Starting phenix.real_space_refine on Thu Feb 15 00:37:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqo_23949/02_2024/7mqo_23949.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqo_23949/02_2024/7mqo_23949.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqo_23949/02_2024/7mqo_23949.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqo_23949/02_2024/7mqo_23949.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqo_23949/02_2024/7mqo_23949.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqo_23949/02_2024/7mqo_23949.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.171 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 94 5.16 5 C 6744 2.51 5 N 1800 2.21 5 O 2004 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 13": "OE1" <-> "OE2" Residue "F GLU 6": "OE1" <-> "OE2" Residue "F PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 239": "OE1" <-> "OE2" Residue "F ASP 250": "OD1" <-> "OD2" Residue "F PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 362": "OE1" <-> "OE2" Residue "F PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 444": "OE1" <-> "OE2" Residue "F PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 6": "OE1" <-> "OE2" Residue "E PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 239": "OE1" <-> "OE2" Residue "E ASP 250": "OD1" <-> "OD2" Residue "E PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 362": "OE1" <-> "OE2" Residue "E PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 444": "OE1" <-> "OE2" Residue "E PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 13": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10642 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 188 Classifications: {'peptide': 24} Modifications used: {'COO': 1} Link IDs: {'TRANS': 23} Chain: "B" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 138 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "F" Number of atoms: 4883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4883 Classifications: {'peptide': 602} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 571} Chain breaks: 4 Chain: "E" Number of atoms: 4883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4883 Classifications: {'peptide': 602} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 571} Chain breaks: 4 Chain: "C" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 188 Classifications: {'peptide': 24} Modifications used: {'COO': 1} Link IDs: {'TRANS': 23} Chain: "D" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 138 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 6.07, per 1000 atoms: 0.57 Number of scatterers: 10642 At special positions: 0 Unit cell: (116.025, 137.865, 84.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 94 16.00 O 2004 8.00 N 1800 7.00 C 6744 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 11 " distance=2.03 Simple disulfide: pdb=" SG CYS A 7 " - pdb=" SG CYS B 7 " distance=1.92 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS B 19 " distance=1.99 Simple disulfide: pdb=" SG CYS F 8 " - pdb=" SG CYS F 26 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 155 " distance=2.03 Simple disulfide: pdb=" SG CYS F 159 " - pdb=" SG CYS F 182 " distance=2.03 Simple disulfide: pdb=" SG CYS F 169 " - pdb=" SG CYS F 188 " distance=2.03 Simple disulfide: pdb=" SG CYS F 192 " - pdb=" SG CYS F 201 " distance=2.03 Simple disulfide: pdb=" SG CYS F 196 " - pdb=" SG CYS F 207 " distance=2.03 Simple disulfide: pdb=" SG CYS F 208 " - pdb=" SG CYS F 216 " distance=2.03 Simple disulfide: pdb=" SG CYS F 212 " - pdb=" SG CYS F 225 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 237 " distance=2.03 Simple disulfide: pdb=" SG CYS F 241 " - pdb=" SG CYS F 253 " distance=2.03 Simple disulfide: pdb=" SG CYS F 259 " - pdb=" SG CYS F 284 " distance=2.03 Simple disulfide: pdb=" SG CYS F 266 " - pdb=" SG CYS F 274 " distance=2.03 Simple disulfide: pdb=" SG CYS F 288 " - pdb=" SG CYS F 301 " distance=2.03 Simple disulfide: pdb=" SG CYS F 304 " - pdb=" SG CYS F 308 " distance=2.03 Simple disulfide: pdb=" SG CYS F 312 " - pdb=" SG CYS F 333 " distance=2.03 Simple disulfide: pdb=" SG CYS F 435 " - pdb=" SG CYS F 468 " distance=2.03 Simple disulfide: pdb=" SG CYS E 8 " - pdb=" SG CYS E 26 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 155 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 182 " distance=2.03 Simple disulfide: pdb=" SG CYS E 169 " - pdb=" SG CYS E 188 " distance=2.03 Simple disulfide: pdb=" SG CYS E 192 " - pdb=" SG CYS E 201 " distance=2.03 Simple disulfide: pdb=" SG CYS E 196 " - pdb=" SG CYS E 207 " distance=2.03 Simple disulfide: pdb=" SG CYS E 208 " - pdb=" SG CYS E 216 " distance=2.03 Simple disulfide: pdb=" SG CYS E 212 " - pdb=" SG CYS E 225 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 237 " distance=2.02 Simple disulfide: pdb=" SG CYS E 241 " - pdb=" SG CYS E 253 " distance=2.03 Simple disulfide: pdb=" SG CYS E 259 " - pdb=" SG CYS E 284 " distance=2.04 Simple disulfide: pdb=" SG CYS E 266 " - pdb=" SG CYS E 274 " distance=2.03 Simple disulfide: pdb=" SG CYS E 288 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 304 " - pdb=" SG CYS E 308 " distance=2.03 Simple disulfide: pdb=" SG CYS E 312 " - pdb=" SG CYS E 333 " distance=2.03 Simple disulfide: pdb=" SG CYS E 435 " - pdb=" SG CYS E 468 " distance=2.03 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 11 " distance=2.03 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS D 7 " distance=2.14 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS D 19 " distance=2.07 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 BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG E1001 " - " ASN E 215 " " NAG E1002 " - " ASN E 418 " " NAG E1003 " - " ASN E 255 " " NAG E1004 " - " ASN E 16 " " NAG E1005 " - " ASN E 397 " " NAG E1006 " - " ASN E 25 " " NAG F1001 " - " ASN F 215 " " NAG F1002 " - " ASN F 418 " " NAG F1003 " - " ASN F 255 " " NAG F1004 " - " ASN F 16 " " NAG F1005 " - " ASN F 397 " " NAG F1006 " - " ASN F 25 " " NAG G 1 " - " ASN F 111 " " NAG H 1 " - " ASN E 111 " Time building additional restraints: 4.12 Conformation dependent library (CDL) restraints added in 1.9 seconds 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2436 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 18 sheets defined 15.9% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 1 through 7 Processing helix chain 'A' and resid 12 through 20 Processing helix chain 'A' and resid 21 through 23 No H-bonds generated for 'chain 'A' and resid 21 through 23' Processing helix chain 'B' and resid 7 through 12 removed outlier: 4.118A pdb=" N VAL B 12 " --> pdb=" O GLY B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 19 Processing helix chain 'F' and resid 148 through 152 Processing helix chain 'F' and resid 255 through 269 removed outlier: 3.752A pdb=" N CYS F 259 " --> pdb=" O ASN F 255 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN F 268 " --> pdb=" O HIS F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 328 Processing helix chain 'F' and resid 351 through 358 Processing helix chain 'F' and resid 435 through 447 removed outlier: 3.650A pdb=" N ILE F 439 " --> pdb=" O CYS F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 498 No H-bonds generated for 'chain 'F' and resid 496 through 498' Processing helix chain 'F' and resid 693 through 714 Processing helix chain 'E' and resid 148 through 152 Processing helix chain 'E' and resid 255 through 269 removed outlier: 3.752A pdb=" N CYS E 259 " --> pdb=" O ASN E 255 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN E 268 " --> pdb=" O HIS E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 328 Processing helix chain 'E' and resid 351 through 358 Processing helix chain 'E' and resid 435 through 447 removed outlier: 3.651A pdb=" N ILE E 439 " --> pdb=" O CYS E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 498 No H-bonds generated for 'chain 'E' and resid 496 through 498' Processing helix chain 'E' and resid 693 through 714 Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 12 through 20 Processing helix chain 'C' and resid 21 through 23 No H-bonds generated for 'chain 'C' and resid 21 through 23' Processing helix chain 'D' and resid 7 through 12 removed outlier: 4.117A pdb=" N VAL D 12 " --> pdb=" O GLY D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 19 Processing sheet with id=AA1, first strand: chain 'F' and resid 7 through 8 Processing sheet with id=AA2, first strand: chain 'F' and resid 11 through 13 removed outlier: 6.440A pdb=" N LEU F 33 " --> pdb=" O LEU F 62 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N LEU F 93 " --> pdb=" O ARG F 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 232 through 233 Processing sheet with id=AA4, first strand: chain 'F' and resid 246 through 248 Processing sheet with id=AA5, first strand: chain 'F' and resid 292 through 294 Processing sheet with id=AA6, first strand: chain 'F' and resid 311 through 313 removed outlier: 3.623A pdb=" N ASN F 337 " --> pdb=" O CYS F 312 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 368 through 370 removed outlier: 6.791A pdb=" N PHE F 400 " --> pdb=" O PHE F 427 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 475 through 480 removed outlier: 6.556A pdb=" N ARG F 488 " --> pdb=" O SER F 476 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ILE F 478 " --> pdb=" O LEU F 486 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU F 486 " --> pdb=" O ILE F 478 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE F 485 " --> pdb=" O MET F 553 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET F 553 " --> pdb=" O ILE F 485 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 530 through 534 removed outlier: 3.610A pdb=" N THR F 530 " --> pdb=" O TYR F 507 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR F 507 " --> pdb=" O THR F 530 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY F 502 " --> pdb=" O LEU F 569 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS F 567 " --> pdb=" O MET F 504 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE F 565 " --> pdb=" O PHE F 506 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA F 563 " --> pdb=" O LYS F 508 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 7 through 8 Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.439A pdb=" N LEU E 33 " --> pdb=" O LEU E 62 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LEU E 93 " --> pdb=" O ARG E 118 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 232 through 233 Processing sheet with id=AB4, first strand: chain 'E' and resid 246 through 248 Processing sheet with id=AB5, first strand: chain 'E' and resid 292 through 294 Processing sheet with id=AB6, first strand: chain 'E' and resid 311 through 313 removed outlier: 3.624A pdb=" N ASN E 337 " --> pdb=" O CYS E 312 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 368 through 370 removed outlier: 6.791A pdb=" N PHE E 400 " --> pdb=" O PHE E 427 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 475 through 480 removed outlier: 6.556A pdb=" N ARG E 488 " --> pdb=" O SER E 476 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ILE E 478 " --> pdb=" O LEU E 486 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU E 486 " --> pdb=" O ILE E 478 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ILE E 485 " --> pdb=" O MET E 553 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET E 553 " --> pdb=" O ILE E 485 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 530 through 534 removed outlier: 3.611A pdb=" N THR E 530 " --> pdb=" O TYR E 507 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR E 507 " --> pdb=" O THR E 530 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY E 502 " --> pdb=" O LEU E 569 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS E 567 " --> pdb=" O MET E 504 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE E 565 " --> pdb=" O PHE E 506 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA E 563 " --> pdb=" O LYS E 508 " (cutoff:3.500A) 177 hydrogen bonds defined for protein. 483 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: 2.98 Time building geometry restraints manager: 4.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3420 1.34 - 1.46: 2464 1.46 - 1.58: 4886 1.58 - 1.70: 2 1.70 - 1.82: 112 Bond restraints: 10884 Sorted by residual: bond pdb=" C1 NAG F1002 " pdb=" O5 NAG F1002 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.25e+00 bond pdb=" C1 NAG E1002 " pdb=" O5 NAG E1002 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.05e+00 bond pdb=" CG PRO E 222 " pdb=" CD PRO E 222 " ideal model delta sigma weight residual 1.503 1.426 0.077 3.40e-02 8.65e+02 5.07e+00 bond pdb=" CG PRO F 222 " pdb=" CD PRO F 222 " ideal model delta sigma weight residual 1.503 1.427 0.076 3.40e-02 8.65e+02 4.97e+00 bond pdb=" C1 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.56e+00 ... (remaining 10879 not shown) Histogram of bond angle deviations from ideal: 95.95 - 103.58: 127 103.58 - 111.21: 4421 111.21 - 118.84: 4354 118.84 - 126.47: 5672 126.47 - 134.10: 168 Bond angle restraints: 14742 Sorted by residual: angle pdb=" N PRO E 222 " pdb=" CD PRO E 222 " pdb=" CG PRO E 222 " ideal model delta sigma weight residual 103.20 95.95 7.25 1.50e+00 4.44e-01 2.34e+01 angle pdb=" N PRO F 222 " pdb=" CD PRO F 222 " pdb=" CG PRO F 222 " ideal model delta sigma weight residual 103.20 95.98 7.22 1.50e+00 4.44e-01 2.32e+01 angle pdb=" N GLU F 22 " pdb=" CA GLU F 22 " pdb=" C GLU F 22 " ideal model delta sigma weight residual 113.01 107.88 5.13 1.20e+00 6.94e-01 1.83e+01 angle pdb=" N GLU E 22 " pdb=" CA GLU E 22 " pdb=" C GLU E 22 " ideal model delta sigma weight residual 113.01 107.89 5.12 1.20e+00 6.94e-01 1.82e+01 angle pdb=" N ALA D 14 " pdb=" CA ALA D 14 " pdb=" C ALA D 14 " ideal model delta sigma weight residual 113.55 108.74 4.81 1.26e+00 6.30e-01 1.46e+01 ... (remaining 14737 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 6041 17.69 - 35.39: 604 35.39 - 53.08: 155 53.08 - 70.77: 26 70.77 - 88.47: 10 Dihedral angle restraints: 6836 sinusoidal: 3070 harmonic: 3766 Sorted by residual: dihedral pdb=" CB CYS F 259 " pdb=" SG CYS F 259 " pdb=" SG CYS F 284 " pdb=" CB CYS F 284 " ideal model delta sinusoidal sigma weight residual -86.00 -152.96 66.96 1 1.00e+01 1.00e-02 5.84e+01 dihedral pdb=" CB CYS E 259 " pdb=" SG CYS E 259 " pdb=" SG CYS E 284 " pdb=" CB CYS E 284 " ideal model delta sinusoidal sigma weight residual -86.00 -152.90 66.90 1 1.00e+01 1.00e-02 5.83e+01 dihedral pdb=" CB CYS F 8 " pdb=" SG CYS F 8 " pdb=" SG CYS F 26 " pdb=" CB CYS F 26 " ideal model delta sinusoidal sigma weight residual 93.00 156.57 -63.57 1 1.00e+01 1.00e-02 5.33e+01 ... (remaining 6833 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1301 0.056 - 0.111: 299 0.111 - 0.167: 56 0.167 - 0.222: 4 0.222 - 0.278: 2 Chirality restraints: 1662 Sorted by residual: chirality pdb=" C1 NAG E1002 " pdb=" ND2 ASN E 418 " pdb=" C2 NAG E1002 " pdb=" O5 NAG E1002 " both_signs ideal model delta sigma weight residual False -2.40 -2.68 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" C1 NAG F1002 " pdb=" ND2 ASN F 418 " pdb=" C2 NAG F1002 " pdb=" O5 NAG F1002 " both_signs ideal model delta sigma weight residual False -2.40 -2.68 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C4 NAG H 1 " pdb=" C3 NAG H 1 " pdb=" C5 NAG H 1 " pdb=" O4 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.34 -0.19 2.00e-01 2.50e+01 8.79e-01 ... (remaining 1659 not shown) Planarity restraints: 1888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS F 8 " 0.042 5.00e-02 4.00e+02 6.43e-02 6.61e+00 pdb=" N PRO F 9 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO F 9 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO F 9 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS E 8 " -0.042 5.00e-02 4.00e+02 6.42e-02 6.59e+00 pdb=" N PRO E 9 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO E 9 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 9 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 221 " -0.043 5.00e-02 4.00e+02 6.34e-02 6.43e+00 pdb=" N PRO E 222 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO E 222 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 222 " -0.035 5.00e-02 4.00e+02 ... (remaining 1885 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 100 2.60 - 3.18: 9047 3.18 - 3.75: 14987 3.75 - 4.33: 21678 4.33 - 4.90: 35591 Nonbonded interactions: 81403 Sorted by model distance: nonbonded pdb=" OE2 GLU F 443 " pdb=" NE2 GLN F 452 " model vdw 2.030 2.520 nonbonded pdb=" OE2 GLU E 443 " pdb=" NE2 GLN E 452 " model vdw 2.031 2.520 nonbonded pdb=" OD1 ASP F 12 " pdb=" NE2 GLN F 34 " model vdw 2.158 2.520 nonbonded pdb=" OD1 ASP E 12 " pdb=" NE2 GLN E 34 " model vdw 2.159 2.520 nonbonded pdb=" O ILE E 29 " pdb=" OG1 THR E 58 " model vdw 2.268 2.440 ... (remaining 81398 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.230 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 30.410 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.080 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 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 : 0.004 0.093 10884 Z= 0.286 Angle : 0.713 7.252 14742 Z= 0.387 Chirality : 0.049 0.278 1662 Planarity : 0.005 0.064 1874 Dihedral : 14.608 88.468 4286 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.10 % Favored : 86.75 % Rotamer: Outliers : 0.17 % Allowed : 0.76 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.87 (0.22), residues: 1260 helix: 0.25 (0.39), residues: 188 sheet: -2.53 (0.49), residues: 106 loop : -2.50 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 251 HIS 0.007 0.001 HIS F 21 PHE 0.017 0.002 PHE E 427 TYR 0.019 0.001 TYR E 430 ARG 0.005 0.000 ARG E 488 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 150 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 372 ARG cc_start: 0.6993 (mtm-85) cc_final: 0.6729 (mtp85) REVERT: E 372 ARG cc_start: 0.6899 (mtm-85) cc_final: 0.6595 (mtp85) REVERT: C 10 ILE cc_start: 0.8519 (mt) cc_final: 0.8309 (mt) outliers start: 2 outliers final: 1 residues processed: 150 average time/residue: 0.2302 time to fit residues: 48.9026 Evaluate side-chains 122 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 0.0970 chunk 60 optimal weight: 0.0980 chunk 73 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 15 ASN ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 462 ASN F 470 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 462 ASN E 470 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10884 Z= 0.313 Angle : 0.679 7.008 14742 Z= 0.350 Chirality : 0.048 0.193 1662 Planarity : 0.005 0.045 1874 Dihedral : 6.953 56.261 1739 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.78 % Favored : 87.06 % Rotamer: Outliers : 1.69 % Allowed : 9.63 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.98 (0.22), residues: 1260 helix: 0.37 (0.39), residues: 176 sheet: -2.34 (0.48), residues: 118 loop : -2.62 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 251 HIS 0.005 0.001 HIS F 209 PHE 0.018 0.002 PHE E 427 TYR 0.015 0.002 TYR F 512 ARG 0.008 0.001 ARG F 409 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 144 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 110 MET cc_start: 0.7463 (mtm) cc_final: 0.7243 (mtm) REVERT: F 131 ILE cc_start: 0.8616 (mt) cc_final: 0.8401 (mt) REVERT: F 294 MET cc_start: 0.6273 (ttt) cc_final: 0.6002 (tpt) REVERT: F 342 ILE cc_start: 0.8415 (pt) cc_final: 0.8153 (mt) REVERT: E 131 ILE cc_start: 0.8632 (mt) cc_final: 0.8390 (mt) REVERT: E 342 ILE cc_start: 0.8423 (pt) cc_final: 0.8141 (mt) REVERT: E 416 LYS cc_start: 0.7051 (pttt) cc_final: 0.6759 (pmtt) outliers start: 20 outliers final: 14 residues processed: 162 average time/residue: 0.2048 time to fit residues: 48.7361 Evaluate side-chains 146 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 132 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 15 ASN Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 50 SER Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 322 ASP Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 322 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 0.1980 chunk 35 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 77 optimal weight: 0.0570 chunk 31 optimal weight: 0.6980 chunk 114 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.5902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10884 Z= 0.211 Angle : 0.589 5.085 14742 Z= 0.307 Chirality : 0.044 0.151 1662 Planarity : 0.004 0.041 1874 Dihedral : 6.557 58.899 1736 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.38 % Favored : 87.46 % Rotamer: Outliers : 1.60 % Allowed : 12.16 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.88 (0.22), residues: 1260 helix: 0.89 (0.41), residues: 162 sheet: -2.15 (0.48), residues: 118 loop : -2.62 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 251 HIS 0.003 0.001 HIS E 21 PHE 0.015 0.002 PHE E 565 TYR 0.011 0.001 TYR F 512 ARG 0.010 0.000 ARG E 409 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 136 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 131 ILE cc_start: 0.8660 (mt) cc_final: 0.8441 (mt) REVERT: F 256 PHE cc_start: 0.7709 (t80) cc_final: 0.7413 (t80) REVERT: F 260 GLN cc_start: 0.6645 (mt0) cc_final: 0.6293 (mt0) REVERT: F 342 ILE cc_start: 0.8364 (pt) cc_final: 0.8007 (mp) REVERT: E 131 ILE cc_start: 0.8666 (mt) cc_final: 0.8440 (mt) REVERT: C 10 ILE cc_start: 0.8636 (mt) cc_final: 0.8385 (mt) outliers start: 19 outliers final: 18 residues processed: 152 average time/residue: 0.1994 time to fit residues: 44.5911 Evaluate side-chains 149 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 131 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 50 SER Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 322 ASP Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 322 ASP Chi-restraints excluded: chain E residue 530 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.7980 chunk 86 optimal weight: 0.0050 chunk 59 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 54 optimal weight: 0.0000 chunk 76 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 405 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 ASN C 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10884 Z= 0.185 Angle : 0.560 4.610 14742 Z= 0.291 Chirality : 0.043 0.146 1662 Planarity : 0.004 0.043 1874 Dihedral : 6.273 54.407 1736 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.98 % Favored : 87.94 % Rotamer: Outliers : 2.79 % Allowed : 13.18 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.77 (0.22), residues: 1260 helix: 1.10 (0.42), residues: 162 sheet: -1.99 (0.48), residues: 118 loop : -2.58 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 251 HIS 0.003 0.001 HIS E 21 PHE 0.013 0.001 PHE F 705 TYR 0.010 0.001 TYR E 507 ARG 0.011 0.000 ARG E 409 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 137 time to evaluate : 1.287 Fit side-chains revert: symmetry clash REVERT: F 111 ASN cc_start: 0.8045 (t0) cc_final: 0.7759 (t0) REVERT: F 131 ILE cc_start: 0.8674 (mt) cc_final: 0.8457 (mt) REVERT: E 111 ASN cc_start: 0.8007 (t0) cc_final: 0.7705 (t0) REVERT: E 131 ILE cc_start: 0.8684 (mt) cc_final: 0.8476 (mt) REVERT: C 10 ILE cc_start: 0.8683 (mt) cc_final: 0.8430 (mt) outliers start: 33 outliers final: 27 residues processed: 160 average time/residue: 0.2061 time to fit residues: 48.4915 Evaluate side-chains 156 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 129 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 HIS Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 266 CYS Chi-restraints excluded: chain F residue 322 ASP Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain F residue 489 TRP Chi-restraints excluded: chain F residue 585 ILE Chi-restraints excluded: chain E residue 21 HIS Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 322 ASP Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 405 ASN Chi-restraints excluded: chain E residue 585 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 103 optimal weight: 0.0570 chunk 84 optimal weight: 6.9990 chunk 0 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10884 Z= 0.229 Angle : 0.579 6.794 14742 Z= 0.300 Chirality : 0.044 0.143 1662 Planarity : 0.004 0.044 1874 Dihedral : 6.267 53.895 1736 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.46 % Favored : 87.54 % Rotamer: Outliers : 2.20 % Allowed : 15.62 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.77 (0.22), residues: 1260 helix: 1.11 (0.41), residues: 166 sheet: -2.11 (0.47), residues: 122 loop : -2.57 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 251 HIS 0.003 0.001 HIS E 21 PHE 0.012 0.001 PHE F 382 TYR 0.010 0.001 TYR F 60 ARG 0.011 0.000 ARG F 409 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 133 time to evaluate : 1.198 Fit side-chains REVERT: B 13 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7262 (mm-30) REVERT: F 111 ASN cc_start: 0.8097 (t0) cc_final: 0.7822 (t0) REVERT: F 131 ILE cc_start: 0.8704 (mt) cc_final: 0.8491 (mt) REVERT: F 256 PHE cc_start: 0.7688 (t80) cc_final: 0.7431 (t80) REVERT: E 111 ASN cc_start: 0.8036 (t0) cc_final: 0.7736 (t0) REVERT: E 131 ILE cc_start: 0.8717 (mt) cc_final: 0.8508 (mt) REVERT: E 260 GLN cc_start: 0.6627 (mt0) cc_final: 0.6055 (mt0) outliers start: 26 outliers final: 26 residues processed: 153 average time/residue: 0.2140 time to fit residues: 48.1279 Evaluate side-chains 150 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 124 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 322 ASP Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain F residue 416 LYS Chi-restraints excluded: chain F residue 489 TRP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 322 ASP Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 405 ASN Chi-restraints excluded: chain E residue 416 LYS Chi-restraints excluded: chain E residue 489 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.9980 chunk 109 optimal weight: 0.4980 chunk 24 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 121 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 0.0870 chunk 10 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 117 optimal weight: 0.0980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 405 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 ASN C 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10884 Z= 0.171 Angle : 0.554 11.052 14742 Z= 0.286 Chirality : 0.043 0.142 1662 Planarity : 0.004 0.046 1874 Dihedral : 6.134 54.332 1736 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 2.36 % Allowed : 16.30 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.66 (0.22), residues: 1260 helix: 1.29 (0.42), residues: 166 sheet: -1.93 (0.47), residues: 122 loop : -2.53 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 251 HIS 0.003 0.001 HIS E 21 PHE 0.014 0.001 PHE E 256 TYR 0.010 0.001 TYR F 507 ARG 0.014 0.000 ARG E 409 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 127 time to evaluate : 1.125 Fit side-chains REVERT: F 111 ASN cc_start: 0.8064 (t0) cc_final: 0.7799 (t0) REVERT: F 131 ILE cc_start: 0.8675 (mt) cc_final: 0.8456 (mt) REVERT: F 239 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7346 (mm-30) REVERT: E 111 ASN cc_start: 0.7996 (t0) cc_final: 0.7710 (t0) REVERT: E 131 ILE cc_start: 0.8685 (mt) cc_final: 0.8469 (mt) REVERT: E 260 GLN cc_start: 0.6561 (mt0) cc_final: 0.6027 (mt0) outliers start: 28 outliers final: 23 residues processed: 149 average time/residue: 0.2219 time to fit residues: 49.5073 Evaluate side-chains 147 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 124 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 50 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 322 ASP Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 585 ILE Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 489 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 121 optimal weight: 0.5980 chunk 76 optimal weight: 0.0020 chunk 74 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10884 Z= 0.196 Angle : 0.566 11.458 14742 Z= 0.293 Chirality : 0.043 0.145 1662 Planarity : 0.004 0.046 1874 Dihedral : 6.082 54.079 1736 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.70 % Favored : 87.30 % Rotamer: Outliers : 2.96 % Allowed : 16.47 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.65 (0.22), residues: 1260 helix: 1.32 (0.42), residues: 166 sheet: -1.88 (0.47), residues: 122 loop : -2.53 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 251 HIS 0.003 0.001 HIS E 440 PHE 0.014 0.001 PHE F 256 TYR 0.013 0.001 TYR F 507 ARG 0.008 0.000 ARG E 409 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 128 time to evaluate : 1.319 Fit side-chains REVERT: F 111 ASN cc_start: 0.8086 (t0) cc_final: 0.7811 (t0) REVERT: F 131 ILE cc_start: 0.8681 (mt) cc_final: 0.8470 (mt) REVERT: F 277 TYR cc_start: 0.6562 (m-80) cc_final: 0.6125 (m-80) REVERT: E 111 ASN cc_start: 0.8042 (t0) cc_final: 0.7738 (t0) REVERT: E 131 ILE cc_start: 0.8689 (mt) cc_final: 0.8474 (mt) outliers start: 35 outliers final: 31 residues processed: 157 average time/residue: 0.2227 time to fit residues: 51.0766 Evaluate side-chains 153 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 122 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 HIS Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 50 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 322 ASP Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain F residue 416 LYS Chi-restraints excluded: chain F residue 489 TRP Chi-restraints excluded: chain E residue 21 HIS Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 322 ASP Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 381 PHE Chi-restraints excluded: chain E residue 405 ASN Chi-restraints excluded: chain E residue 416 LYS Chi-restraints excluded: chain E residue 489 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 60 optimal weight: 0.0040 chunk 11 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10884 Z= 0.227 Angle : 0.590 11.410 14742 Z= 0.305 Chirality : 0.044 0.169 1662 Planarity : 0.004 0.051 1874 Dihedral : 6.117 53.737 1736 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.06 % Favored : 87.86 % Rotamer: Outliers : 3.72 % Allowed : 16.30 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.63 (0.23), residues: 1260 helix: 1.34 (0.42), residues: 166 sheet: -1.81 (0.49), residues: 122 loop : -2.53 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 251 HIS 0.003 0.001 HIS F 440 PHE 0.018 0.001 PHE E 256 TYR 0.012 0.001 TYR F 507 ARG 0.012 0.000 ARG F 409 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 130 time to evaluate : 1.115 Fit side-chains REVERT: F 111 ASN cc_start: 0.8110 (t0) cc_final: 0.7837 (t0) REVERT: F 123 ASN cc_start: 0.8120 (m110) cc_final: 0.7880 (m110) REVERT: F 131 ILE cc_start: 0.8695 (mt) cc_final: 0.8485 (mt) REVERT: E 111 ASN cc_start: 0.8094 (t0) cc_final: 0.7801 (t0) REVERT: E 123 ASN cc_start: 0.8117 (m110) cc_final: 0.7887 (m110) REVERT: E 131 ILE cc_start: 0.8712 (mt) cc_final: 0.8491 (mt) outliers start: 44 outliers final: 35 residues processed: 164 average time/residue: 0.2158 time to fit residues: 51.3718 Evaluate side-chains 161 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 126 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 HIS Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 50 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 322 ASP Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 381 PHE Chi-restraints excluded: chain F residue 404 ASP Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain F residue 416 LYS Chi-restraints excluded: chain F residue 489 TRP Chi-restraints excluded: chain E residue 21 HIS Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 322 ASP Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 348 ASN Chi-restraints excluded: chain E residue 381 PHE Chi-restraints excluded: chain E residue 405 ASN Chi-restraints excluded: chain E residue 489 TRP Chi-restraints excluded: chain E residue 585 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 4.9990 chunk 116 optimal weight: 0.0980 chunk 68 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 119 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10884 Z= 0.210 Angle : 0.592 12.141 14742 Z= 0.305 Chirality : 0.044 0.172 1662 Planarity : 0.004 0.050 1874 Dihedral : 6.103 53.726 1736 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.86 % Favored : 87.06 % Rotamer: Outliers : 3.55 % Allowed : 16.55 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.59 (0.23), residues: 1260 helix: 1.40 (0.42), residues: 166 sheet: -1.76 (0.49), residues: 122 loop : -2.51 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 251 HIS 0.003 0.001 HIS E 440 PHE 0.014 0.001 PHE F 256 TYR 0.013 0.001 TYR F 507 ARG 0.012 0.000 ARG E 409 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 133 time to evaluate : 1.749 Fit side-chains revert: symmetry clash REVERT: F 111 ASN cc_start: 0.8102 (t0) cc_final: 0.7815 (t0) REVERT: F 131 ILE cc_start: 0.8675 (mt) cc_final: 0.8465 (mt) REVERT: E 111 ASN cc_start: 0.8093 (t0) cc_final: 0.7803 (t0) REVERT: E 131 ILE cc_start: 0.8690 (mt) cc_final: 0.8474 (mt) REVERT: E 277 TYR cc_start: 0.6621 (m-80) cc_final: 0.6276 (m-80) outliers start: 42 outliers final: 33 residues processed: 164 average time/residue: 0.2436 time to fit residues: 59.5565 Evaluate side-chains 155 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 122 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 50 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 348 ASN Chi-restraints excluded: chain F residue 404 ASP Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain F residue 489 TRP Chi-restraints excluded: chain F residue 531 VAL Chi-restraints excluded: chain E residue 21 HIS Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 348 ASN Chi-restraints excluded: chain E residue 381 PHE Chi-restraints excluded: chain E residue 405 ASN Chi-restraints excluded: chain E residue 489 TRP Chi-restraints excluded: chain E residue 531 VAL Chi-restraints excluded: chain E residue 585 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.0040 chunk 56 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 79 optimal weight: 0.0970 chunk 106 optimal weight: 2.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 429 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 HIS C 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10884 Z= 0.194 Angle : 0.587 11.135 14742 Z= 0.303 Chirality : 0.044 0.155 1662 Planarity : 0.004 0.052 1874 Dihedral : 6.057 53.699 1736 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.54 % Favored : 87.38 % Rotamer: Outliers : 3.12 % Allowed : 17.06 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.55 (0.23), residues: 1260 helix: 1.43 (0.42), residues: 166 sheet: -1.71 (0.50), residues: 122 loop : -2.49 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 412 HIS 0.005 0.001 HIS C 21 PHE 0.020 0.001 PHE E 256 TYR 0.013 0.001 TYR F 507 ARG 0.014 0.000 ARG E 409 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 126 time to evaluate : 1.332 Fit side-chains REVERT: F 111 ASN cc_start: 0.8105 (t0) cc_final: 0.7816 (t0) REVERT: F 131 ILE cc_start: 0.8648 (mt) cc_final: 0.8447 (mt) REVERT: F 277 TYR cc_start: 0.6576 (m-80) cc_final: 0.6238 (m-80) REVERT: E 111 ASN cc_start: 0.8087 (t0) cc_final: 0.7784 (t0) REVERT: E 131 ILE cc_start: 0.8667 (mt) cc_final: 0.8462 (mt) REVERT: E 256 PHE cc_start: 0.7639 (t80) cc_final: 0.6872 (t80) REVERT: E 260 GLN cc_start: 0.6732 (mt0) cc_final: 0.6460 (mp10) REVERT: E 294 MET cc_start: 0.5599 (tpt) cc_final: 0.5244 (ttt) outliers start: 37 outliers final: 33 residues processed: 152 average time/residue: 0.2177 time to fit residues: 48.2640 Evaluate side-chains 154 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 121 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 50 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 381 PHE Chi-restraints excluded: chain F residue 404 ASP Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain F residue 489 TRP Chi-restraints excluded: chain F residue 531 VAL Chi-restraints excluded: chain E residue 21 HIS Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 381 PHE Chi-restraints excluded: chain E residue 405 ASN Chi-restraints excluded: chain E residue 429 HIS Chi-restraints excluded: chain E residue 489 TRP Chi-restraints excluded: chain E residue 531 VAL Chi-restraints excluded: chain E residue 585 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 12 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 429 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.216233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.191355 restraints weight = 11230.567| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 1.57 r_work: 0.3463 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10884 Z= 0.258 Angle : 0.624 14.673 14742 Z= 0.320 Chirality : 0.045 0.153 1662 Planarity : 0.004 0.054 1874 Dihedral : 6.147 52.832 1736 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.02 % Favored : 86.83 % Rotamer: Outliers : 3.21 % Allowed : 17.23 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.60 (0.23), residues: 1260 helix: 1.48 (0.42), residues: 160 sheet: -1.76 (0.50), residues: 122 loop : -2.51 (0.18), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 251 HIS 0.006 0.001 HIS F 429 PHE 0.017 0.002 PHE F 256 TYR 0.014 0.001 TYR E 507 ARG 0.014 0.000 ARG E 409 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2429.07 seconds wall clock time: 44 minutes 55.50 seconds (2695.50 seconds total)