Starting phenix.real_space_refine on Thu Apr 11 14:04:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wxb_21954/04_2024/6wxb_21954_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wxb_21954/04_2024/6wxb_21954.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wxb_21954/04_2024/6wxb_21954.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wxb_21954/04_2024/6wxb_21954.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wxb_21954/04_2024/6wxb_21954_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wxb_21954/04_2024/6wxb_21954_trim.pdb" } resolution = 2.9 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= -0.001 sd= 0.298 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 57 5.16 5 C 7251 2.51 5 N 2025 2.21 5 O 2316 1.98 5 H 11049 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A ARG 208": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 325": "OE1" <-> "OE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A GLU 359": "OE1" <-> "OE2" Residue "A ASP 375": "OD1" <-> "OD2" Residue "A PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 419": "OD1" <-> "OD2" Residue "A GLU 432": "OE1" <-> "OE2" Residue "A PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 489": "OD1" <-> "OD2" Residue "B PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "B ARG 208": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 325": "OE1" <-> "OE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B GLU 359": "OE1" <-> "OE2" Residue "B ASP 375": "OD1" <-> "OD2" Residue "B PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 419": "OD1" <-> "OD2" Residue "B GLU 432": "OE1" <-> "OE2" Residue "B PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 489": "OD1" <-> "OD2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 119": "OE1" <-> "OE2" Residue "C GLU 190": "OE1" <-> "OE2" Residue "C ARG 208": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 325": "OE1" <-> "OE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C GLU 359": "OE1" <-> "OE2" Residue "C ASP 375": "OD1" <-> "OD2" Residue "C PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 419": "OD1" <-> "OD2" Residue "C GLU 432": "OE1" <-> "OE2" Residue "C PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 489": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 22698 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 7499 Classifications: {'peptide': 485} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "B" Number of atoms: 7499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 7499 Classifications: {'peptide': 485} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "C" Number of atoms: 7499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 7499 Classifications: {'peptide': 485} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 67 Unusual residues: {'BMA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 67 Unusual residues: {'BMA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 67 Unusual residues: {'BMA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 10.61, per 1000 atoms: 0.47 Number of scatterers: 22698 At special positions: 0 Unit cell: (83.43, 85.49, 145.23, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 O 2316 8.00 N 2025 7.00 C 7251 6.00 H 11049 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS A 466 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.04 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.02 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 466 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 76 " distance=2.03 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 139 " distance=2.04 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 305 " distance=2.02 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 466 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 285 " " NAG A 602 " - " ASN A 165 " " NAG A 603 " - " ASN A 81 " " NAG B 601 " - " ASN B 285 " " NAG B 602 " - " ASN B 165 " " NAG B 603 " - " ASN B 81 " " NAG C 603 " - " ASN C 285 " " NAG C 604 " - " ASN C 165 " " NAG C 605 " - " ASN C 81 " Time building additional restraints: 19.66 Conformation dependent library (CDL) restraints added in 2.5 seconds 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2688 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 30 sheets defined 27.6% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.01 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 4.787A pdb=" N VAL A 78 " --> pdb=" O HIS A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'A' and resid 366 through 379 removed outlier: 4.344A pdb=" N GLY A 379 " --> pdb=" O ASP A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 404 through 455 Processing helix chain 'A' and resid 474 through 484 Processing helix chain 'A' and resid 487 through 490 removed outlier: 3.656A pdb=" N VAL A 490 " --> pdb=" O ASP A 487 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 487 through 490' Processing helix chain 'A' and resid 491 through 500 removed outlier: 3.703A pdb=" N ASN A 497 " --> pdb=" O ASP A 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 72 Processing helix chain 'B' and resid 73 through 80 removed outlier: 4.787A pdb=" N VAL B 78 " --> pdb=" O HIS B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 116 Processing helix chain 'B' and resid 187 through 195 Processing helix chain 'B' and resid 366 through 379 removed outlier: 4.344A pdb=" N GLY B 379 " --> pdb=" O ASP B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 384 Processing helix chain 'B' and resid 404 through 455 Processing helix chain 'B' and resid 474 through 484 Processing helix chain 'B' and resid 487 through 490 removed outlier: 3.657A pdb=" N VAL B 490 " --> pdb=" O ASP B 487 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 487 through 490' Processing helix chain 'B' and resid 491 through 500 removed outlier: 3.703A pdb=" N ASN B 497 " --> pdb=" O ASP B 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 4.787A pdb=" N VAL C 78 " --> pdb=" O HIS C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'C' and resid 366 through 379 removed outlier: 4.344A pdb=" N GLY C 379 " --> pdb=" O ASP C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 384 Processing helix chain 'C' and resid 404 through 455 Processing helix chain 'C' and resid 474 through 484 Processing helix chain 'C' and resid 487 through 490 removed outlier: 3.656A pdb=" N VAL C 490 " --> pdb=" O ASP C 487 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 487 through 490' Processing helix chain 'C' and resid 491 through 500 removed outlier: 3.702A pdb=" N ASN C 497 " --> pdb=" O ASP C 493 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 362 through 365 Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 40 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 52 removed outlier: 5.901A pdb=" N ILE A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 61 Processing sheet with id=AA7, first strand: chain 'A' and resid 100 through 101 removed outlier: 5.029A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 100 through 101 removed outlier: 7.674A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LEU A 251 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 154 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N TRP A 153 " --> pdb=" O ASN A 133 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN A 133 " --> pdb=" O TRP A 153 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 164 through 169 removed outlier: 4.976A pdb=" N ARG A 201 " --> pdb=" O ASN A 248 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 286 through 288 removed outlier: 4.133A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 362 through 365 Processing sheet with id=AB3, first strand: chain 'B' and resid 24 through 26 Processing sheet with id=AB4, first strand: chain 'B' and resid 40 through 41 Processing sheet with id=AB5, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AB6, first strand: chain 'B' and resid 51 through 52 removed outlier: 5.901A pdb=" N ILE B 51 " --> pdb=" O ASP B 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 58 through 61 Processing sheet with id=AB8, first strand: chain 'B' and resid 100 through 101 removed outlier: 5.029A pdb=" N ILE B 179 " --> pdb=" O GLY B 256 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLY B 256 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 100 through 101 removed outlier: 7.675A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LEU B 251 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU B 154 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N TRP B 153 " --> pdb=" O ASN B 133 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN B 133 " --> pdb=" O TRP B 153 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 164 through 169 removed outlier: 4.976A pdb=" N ARG B 201 " --> pdb=" O ASN B 248 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 286 through 288 removed outlier: 4.134A pdb=" N CYS B 281 " --> pdb=" O ILE B 288 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 362 through 365 Processing sheet with id=AC4, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AC5, first strand: chain 'C' and resid 40 through 41 Processing sheet with id=AC6, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AC7, first strand: chain 'C' and resid 51 through 52 removed outlier: 5.902A pdb=" N ILE C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 58 through 61 Processing sheet with id=AC9, first strand: chain 'C' and resid 100 through 101 removed outlier: 5.030A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 100 through 101 removed outlier: 7.674A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LEU C 251 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU C 154 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N TRP C 153 " --> pdb=" O ASN C 133 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN C 133 " --> pdb=" O TRP C 153 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 164 through 169 removed outlier: 4.975A pdb=" N ARG C 201 " --> pdb=" O ASN C 248 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 286 through 288 removed outlier: 4.133A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) 534 hydrogen bonds defined for protein. 1440 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.79 Time building geometry restraints manager: 20.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 11037 1.03 - 1.23: 96 1.23 - 1.43: 5006 1.43 - 1.63: 6718 1.63 - 1.83: 78 Bond restraints: 22935 Sorted by residual: bond pdb=" C1 NAG A 603 " pdb=" O5 NAG A 603 " ideal model delta sigma weight residual 1.406 1.526 -0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" C1 NAG B 603 " pdb=" O5 NAG B 603 " ideal model delta sigma weight residual 1.406 1.526 -0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" C1 NAG C 605 " pdb=" O5 NAG C 605 " ideal model delta sigma weight residual 1.406 1.526 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" C1 NAG C 604 " pdb=" O5 NAG C 604 " ideal model delta sigma weight residual 1.406 1.346 0.060 2.00e-02 2.50e+03 8.89e+00 bond pdb=" C1 NAG A 602 " pdb=" O5 NAG A 602 " ideal model delta sigma weight residual 1.406 1.347 0.059 2.00e-02 2.50e+03 8.84e+00 ... (remaining 22930 not shown) Histogram of bond angle deviations from ideal: 99.77 - 106.62: 556 106.62 - 113.47: 26585 113.47 - 120.31: 6978 120.31 - 127.16: 6923 127.16 - 134.00: 160 Bond angle restraints: 41202 Sorted by residual: angle pdb=" N THR B 388 " pdb=" CA THR B 388 " pdb=" C THR B 388 " ideal model delta sigma weight residual 110.80 101.42 9.38 2.13e+00 2.20e-01 1.94e+01 angle pdb=" N THR A 388 " pdb=" CA THR A 388 " pdb=" C THR A 388 " ideal model delta sigma weight residual 110.80 101.42 9.38 2.13e+00 2.20e-01 1.94e+01 angle pdb=" N THR C 388 " pdb=" CA THR C 388 " pdb=" C THR C 388 " ideal model delta sigma weight residual 110.80 101.45 9.35 2.13e+00 2.20e-01 1.93e+01 angle pdb=" C1 NAG B 603 " pdb=" O5 NAG B 603 " pdb=" C5 NAG B 603 " ideal model delta sigma weight residual 113.21 126.29 -13.08 3.00e+00 1.11e-01 1.90e+01 angle pdb=" C1 NAG C 605 " pdb=" O5 NAG C 605 " pdb=" C5 NAG C 605 " ideal model delta sigma weight residual 113.21 126.27 -13.06 3.00e+00 1.11e-01 1.90e+01 ... (remaining 41197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.52: 10317 21.52 - 43.04: 546 43.04 - 64.56: 159 64.56 - 86.08: 36 86.08 - 107.60: 18 Dihedral angle restraints: 11076 sinusoidal: 6183 harmonic: 4893 Sorted by residual: dihedral pdb=" CA ARG A 141 " pdb=" C ARG A 141 " pdb=" N GLY A 142 " pdb=" CA GLY A 142 " ideal model delta harmonic sigma weight residual 180.00 144.84 35.16 0 5.00e+00 4.00e-02 4.95e+01 dihedral pdb=" CA ARG B 141 " pdb=" C ARG B 141 " pdb=" N GLY B 142 " pdb=" CA GLY B 142 " ideal model delta harmonic sigma weight residual 180.00 144.87 35.13 0 5.00e+00 4.00e-02 4.94e+01 dihedral pdb=" CA ARG C 141 " pdb=" C ARG C 141 " pdb=" N GLY C 142 " pdb=" CA GLY C 142 " ideal model delta harmonic sigma weight residual 180.00 144.92 35.08 0 5.00e+00 4.00e-02 4.92e+01 ... (remaining 11073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1545 0.067 - 0.134: 236 0.134 - 0.201: 22 0.201 - 0.268: 3 0.268 - 0.335: 6 Chirality restraints: 1812 Sorted by residual: chirality pdb=" C1 NAG B 602 " pdb=" ND2 ASN B 165 " pdb=" C2 NAG B 602 " pdb=" O5 NAG B 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" C1 NAG A 602 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A 602 " pdb=" O5 NAG A 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" C1 NAG C 604 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG C 604 " pdb=" O5 NAG C 604 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.77e+00 ... (remaining 1809 not shown) Planarity restraints: 3495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 168 " -0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO B 169 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 169 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 169 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 81 " -0.012 2.00e-02 2.50e+03 1.33e-02 2.20e+00 pdb=" CG ASN C 81 " 0.003 2.00e-02 2.50e+03 pdb=" OD1 ASN C 81 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN C 81 " 0.021 2.00e-02 2.50e+03 pdb=" C1 NAG C 605 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET C 168 " -0.025 5.00e-02 4.00e+02 3.70e-02 2.20e+00 pdb=" N PRO C 169 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 169 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 169 " -0.021 5.00e-02 4.00e+02 ... (remaining 3492 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 3085 2.26 - 2.85: 51881 2.85 - 3.43: 60045 3.43 - 4.02: 88158 4.02 - 4.60: 132800 Nonbonded interactions: 335969 Sorted by model distance: nonbonded pdb="HH12 ARG A 405 " pdb=" OE1 GLU B 403 " model vdw 1.677 1.850 nonbonded pdb=" OE1 GLU A 403 " pdb="HH12 ARG C 405 " model vdw 1.683 1.850 nonbonded pdb=" O CYS B 477 " pdb=" HG SER B 480 " model vdw 1.690 1.850 nonbonded pdb=" O CYS C 477 " pdb=" HG SER C 480 " model vdw 1.690 1.850 nonbonded pdb=" O CYS A 477 " pdb=" HG SER A 480 " model vdw 1.691 1.850 ... (remaining 335964 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' and (resid 9 through 501 or resid 601 or resid 603 through 604)) selection = (chain 'B' and (resid 9 through 501 or resid 601 or resid 603 through 604)) selection = (chain 'C' and (resid 9 through 501 or resid 601 or resid 603 through 604)) } 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.320 Extract box with map and model: 5.080 Check model and map are aligned: 0.350 Set scattering table: 0.210 Process input model: 77.710 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 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 : 0.007 0.120 11886 Z= 0.452 Angle : 0.849 13.082 16122 Z= 0.421 Chirality : 0.051 0.335 1812 Planarity : 0.004 0.037 2094 Dihedral : 15.835 107.597 4599 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.71 % Allowed : 2.36 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -2.98 (0.18), residues: 1443 helix: -0.78 (0.23), residues: 333 sheet: -2.35 (0.26), residues: 255 loop : -2.44 (0.17), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 222 HIS 0.006 0.002 HIS B 488 PHE 0.017 0.002 PHE C 353 TYR 0.014 0.002 TYR A 105 ARG 0.005 0.001 ARG B 383 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 250 time to evaluate : 1.945 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: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8088 (ttmt) cc_final: 0.7879 (ttmm) REVERT: A 163 VAL cc_start: 0.9119 (t) cc_final: 0.8874 (p) REVERT: A 301 THR cc_start: 0.8308 (p) cc_final: 0.8061 (p) REVERT: A 368 LYS cc_start: 0.8006 (tttp) cc_final: 0.7628 (mppt) REVERT: A 383 ARG cc_start: 0.7320 (ptt-90) cc_final: 0.7015 (ptt180) REVERT: A 424 ASN cc_start: 0.7976 (m-40) cc_final: 0.7575 (m-40) REVERT: A 493 ASP cc_start: 0.8131 (m-30) cc_final: 0.7793 (m-30) REVERT: B 27 LYS cc_start: 0.8015 (ttmt) cc_final: 0.7579 (ttpp) REVERT: B 101 ASP cc_start: 0.8295 (p0) cc_final: 0.8010 (p0) REVERT: B 247 SER cc_start: 0.8592 (t) cc_final: 0.8372 (p) REVERT: B 248 ASN cc_start: 0.7538 (t0) cc_final: 0.7101 (t0) REVERT: B 368 LYS cc_start: 0.7839 (tttp) cc_final: 0.7535 (mppt) REVERT: B 457 GLU cc_start: 0.6751 (mm-30) cc_final: 0.6029 (mm-30) REVERT: B 493 ASP cc_start: 0.8194 (m-30) cc_final: 0.7964 (m-30) REVERT: C 248 ASN cc_start: 0.7627 (t0) cc_final: 0.7365 (t0) REVERT: C 291 ASP cc_start: 0.8217 (p0) cc_final: 0.7974 (p0) REVERT: C 301 THR cc_start: 0.8349 (p) cc_final: 0.8086 (p) REVERT: C 368 LYS cc_start: 0.7694 (tttp) cc_final: 0.7475 (mppt) REVERT: C 493 ASP cc_start: 0.8113 (m-30) cc_final: 0.7824 (m-30) outliers start: 9 outliers final: 3 residues processed: 259 average time/residue: 2.3298 time to fit residues: 662.7467 Evaluate side-chains 152 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 149 time to evaluate : 1.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 400 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 0.0670 chunk 58 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 0.0980 chunk 84 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN B 454 GLN B 498 ASN ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 GLN C 458 ASN C 498 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11886 Z= 0.188 Angle : 0.548 6.100 16122 Z= 0.282 Chirality : 0.045 0.202 1812 Planarity : 0.004 0.056 2094 Dihedral : 8.186 59.657 1887 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.34 % Allowed : 10.30 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.81 (0.20), residues: 1443 helix: 1.07 (0.26), residues: 333 sheet: -1.93 (0.29), residues: 255 loop : -1.98 (0.19), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 421 HIS 0.003 0.001 HIS A 75 PHE 0.010 0.001 PHE A 353 TYR 0.011 0.001 TYR A 470 ARG 0.009 0.001 ARG A 57 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 149 time to evaluate : 1.917 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: A 101 ASP cc_start: 0.8059 (p0) cc_final: 0.7858 (p0) REVERT: A 368 LYS cc_start: 0.8012 (tttp) cc_final: 0.7598 (mppt) REVERT: B 27 LYS cc_start: 0.7898 (ttmt) cc_final: 0.7509 (ttpp) REVERT: B 368 LYS cc_start: 0.7837 (tttp) cc_final: 0.7490 (mppt) outliers start: 17 outliers final: 7 residues processed: 164 average time/residue: 1.9658 time to fit residues: 361.0438 Evaluate side-chains 139 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 132 time to evaluate : 2.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 388 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 ASN ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11886 Z= 0.277 Angle : 0.529 4.953 16122 Z= 0.274 Chirality : 0.044 0.190 1812 Planarity : 0.004 0.033 2094 Dihedral : 6.618 53.582 1886 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 1.65 % Allowed : 10.77 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.43 (0.21), residues: 1443 helix: 1.63 (0.26), residues: 333 sheet: -2.00 (0.27), residues: 282 loop : -1.71 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 421 HIS 0.003 0.001 HIS C 183 PHE 0.012 0.001 PHE C 353 TYR 0.011 0.001 TYR B 105 ARG 0.005 0.000 ARG A 57 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 134 time to evaluate : 1.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 LYS cc_start: 0.8007 (tttp) cc_final: 0.7617 (mppt) REVERT: B 27 LYS cc_start: 0.7775 (ttmt) cc_final: 0.7408 (ttpp) REVERT: B 368 LYS cc_start: 0.7836 (tttp) cc_final: 0.7514 (mppt) REVERT: C 208 ARG cc_start: 0.7843 (ptm-80) cc_final: 0.7440 (ptp-170) REVERT: C 344 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7560 (mm-30) REVERT: C 367 LEU cc_start: 0.7864 (mm) cc_final: 0.7620 (mm) REVERT: C 368 LYS cc_start: 0.7959 (mppt) cc_final: 0.7473 (mtpp) REVERT: C 398 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7980 (mt-10) REVERT: C 449 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.5886 (mp0) outliers start: 21 outliers final: 9 residues processed: 149 average time/residue: 2.0038 time to fit residues: 333.7291 Evaluate side-chains 140 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 129 time to evaluate : 1.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 398 GLU Chi-restraints excluded: chain C residue 449 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11886 Z= 0.275 Angle : 0.512 5.023 16122 Z= 0.264 Chirality : 0.043 0.178 1812 Planarity : 0.003 0.033 2094 Dihedral : 5.943 51.247 1878 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.42 % Allowed : 11.95 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.17 (0.21), residues: 1443 helix: 1.99 (0.26), residues: 333 sheet: -1.90 (0.28), residues: 282 loop : -1.58 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 421 HIS 0.007 0.001 HIS C 17 PHE 0.011 0.001 PHE C 353 TYR 0.009 0.001 TYR B 105 ARG 0.003 0.000 ARG A 57 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 130 time to evaluate : 1.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 LYS cc_start: 0.7984 (tttp) cc_final: 0.7613 (mppt) REVERT: B 27 LYS cc_start: 0.7812 (ttmt) cc_final: 0.7334 (ttpp) REVERT: B 274 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8324 (mp) REVERT: B 368 LYS cc_start: 0.7840 (tttp) cc_final: 0.7517 (mppt) REVERT: C 208 ARG cc_start: 0.7889 (ptm-80) cc_final: 0.7493 (ptp-170) REVERT: C 248 ASN cc_start: 0.7695 (t0) cc_final: 0.7446 (t0) REVERT: C 344 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7509 (mm-30) REVERT: C 368 LYS cc_start: 0.8030 (mppt) cc_final: 0.7530 (mtpp) outliers start: 18 outliers final: 14 residues processed: 141 average time/residue: 1.7977 time to fit residues: 286.8615 Evaluate side-chains 140 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 125 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 388 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 11886 Z= 0.238 Angle : 0.491 5.223 16122 Z= 0.253 Chirality : 0.043 0.174 1812 Planarity : 0.003 0.027 2094 Dihedral : 5.685 53.098 1878 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 1.49 % Allowed : 11.48 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.02 (0.21), residues: 1443 helix: 2.16 (0.27), residues: 342 sheet: -1.84 (0.28), residues: 282 loop : -1.54 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 421 HIS 0.004 0.001 HIS C 17 PHE 0.010 0.001 PHE C 353 TYR 0.012 0.001 TYR A 470 ARG 0.002 0.000 ARG B 57 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 time to evaluate : 1.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 LYS cc_start: 0.7967 (tttp) cc_final: 0.7606 (mppt) REVERT: A 398 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8256 (mt-10) REVERT: A 475 ASN cc_start: 0.8574 (m-40) cc_final: 0.8372 (m110) REVERT: B 27 LYS cc_start: 0.7836 (ttmt) cc_final: 0.7365 (ttpp) REVERT: B 274 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8337 (mp) REVERT: B 280 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8171 (mm-30) REVERT: B 368 LYS cc_start: 0.7722 (tttp) cc_final: 0.7413 (mppt) REVERT: C 208 ARG cc_start: 0.7901 (ptm-80) cc_final: 0.7530 (ptp-170) REVERT: C 248 ASN cc_start: 0.7648 (t0) cc_final: 0.7368 (t0) REVERT: C 368 LYS cc_start: 0.7995 (mppt) cc_final: 0.7490 (mtpp) REVERT: C 406 ILE cc_start: 0.8062 (mm) cc_final: 0.7827 (mp) outliers start: 19 outliers final: 15 residues processed: 140 average time/residue: 1.7728 time to fit residues: 281.5373 Evaluate side-chains 139 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 123 time to evaluate : 2.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 287 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 134 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: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 11886 Z= 0.401 Angle : 0.554 6.250 16122 Z= 0.285 Chirality : 0.045 0.168 1812 Planarity : 0.004 0.048 2094 Dihedral : 5.990 46.724 1878 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.12 % Allowed : 11.56 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 (0.21), residues: 1443 helix: 1.96 (0.26), residues: 342 sheet: -1.69 (0.28), residues: 270 loop : -1.60 (0.20), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 421 HIS 0.004 0.001 HIS C 17 PHE 0.012 0.002 PHE A 353 TYR 0.021 0.002 TYR B 195 ARG 0.002 0.000 ARG C 90 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 122 time to evaluate : 1.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 ARG cc_start: 0.7994 (ptm-80) cc_final: 0.7473 (ptp-170) REVERT: A 368 LYS cc_start: 0.7962 (tttp) cc_final: 0.7576 (mppt) REVERT: A 475 ASN cc_start: 0.8630 (m-40) cc_final: 0.8410 (m110) REVERT: B 27 LYS cc_start: 0.7818 (ttmt) cc_final: 0.7347 (ttpp) REVERT: B 368 LYS cc_start: 0.7712 (tttp) cc_final: 0.7419 (mppt) REVERT: C 208 ARG cc_start: 0.8038 (ptm-80) cc_final: 0.7586 (ptp-170) REVERT: C 248 ASN cc_start: 0.7797 (t0) cc_final: 0.7518 (t0) REVERT: C 368 LYS cc_start: 0.7990 (mppt) cc_final: 0.7485 (mtpp) outliers start: 27 outliers final: 20 residues processed: 141 average time/residue: 1.8030 time to fit residues: 287.5206 Evaluate side-chains 137 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 439 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 117 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7495 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 11886 Z= 0.195 Angle : 0.480 6.159 16122 Z= 0.248 Chirality : 0.042 0.173 1812 Planarity : 0.003 0.036 2094 Dihedral : 5.590 51.528 1878 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.94 % Allowed : 13.05 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.22), residues: 1443 helix: 2.31 (0.27), residues: 342 sheet: -1.81 (0.28), residues: 282 loop : -1.46 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 421 HIS 0.004 0.001 HIS A 17 PHE 0.010 0.001 PHE B 353 TYR 0.015 0.001 TYR A 195 ARG 0.004 0.000 ARG B 321 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 127 time to evaluate : 1.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 ARG cc_start: 0.7946 (ptm-80) cc_final: 0.7449 (ptp-170) REVERT: A 368 LYS cc_start: 0.7954 (tttp) cc_final: 0.7595 (mppt) REVERT: A 475 ASN cc_start: 0.8654 (m-40) cc_final: 0.8428 (m110) REVERT: B 27 LYS cc_start: 0.7875 (ttmt) cc_final: 0.7425 (ttpp) REVERT: B 368 LYS cc_start: 0.7696 (tttp) cc_final: 0.7414 (mppt) REVERT: C 208 ARG cc_start: 0.7987 (ptm-80) cc_final: 0.7550 (ptp-170) REVERT: C 248 ASN cc_start: 0.7643 (t0) cc_final: 0.7401 (t0) REVERT: C 368 LYS cc_start: 0.7983 (mppt) cc_final: 0.7472 (mtpp) REVERT: C 406 ILE cc_start: 0.8026 (mm) cc_final: 0.7795 (mp) outliers start: 12 outliers final: 12 residues processed: 136 average time/residue: 1.8143 time to fit residues: 279.4977 Evaluate side-chains 133 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 121 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 205 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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: 0.7499 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 11886 Z= 0.234 Angle : 0.484 5.893 16122 Z= 0.249 Chirality : 0.043 0.170 1812 Planarity : 0.003 0.037 2094 Dihedral : 5.487 50.764 1878 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.26 % Allowed : 13.21 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.80 (0.22), residues: 1443 helix: 2.43 (0.27), residues: 342 sheet: -1.77 (0.28), residues: 282 loop : -1.42 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 421 HIS 0.003 0.001 HIS A 17 PHE 0.009 0.001 PHE A 353 TYR 0.014 0.001 TYR A 195 ARG 0.004 0.000 ARG B 321 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 126 time to evaluate : 1.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 LYS cc_start: 0.7934 (tttp) cc_final: 0.7581 (mppt) REVERT: A 475 ASN cc_start: 0.8654 (m-40) cc_final: 0.8429 (m110) REVERT: B 27 LYS cc_start: 0.7827 (ttmt) cc_final: 0.7377 (ttpp) REVERT: B 368 LYS cc_start: 0.7661 (tttp) cc_final: 0.7377 (mppt) REVERT: C 208 ARG cc_start: 0.8010 (ptm-80) cc_final: 0.7578 (ptp-170) REVERT: C 248 ASN cc_start: 0.7635 (t0) cc_final: 0.7391 (t0) REVERT: C 368 LYS cc_start: 0.7976 (mppt) cc_final: 0.7467 (mtpp) REVERT: C 406 ILE cc_start: 0.8023 (mm) cc_final: 0.7789 (mp) outliers start: 16 outliers final: 15 residues processed: 139 average time/residue: 1.6719 time to fit residues: 265.3728 Evaluate side-chains 136 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 1.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 388 THR 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: 2.9990 chunk 129 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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: 0.7506 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 11886 Z= 0.278 Angle : 0.497 5.713 16122 Z= 0.256 Chirality : 0.043 0.163 1812 Planarity : 0.004 0.072 2094 Dihedral : 5.530 50.856 1878 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.26 % Allowed : 13.52 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.80 (0.22), residues: 1443 helix: 2.41 (0.27), residues: 342 sheet: -1.76 (0.28), residues: 282 loop : -1.40 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 421 HIS 0.004 0.001 HIS A 17 PHE 0.010 0.001 PHE B 353 TYR 0.014 0.001 TYR A 195 ARG 0.010 0.000 ARG B 321 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 121 time to evaluate : 2.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 LYS cc_start: 0.7935 (tttp) cc_final: 0.7584 (mppt) REVERT: A 475 ASN cc_start: 0.8642 (m-40) cc_final: 0.8428 (m110) REVERT: B 27 LYS cc_start: 0.7820 (ttmt) cc_final: 0.7368 (ttpp) REVERT: B 368 LYS cc_start: 0.7663 (tttp) cc_final: 0.7380 (mppt) REVERT: C 208 ARG cc_start: 0.8030 (ptm-80) cc_final: 0.7600 (ptp-170) REVERT: C 248 ASN cc_start: 0.7663 (t0) cc_final: 0.7411 (t0) REVERT: C 368 LYS cc_start: 0.7980 (mppt) cc_final: 0.7470 (mtpp) REVERT: C 406 ILE cc_start: 0.8031 (mm) cc_final: 0.7799 (mp) outliers start: 16 outliers final: 15 residues processed: 132 average time/residue: 1.8516 time to fit residues: 283.2030 Evaluate side-chains 136 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 1.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 388 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 95 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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: 0.7506 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 11886 Z= 0.268 Angle : 0.492 5.755 16122 Z= 0.254 Chirality : 0.043 0.162 1812 Planarity : 0.004 0.068 2094 Dihedral : 5.515 50.180 1878 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.42 % Allowed : 13.36 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.22), residues: 1443 helix: 2.43 (0.27), residues: 342 sheet: -1.77 (0.28), residues: 282 loop : -1.37 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 421 HIS 0.004 0.001 HIS A 17 PHE 0.011 0.001 PHE B 353 TYR 0.013 0.001 TYR A 195 ARG 0.007 0.000 ARG B 321 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 120 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 LYS cc_start: 0.7927 (tttp) cc_final: 0.7575 (mppt) REVERT: B 27 LYS cc_start: 0.7818 (ttmt) cc_final: 0.7367 (ttpp) REVERT: B 274 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8403 (mp) REVERT: B 321 ARG cc_start: 0.8685 (ttm-80) cc_final: 0.8443 (ttm-80) REVERT: B 368 LYS cc_start: 0.7660 (tttp) cc_final: 0.7391 (mppt) REVERT: C 208 ARG cc_start: 0.7973 (ptm-80) cc_final: 0.7556 (ptp-170) REVERT: C 248 ASN cc_start: 0.7656 (t0) cc_final: 0.7395 (t0) REVERT: C 344 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7505 (mm-30) REVERT: C 368 LYS cc_start: 0.7965 (mppt) cc_final: 0.7446 (mtpp) REVERT: C 406 ILE cc_start: 0.8038 (mm) cc_final: 0.7807 (mp) outliers start: 18 outliers final: 15 residues processed: 134 average time/residue: 1.7881 time to fit residues: 272.1555 Evaluate side-chains 131 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 115 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 388 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 105 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 117 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 376 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.110834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.092031 restraints weight = 41821.711| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.00 r_work: 0.2919 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 11886 Z= 0.208 Angle : 0.473 5.812 16122 Z= 0.245 Chirality : 0.043 0.166 1812 Planarity : 0.003 0.067 2094 Dihedral : 5.431 50.660 1878 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.10 % Allowed : 13.99 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.22), residues: 1443 helix: 2.50 (0.27), residues: 342 sheet: -1.75 (0.28), residues: 282 loop : -1.33 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 421 HIS 0.004 0.001 HIS A 17 PHE 0.010 0.001 PHE B 353 TYR 0.013 0.001 TYR B 195 ARG 0.009 0.000 ARG B 321 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7250.66 seconds wall clock time: 129 minutes 49.79 seconds (7789.79 seconds total)