Conformation dependent library (CDL) restraints added in 2.2 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... Secondary structure from input PDB file: 61 helices and 12 sheets defined 65.3% alpha, 5.6% beta 38 base pairs and 190 stacking pairs defined. Time for finding SS restraints: 12.70 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.581A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.502A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) 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 85 through 113 removed outlier: 3.645A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.653A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 19 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 removed outlier: 3.666A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.554A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.600A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.868A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.691A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.732A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.634A pdb=" N ALA D 78 " --> pdb=" O ALA D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 120 removed outlier: 3.518A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 removed outlier: 3.534A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.636A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.570A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.689A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.532A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.513A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.612A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.569A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.789A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 122 Processing helix chain 'W' and resid 181 through 198 Processing helix chain 'W' and resid 210 through 225 Processing helix chain 'W' and resid 237 through 239 No H-bonds generated for 'chain 'W' and resid 237 through 239' Processing helix chain 'W' and resid 240 through 252 removed outlier: 3.523A pdb=" N MET W 245 " --> pdb=" O LEU W 241 " (cutoff:3.500A) Processing helix chain 'W' and resid 263 through 274 Processing helix chain 'W' and resid 287 through 293 Processing helix chain 'W' and resid 293 through 298 Processing helix chain 'W' and resid 310 through 314 Processing helix chain 'W' and resid 318 through 325 removed outlier: 3.575A pdb=" N ARG W 325 " --> pdb=" O SER W 321 " (cutoff:3.500A) Processing helix chain 'W' and resid 344 through 355 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 361 through 369 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 387 through 391 removed outlier: 4.443A pdb=" N PHE W 391 " --> pdb=" O VAL W 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 387 through 391' Processing helix chain 'W' and resid 396 through 401 Processing helix chain 'W' and resid 417 through 430 Processing helix chain 'W' and resid 438 through 442 Processing helix chain 'W' and resid 448 through 459 removed outlier: 4.059A pdb=" N GLN W 452 " --> pdb=" O ASN W 448 " (cutoff:3.500A) Processing helix chain 'W' and resid 460 through 463 Processing helix chain 'W' and resid 475 through 481 removed outlier: 3.662A pdb=" N VAL W 479 " --> pdb=" O ASP W 475 " (cutoff:3.500A) Processing helix chain 'W' and resid 482 through 489 removed outlier: 3.613A pdb=" N ASP W 489 " --> pdb=" O MET W 485 " (cutoff:3.500A) Processing helix chain 'W' and resid 490 through 497 Processing helix chain 'W' and resid 508 through 523 removed outlier: 3.724A pdb=" N LEU W 512 " --> pdb=" O MET W 508 " (cutoff:3.500A) Processing helix chain 'W' and resid 534 through 547 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 563 Processing helix chain 'W' and resid 582 through 592 removed outlier: 4.084A pdb=" N ASP W 586 " --> pdb=" O ASN W 582 " (cutoff:3.500A) Processing helix chain 'W' and resid 612 through 629 removed outlier: 4.182A pdb=" N ARG W 616 " --> pdb=" O THR W 612 " (cutoff:3.500A) 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=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.643A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.837A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.893A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.822A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.956A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'W' and resid 257 through 260 removed outlier: 6.614A pdb=" N VAL W 258 " --> pdb=" O VAL W 284 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N SER W 286 " --> pdb=" O VAL W 258 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N LEU W 260 " --> pdb=" O SER W 286 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE W 202 " --> pdb=" O LEU W 393 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'W' and resid 408 through 414 removed outlier: 6.570A pdb=" N CYS W 527 " --> pdb=" O MET W 556 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N SER W 558 " --> pdb=" O CYS W 527 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N LEU W 529 " --> pdb=" O SER W 558 " (cutoff:3.500A) 547 hydrogen bonds defined for protein. 1599 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: 11.36 Time building geometry restraints manager: 23.97 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=" F1 BEF W1103 " pdb="BE 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=" F2 BEF W1103 " pdb="BE 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=" F3 BEF W1103 " pdb="BE 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: 13051 2.44 - 3.16: 83161 3.16 - 3.88: 111052 3.88 - 4.60: 180703 Nonbonded interactions: 387981 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 2.450 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 387976 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.370 Extract box with map and model: 1.050 Check model and map are aligned: 0.220 Set scattering table: 0.270 Process input model: 97.740 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.090 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:10.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.100 ------------------------------------------------------------------------------- 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= 0.720 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 : 1.867 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: 4.3001 time to fit residues: 1063.4792 Evaluate side-chains 136 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 134 time to evaluate : 1.848 ------------------------------------------------------------------------------- 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: 0.8980 chunk 109 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 93 GLN W 477 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16768 Z= 0.219 Angle : 0.662 6.105 23904 Z= 0.391 Chirality : 0.042 0.149 2704 Planarity : 0.006 0.063 1995 Dihedral : 23.053 166.130 4579 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.34 % Favored : 97.58 % Rotamer: Outliers : 1.52 % Allowed : 12.84 % 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: 0.79 (0.23), residues: 1199 helix: 1.48 (0.19), residues: 730 sheet: 0.76 (0.58), residues: 72 loop : -1.35 (0.27), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP W 280 HIS 0.023 0.001 HIS W 477 PHE 0.009 0.001 PHE E 78 TYR 0.014 0.001 TYR W 195 ARG 0.008 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 164 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 148 time to evaluate : 2.086 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: C 95 LYS cc_start: 0.8765 (ttmt) cc_final: 0.8516 (tmtt) REVERT: D 65 ASP cc_start: 0.7944 (t0) cc_final: 0.7671 (t0) REVERT: E 115 LYS cc_start: 0.8718 (mttt) cc_final: 0.8426 (mtmp) outliers start: 16 outliers final: 2 residues processed: 155 average time/residue: 3.3882 time to fit residues: 571.3413 Evaluate side-chains 133 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 131 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 108 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 44 optimal weight: 0.0070 chunk 105 optimal weight: 4.9990 overall best weight: 2.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN W 341 GLN W 598 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 16768 Z= 0.396 Angle : 0.689 7.287 23904 Z= 0.406 Chirality : 0.047 0.173 2704 Planarity : 0.006 0.048 1995 Dihedral : 24.977 166.036 4578 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.42 % Favored : 96.41 % Rotamer: Outliers : 2.09 % Allowed : 13.51 % 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: 1.12 (0.24), residues: 1199 helix: 1.86 (0.19), residues: 731 sheet: 0.40 (0.61), residues: 74 loop : -1.40 (0.27), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP W 280 HIS 0.007 0.001 HIS W 477 PHE 0.011 0.002 PHE E 84 TYR 0.012 0.002 TYR E 54 ARG 0.009 0.001 ARG E 83 *********************** 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 158 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 136 time to evaluate : 1.849 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: C 41 GLU cc_start: 0.7927 (tt0) cc_final: 0.7696 (tt0) REVERT: C 95 LYS cc_start: 0.8790 (ttmt) cc_final: 0.8499 (tptt) REVERT: D 65 ASP cc_start: 0.7980 (t0) cc_final: 0.7620 (t0) REVERT: E 94 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7088 (mp0) REVERT: E 115 LYS cc_start: 0.8678 (mttt) cc_final: 0.8375 (mtmp) REVERT: F 91 LYS cc_start: 0.8495 (tttp) cc_final: 0.8216 (ttpp) REVERT: G 74 LYS cc_start: 0.8540 (mtpt) cc_final: 0.8260 (mmmt) REVERT: H 90 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8128 (mp0) REVERT: W 233 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7504 (ttm) REVERT: W 620 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.6982 (mmm160) outliers start: 22 outliers final: 7 residues processed: 149 average time/residue: 3.8812 time to fit residues: 618.8053 Evaluate side-chains 141 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 130 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain W residue 233 MET Chi-restraints excluded: chain W residue 367 SER Chi-restraints excluded: chain W residue 429 MET Chi-restraints excluded: chain W residue 600 LYS 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: 1.9990 chunk 14 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 87 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 75 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16768 Z= 0.213 Angle : 0.605 5.959 23904 Z= 0.361 Chirality : 0.041 0.146 2704 Planarity : 0.004 0.048 1995 Dihedral : 25.156 160.159 4576 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 1.19 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.17 % Favored : 96.66 % Rotamer: Outliers : 1.24 % Allowed : 14.37 % 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: 1.56 (0.25), residues: 1199 helix: 2.32 (0.20), residues: 726 sheet: 0.55 (0.62), residues: 76 loop : -1.41 (0.28), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP W 348 HIS 0.003 0.001 HIS W 535 PHE 0.007 0.001 PHE B 61 TYR 0.012 0.001 TYR W 195 ARG 0.008 0.000 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 152 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 139 time to evaluate : 1.844 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: 0.8155 (mttp) cc_final: 0.7906 (mttp) REVERT: C 41 GLU cc_start: 0.7914 (tt0) cc_final: 0.7688 (tt0) REVERT: C 95 LYS cc_start: 0.8774 (ttmt) cc_final: 0.8498 (tptt) REVERT: C 114 VAL cc_start: 0.8316 (t) cc_final: 0.8029 (p) REVERT: D 65 ASP cc_start: 0.7958 (t0) cc_final: 0.7583 (t0) REVERT: E 94 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.6995 (mp0) REVERT: E 115 LYS cc_start: 0.8615 (mttt) cc_final: 0.8356 (mtmp) REVERT: F 91 LYS cc_start: 0.8498 (tttp) cc_final: 0.8184 (ttpp) REVERT: G 74 LYS cc_start: 0.8542 (mtpt) cc_final: 0.8307 (mmpt) REVERT: W 620 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.6875 (mmm160) outliers start: 13 outliers final: 2 residues processed: 147 average time/residue: 3.4835 time to fit residues: 552.2634 Evaluate side-chains 133 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 129 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain W residue 429 MET Chi-restraints excluded: chain W residue 442 ASP Chi-restraints excluded: chain W residue 620 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 4.9990 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: 0.9990 chunk 96 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 124 optimal weight: 0.0470 chunk 35 optimal weight: 2.9990 overall best weight: 1.6086 ------------------------------------------------------------------------------- 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: 0.7225 moved from start: 0.5071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16768 Z= 0.275 Angle : 0.603 6.008 23904 Z= 0.359 Chirality : 0.042 0.155 2704 Planarity : 0.005 0.052 1995 Dihedral : 25.649 159.347 4576 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.92 % Favored : 95.91 % Rotamer: Outliers : 1.43 % Allowed : 14.46 % Favored : 84.11 % 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: 1.61 (0.25), residues: 1199 helix: 2.36 (0.20), residues: 726 sheet: 0.54 (0.62), residues: 76 loop : -1.38 (0.28), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP W 348 HIS 0.004 0.001 HIS F 75 PHE 0.023 0.001 PHE W 391 TYR 0.011 0.001 TYR W 195 ARG 0.008 0.000 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 149 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 134 time to evaluate : 1.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 GLU cc_start: 0.7920 (tt0) cc_final: 0.7687 (tt0) REVERT: C 95 LYS cc_start: 0.8780 (ttmt) cc_final: 0.8501 (tptt) REVERT: C 114 VAL cc_start: 0.8359 (t) cc_final: 0.8029 (p) REVERT: D 65 ASP cc_start: 0.7981 (t0) cc_final: 0.7595 (t0) REVERT: E 115 LYS cc_start: 0.8552 (mttt) cc_final: 0.8293 (mtmp) REVERT: E 120 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7737 (mtp) REVERT: F 91 LYS cc_start: 0.8483 (tttp) cc_final: 0.8208 (ttpp) REVERT: G 74 LYS cc_start: 0.8552 (mtpt) cc_final: 0.8315 (mmpt) REVERT: H 90 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8121 (mp0) REVERT: W 620 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.6915 (mmm160) outliers start: 15 outliers final: 5 residues processed: 145 average time/residue: 3.5249 time to fit residues: 552.2604 Evaluate side-chains 134 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 126 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain W residue 429 MET Chi-restraints excluded: chain W residue 620 ARG Chi-restraints excluded: chain W residue 628 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 134 optimal weight: 0.0370 overall best weight: 1.0064 ------------------------------------------------------------------------------- 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: 0.7194 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16768 Z= 0.194 Angle : 0.589 7.776 23904 Z= 0.349 Chirality : 0.040 0.149 2704 Planarity : 0.004 0.064 1995 Dihedral : 25.769 159.430 4576 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.42 % Favored : 96.41 % Rotamer: Outliers : 1.05 % Allowed : 15.41 % Favored : 83.54 % 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: 1.80 (0.25), residues: 1199 helix: 2.51 (0.20), residues: 727 sheet: 0.54 (0.62), residues: 76 loop : -1.31 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP W 348 HIS 0.002 0.001 HIS F 75 PHE 0.007 0.001 PHE B 61 TYR 0.012 0.001 TYR W 195 ARG 0.015 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 138 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 127 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8193 (mttp) cc_final: 0.7962 (mttp) REVERT: C 95 LYS cc_start: 0.8781 (ttmt) cc_final: 0.8506 (tptt) REVERT: D 65 ASP cc_start: 0.7942 (t0) cc_final: 0.7568 (t0) REVERT: E 115 LYS cc_start: 0.8523 (mttt) cc_final: 0.8272 (mtmp) REVERT: F 84 MET cc_start: 0.7911 (mmm) cc_final: 0.7705 (mmm) REVERT: F 91 LYS cc_start: 0.8486 (tttp) cc_final: 0.8208 (ttpp) REVERT: G 74 LYS cc_start: 0.8519 (mtpt) cc_final: 0.8297 (mmpt) REVERT: H 90 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.8040 (mp0) REVERT: W 620 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.6895 (mmm160) outliers start: 11 outliers final: 6 residues processed: 134 average time/residue: 2.9694 time to fit residues: 427.7668 Evaluate side-chains 133 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 125 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 90 GLU 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 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: 5.9990 chunk 78 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 85 optimal weight: 6.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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: 0.7265 moved from start: 0.5326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 16768 Z= 0.338 Angle : 0.614 6.633 23904 Z= 0.364 Chirality : 0.044 0.166 2704 Planarity : 0.005 0.051 1995 Dihedral : 26.111 159.255 4576 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.42 % Favored : 95.41 % Rotamer: Outliers : 1.05 % Allowed : 15.22 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.25), residues: 1199 helix: 2.29 (0.19), residues: 726 sheet: 0.38 (0.62), residues: 75 loop : -1.39 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP W 368 HIS 0.003 0.001 HIS H 106 PHE 0.019 0.001 PHE W 391 TYR 0.009 0.001 TYR W 183 ARG 0.007 0.001 ARG E 42 *********************** 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 141 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 130 time to evaluate : 1.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8237 (mttp) cc_final: 0.8025 (mttp) REVERT: C 95 LYS cc_start: 0.8780 (ttmt) cc_final: 0.8512 (tptt) REVERT: D 65 ASP cc_start: 0.7937 (t0) cc_final: 0.7580 (t0) REVERT: E 115 LYS cc_start: 0.8576 (mttt) cc_final: 0.8266 (mtmp) REVERT: E 120 MET cc_start: 0.8065 (mmm) cc_final: 0.7779 (mtp) REVERT: F 91 LYS cc_start: 0.8490 (tttp) cc_final: 0.8214 (ttpp) REVERT: G 74 LYS cc_start: 0.8651 (mtpt) cc_final: 0.8394 (mmpt) REVERT: W 620 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.6923 (mmm160) outliers start: 11 outliers final: 6 residues processed: 137 average time/residue: 3.7440 time to fit residues: 550.5519 Evaluate side-chains 132 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 125 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain G residue 100 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 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: 3.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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: 0.7257 moved from start: 0.5478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16768 Z= 0.298 Angle : 0.603 6.393 23904 Z= 0.356 Chirality : 0.043 0.150 2704 Planarity : 0.004 0.051 1995 Dihedral : 26.315 160.699 4576 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.84 % Favored : 96.00 % Rotamer: Outliers : 1.33 % Allowed : 15.41 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.25), residues: 1199 helix: 2.36 (0.19), residues: 726 sheet: 0.68 (0.64), residues: 65 loop : -1.45 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP W 348 HIS 0.003 0.001 HIS W 535 PHE 0.009 0.001 PHE B 61 TYR 0.008 0.001 TYR W 183 ARG 0.008 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 145 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 131 time to evaluate : 2.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8245 (mttp) cc_final: 0.8040 (mttp) REVERT: C 95 LYS cc_start: 0.8781 (ttmt) cc_final: 0.8514 (tptt) REVERT: D 65 ASP cc_start: 0.7947 (t0) cc_final: 0.7576 (t0) REVERT: E 115 LYS cc_start: 0.8569 (mttt) cc_final: 0.8280 (mtmp) REVERT: E 120 MET cc_start: 0.8036 (mmm) cc_final: 0.7814 (mtp) REVERT: F 91 LYS cc_start: 0.8500 (tttp) cc_final: 0.8210 (ttpp) REVERT: G 74 LYS cc_start: 0.8664 (mtpt) cc_final: 0.8399 (mmpt) REVERT: W 620 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.6915 (mmm160) outliers start: 14 outliers final: 7 residues processed: 139 average time/residue: 3.6513 time to fit residues: 550.9079 Evaluate side-chains 135 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 127 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain W residue 367 SER Chi-restraints excluded: chain W residue 429 MET Chi-restraints excluded: chain W residue 620 ARG 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: 0.5980 chunk 129 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 128 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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: 0.7220 moved from start: 0.5560 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= 0.198 Angle : 0.580 7.754 23904 Z= 0.342 Chirality : 0.039 0.157 2704 Planarity : 0.004 0.052 1995 Dihedral : 26.343 161.330 4576 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.67 % Favored : 96.16 % Rotamer: Outliers : 0.86 % Allowed : 15.79 % Favored : 83.35 % 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: 1.82 (0.25), residues: 1199 helix: 2.56 (0.20), residues: 730 sheet: 0.74 (0.65), residues: 67 loop : -1.40 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP W 348 HIS 0.003 0.001 HIS W 535 PHE 0.029 0.001 PHE W 391 TYR 0.009 0.001 TYR W 195 ARG 0.009 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: 9 poor density : 133 time to evaluate : 2.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 95 LYS cc_start: 0.8778 (ttmt) cc_final: 0.8512 (tptt) REVERT: D 65 ASP cc_start: 0.7930 (t0) cc_final: 0.7548 (t0) REVERT: E 115 LYS cc_start: 0.8526 (mttt) cc_final: 0.8258 (mtmp) REVERT: E 120 MET cc_start: 0.7973 (mmm) cc_final: 0.7681 (mtp) REVERT: F 91 LYS cc_start: 0.8504 (tttp) cc_final: 0.8223 (ttpp) REVERT: G 74 LYS cc_start: 0.8609 (mtpt) cc_final: 0.8374 (mmpt) REVERT: W 620 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.6856 (mmm160) outliers start: 9 outliers final: 6 residues processed: 140 average time/residue: 3.6618 time to fit residues: 550.9575 Evaluate side-chains 136 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 129 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain W residue 367 SER Chi-restraints excluded: chain W residue 429 MET Chi-restraints excluded: chain W residue 620 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.5636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16768 Z= 0.261 Angle : 0.597 8.586 23904 Z= 0.350 Chirality : 0.041 0.150 2704 Planarity : 0.004 0.053 1995 Dihedral : 26.411 161.308 4576 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.84 % Favored : 96.00 % Rotamer: Outliers : 0.95 % Allowed : 15.98 % Favored : 83.06 % 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: 1.74 (0.25), residues: 1199 helix: 2.53 (0.20), residues: 725 sheet: 0.72 (0.63), residues: 65 loop : -1.42 (0.28), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP W 348 HIS 0.002 0.001 HIS W 535 PHE 0.009 0.001 PHE B 61 TYR 0.008 0.001 TYR W 183 ARG 0.009 0.000 ARG E 42 ********************** 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: 10 poor density : 130 time to evaluate : 1.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8231 (mttp) cc_final: 0.8030 (mttp) REVERT: C 95 LYS cc_start: 0.8757 (ttmt) cc_final: 0.8508 (tptt) REVERT: D 65 ASP cc_start: 0.7957 (t0) cc_final: 0.7581 (t0) REVERT: E 115 LYS cc_start: 0.8549 (mttt) cc_final: 0.8264 (mtmp) REVERT: E 120 MET cc_start: 0.8025 (mmm) cc_final: 0.7740 (mtp) REVERT: F 91 LYS cc_start: 0.8497 (tttp) cc_final: 0.8215 (ttpp) REVERT: G 74 LYS cc_start: 0.8631 (mtpt) cc_final: 0.8388 (mmpt) REVERT: W 620 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.6858 (mmm160) outliers start: 10 outliers final: 6 residues processed: 137 average time/residue: 3.5411 time to fit residues: 522.8385 Evaluate side-chains 135 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 128 time to evaluate : 1.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain W residue 367 SER Chi-restraints excluded: chain W residue 429 MET Chi-restraints excluded: chain W residue 620 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 117 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 100 optimal weight: 0.0570 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.084312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.063708 restraints weight = 88951.005| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.48 r_work: 0.2890 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.5661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16768 Z= 0.176 Angle : 0.589 9.834 23904 Z= 0.345 Chirality : 0.038 0.153 2704 Planarity : 0.004 0.060 1995 Dihedral : 26.415 161.697 4576 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.67 % Favored : 96.16 % Rotamer: Outliers : 0.76 % Allowed : 15.79 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.25), residues: 1199 helix: 2.59 (0.20), residues: 729 sheet: 0.77 (0.64), residues: 67 loop : -1.37 (0.28), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP W 348 HIS 0.003 0.001 HIS W 535 PHE 0.031 0.001 PHE W 391 TYR 0.007 0.001 TYR W 195 ARG 0.009 0.000 ARG E 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11640.21 seconds wall clock time: 245 minutes 25.55 seconds (14725.55 seconds total)