Starting phenix.real_space_refine on Fri Feb 16 07:32:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhj_24463/02_2024/7rhj_24463_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhj_24463/02_2024/7rhj_24463.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhj_24463/02_2024/7rhj_24463_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhj_24463/02_2024/7rhj_24463_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhj_24463/02_2024/7rhj_24463_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhj_24463/02_2024/7rhj_24463.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhj_24463/02_2024/7rhj_24463.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhj_24463/02_2024/7rhj_24463_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhj_24463/02_2024/7rhj_24463_updated.pdb" } resolution = 2.88 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= 0.006 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 P 4 5.49 5 S 83 5.16 5 C 9618 2.51 5 N 2397 2.21 5 O 2636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 159": "OD1" <-> "OD2" Residue "A TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 429": "OD1" <-> "OD2" Residue "A GLU 452": "OE1" <-> "OE2" Residue "A ASP 540": "OD1" <-> "OD2" Residue "B TYR 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 994": "OE1" <-> "OE2" Residue "B PHE 1051": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1069": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 232": "OE1" <-> "OE2" Residue "C TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14738 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3688 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3553 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 14, 'TRANS': 418} Chain breaks: 1 Chain: "C" Number of atoms: 3688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3688 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 3688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3688 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'5H0': 1, 'PCG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.97, per 1000 atoms: 0.54 Number of scatterers: 14738 At special positions: 0 Unit cell: (99.002, 97.324, 119.977, 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 83 16.00 P 4 15.00 O 2636 8.00 N 2397 7.00 C 9618 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.35 Conformation dependent library (CDL) restraints added in 3.0 seconds 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3370 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 73 helices and 8 sheets defined 59.9% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.64 Creating SS restraints... Processing helix chain 'A' and resid 163 through 188 Proline residue: A 175 - end of helix removed outlier: 5.080A pdb=" N ILE A 184 " --> pdb=" O TRP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 197 through 220 Processing helix chain 'A' and resid 233 through 242 Processing helix chain 'A' and resid 244 through 252 Processing helix chain 'A' and resid 257 through 261 Processing helix chain 'A' and resid 268 through 291 removed outlier: 3.592A pdb=" N ARG A 271 " --> pdb=" O PRO A 268 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASN A 273 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG A 274 " --> pdb=" O ARG A 271 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG A 277 " --> pdb=" O ARG A 274 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N SER A 279 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A 288 " --> pdb=" O PHE A 285 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU A 289 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A 290 " --> pdb=" O ARG A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 325 Processing helix chain 'A' and resid 345 through 360 Processing helix chain 'A' and resid 372 through 387 Processing helix chain 'A' and resid 389 through 403 Processing helix chain 'A' and resid 405 through 423 Processing helix chain 'A' and resid 428 through 443 Processing helix chain 'A' and resid 450 through 453 No H-bonds generated for 'chain 'A' and resid 450 through 453' Processing helix chain 'A' and resid 459 through 469 Processing helix chain 'A' and resid 471 through 475 Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 578 through 585 Processing helix chain 'A' and resid 589 through 604 removed outlier: 3.503A pdb=" N ILE A 602 " --> pdb=" O LYS A 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 679 Proline residue: B 675 - end of helix Processing helix chain 'B' and resid 688 through 708 Processing helix chain 'B' and resid 727 through 734 removed outlier: 3.642A pdb=" N TYR B 732 " --> pdb=" O MET B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 744 Processing helix chain 'B' and resid 759 through 767 Proline residue: B 764 - end of helix Processing helix chain 'B' and resid 769 through 782 removed outlier: 3.559A pdb=" N SER B 781 " --> pdb=" O SER B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 815 Processing helix chain 'B' and resid 831 through 843 Processing helix chain 'B' and resid 855 through 886 Processing helix chain 'B' and resid 888 through 906 Processing helix chain 'B' and resid 911 through 927 Processing helix chain 'B' and resid 933 through 939 removed outlier: 3.501A pdb=" N GLN B 939 " --> pdb=" O GLU B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 958 removed outlier: 7.185A pdb=" N ASN B 955 " --> pdb=" O ASP B 951 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ILE B 956 " --> pdb=" O VAL B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 977 Processing helix chain 'B' and resid 1031 through 1034 No H-bonds generated for 'chain 'B' and resid 1031 through 1034' Processing helix chain 'B' and resid 1062 through 1066 Processing helix chain 'B' and resid 1070 through 1082 Processing helix chain 'C' and resid 163 through 188 Proline residue: C 175 - end of helix removed outlier: 4.984A pdb=" N ILE C 184 " --> pdb=" O TRP C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 195 Processing helix chain 'C' and resid 197 through 218 Processing helix chain 'C' and resid 233 through 242 Processing helix chain 'C' and resid 244 through 252 Processing helix chain 'C' and resid 257 through 263 Processing helix chain 'C' and resid 268 through 291 removed outlier: 3.596A pdb=" N ARG C 271 " --> pdb=" O PRO C 268 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ASN C 273 " --> pdb=" O ILE C 270 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG C 274 " --> pdb=" O ARG C 271 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG C 277 " --> pdb=" O ARG C 274 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N SER C 279 " --> pdb=" O LEU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 325 Processing helix chain 'C' and resid 345 through 360 Processing helix chain 'C' and resid 372 through 423 removed outlier: 4.971A pdb=" N ALA C 406 " --> pdb=" O ASN C 402 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ARG C 407 " --> pdb=" O MET C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 443 Processing helix chain 'C' and resid 450 through 453 No H-bonds generated for 'chain 'C' and resid 450 through 453' Processing helix chain 'C' and resid 459 through 469 removed outlier: 3.633A pdb=" N GLU C 464 " --> pdb=" O LYS C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 476 removed outlier: 3.699A pdb=" N LYS C 476 " --> pdb=" O ASP C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 494 removed outlier: 3.623A pdb=" N VAL C 492 " --> pdb=" O LEU C 488 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LEU C 493 " --> pdb=" O VAL C 489 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LYS C 494 " --> pdb=" O GLU C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 549 No H-bonds generated for 'chain 'C' and resid 546 through 549' Processing helix chain 'C' and resid 578 through 585 Processing helix chain 'C' and resid 589 through 603 removed outlier: 4.311A pdb=" N GLU C 596 " --> pdb=" O LYS C 592 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN C 601 " --> pdb=" O GLU C 597 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE C 602 " --> pdb=" O LYS C 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 188 Proline residue: D 175 - end of helix removed outlier: 5.073A pdb=" N ILE D 184 " --> pdb=" O TRP D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 195 Processing helix chain 'D' and resid 197 through 220 Processing helix chain 'D' and resid 233 through 242 Processing helix chain 'D' and resid 244 through 252 Processing helix chain 'D' and resid 256 through 263 removed outlier: 3.592A pdb=" N PHE D 261 " --> pdb=" O LEU D 258 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU D 263 " --> pdb=" O TYR D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 291 removed outlier: 4.273A pdb=" N ASN D 273 " --> pdb=" O ILE D 270 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG D 277 " --> pdb=" O ARG D 274 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N SER D 279 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR D 288 " --> pdb=" O PHE D 285 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU D 289 " --> pdb=" O GLN D 286 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR D 290 " --> pdb=" O ARG D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 325 Processing helix chain 'D' and resid 345 through 360 Processing helix chain 'D' and resid 372 through 401 removed outlier: 4.123A pdb=" N PHE D 389 " --> pdb=" O GLY D 385 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA D 390 " --> pdb=" O VAL D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 424 Processing helix chain 'D' and resid 428 through 443 Processing helix chain 'D' and resid 450 through 456 removed outlier: 5.092A pdb=" N TYR D 456 " --> pdb=" O GLU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 469 Processing helix chain 'D' and resid 471 through 474 No H-bonds generated for 'chain 'D' and resid 471 through 474' Processing helix chain 'D' and resid 487 through 490 No H-bonds generated for 'chain 'D' and resid 487 through 490' Processing helix chain 'D' and resid 546 through 549 No H-bonds generated for 'chain 'D' and resid 546 through 549' Processing helix chain 'D' and resid 578 through 585 Processing helix chain 'D' and resid 589 through 604 removed outlier: 3.720A pdb=" N LYS D 598 " --> pdb=" O MET D 594 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 496 through 500 removed outlier: 6.038A pdb=" N PHE A 574 " --> pdb=" O ILE A 519 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ILE A 519 " --> pdb=" O PHE A 574 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU A 576 " --> pdb=" O TYR A 517 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N TYR A 517 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 523 through 526 removed outlier: 3.971A pdb=" N LYS A 523 " --> pdb=" O ILE A 568 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 979 through 983 removed outlier: 6.371A pdb=" N PHE B1055 " --> pdb=" O ILE B1002 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ILE B1002 " --> pdb=" O PHE B1055 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N LEU B1057 " --> pdb=" O TYR B1000 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N TYR B1000 " --> pdb=" O LEU B1057 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 987 through 990 removed outlier: 4.092A pdb=" N ASP B 987 " --> pdb=" O ALA B1048 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N VAL B1046 " --> pdb=" O VAL B 989 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLN B1006 " --> pdb=" O HIS B1049 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL B1020 " --> pdb=" O VAL B1009 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 496 through 500 Processing sheet with id= F, first strand: chain 'C' and resid 523 through 527 removed outlier: 4.198A pdb=" N LYS C 523 " --> pdb=" O ILE C 568 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE C 568 " --> pdb=" O LYS C 523 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN C 564 " --> pdb=" O VAL C 527 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 496 through 500 removed outlier: 6.108A pdb=" N PHE D 574 " --> pdb=" O ILE D 519 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ILE D 519 " --> pdb=" O PHE D 574 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 524 through 527 removed outlier: 4.271A pdb=" N ASN D 564 " --> pdb=" O VAL D 527 " (cutoff:3.500A) 775 hydrogen bonds defined for protein. 2133 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: 4.64 Time building geometry restraints manager: 6.85 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: 4534 1.34 - 1.47: 3822 1.47 - 1.59: 6594 1.59 - 1.71: 9 1.71 - 1.84: 140 Bond restraints: 15099 Sorted by residual: bond pdb=" C3' PCG A 701 " pdb=" C4' PCG A 701 " ideal model delta sigma weight residual 1.808 1.494 0.314 2.00e-02 2.50e+03 2.46e+02 bond pdb=" C3' PCG D 802 " pdb=" C4' PCG D 802 " ideal model delta sigma weight residual 1.808 1.494 0.314 2.00e-02 2.50e+03 2.46e+02 bond pdb=" C3' PCG C 701 " pdb=" C4' PCG C 701 " ideal model delta sigma weight residual 1.808 1.495 0.313 2.00e-02 2.50e+03 2.45e+02 bond pdb=" C3' PCG B1301 " pdb=" C4' PCG B1301 " ideal model delta sigma weight residual 1.808 1.495 0.313 2.00e-02 2.50e+03 2.44e+02 bond pdb=" C2' PCG A 701 " pdb=" C3' PCG A 701 " ideal model delta sigma weight residual 1.200 1.504 -0.304 2.00e-02 2.50e+03 2.31e+02 ... (remaining 15094 not shown) Histogram of bond angle deviations from ideal: 98.80 - 105.91: 276 105.91 - 113.03: 8053 113.03 - 120.14: 5565 120.14 - 127.26: 6436 127.26 - 134.37: 148 Bond angle restraints: 20478 Sorted by residual: angle pdb=" CA PRO C 497 " pdb=" N PRO C 497 " pdb=" CD PRO C 497 " ideal model delta sigma weight residual 112.00 105.56 6.44 1.40e+00 5.10e-01 2.11e+01 angle pdb=" C LYS B1059 " pdb=" N LYS B1060 " pdb=" CA LYS B1060 " ideal model delta sigma weight residual 121.54 129.79 -8.25 1.91e+00 2.74e-01 1.86e+01 angle pdb=" N GLU D 464 " pdb=" CA GLU D 464 " pdb=" CB GLU D 464 " ideal model delta sigma weight residual 110.41 117.10 -6.69 1.68e+00 3.54e-01 1.59e+01 angle pdb=" N GLU B 780 " pdb=" CA GLU B 780 " pdb=" CB GLU B 780 " ideal model delta sigma weight residual 110.39 117.11 -6.72 1.75e+00 3.27e-01 1.47e+01 angle pdb=" C ALA D 463 " pdb=" N GLU D 464 " pdb=" CA GLU D 464 " ideal model delta sigma weight residual 121.58 114.12 7.46 1.95e+00 2.63e-01 1.46e+01 ... (remaining 20473 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 8138 17.98 - 35.95: 690 35.95 - 53.93: 97 53.93 - 71.91: 12 71.91 - 89.89: 9 Dihedral angle restraints: 8946 sinusoidal: 3685 harmonic: 5261 Sorted by residual: dihedral pdb=" CA THR D 181 " pdb=" C THR D 181 " pdb=" N MET D 182 " pdb=" CA MET D 182 " ideal model delta harmonic sigma weight residual -180.00 -161.90 -18.10 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA GLU C 464 " pdb=" C GLU C 464 " pdb=" N ILE C 465 " pdb=" CA ILE C 465 " ideal model delta harmonic sigma weight residual 180.00 162.02 17.98 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA LEU D 491 " pdb=" C LEU D 491 " pdb=" N VAL D 492 " pdb=" CA VAL D 492 " ideal model delta harmonic sigma weight residual 180.00 162.13 17.87 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 8943 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2156 0.094 - 0.188: 114 0.188 - 0.281: 4 0.281 - 0.375: 4 0.375 - 0.469: 4 Chirality restraints: 2282 Sorted by residual: chirality pdb=" C3' PCG C 701 " pdb=" C2' PCG C 701 " pdb=" C4' PCG C 701 " pdb=" O3' PCG C 701 " both_signs ideal model delta sigma weight residual False -2.10 -2.57 0.47 2.00e-01 2.50e+01 5.50e+00 chirality pdb=" C3' PCG A 701 " pdb=" C2' PCG A 701 " pdb=" C4' PCG A 701 " pdb=" O3' PCG A 701 " both_signs ideal model delta sigma weight residual False -2.10 -2.57 0.47 2.00e-01 2.50e+01 5.44e+00 chirality pdb=" C3' PCG B1301 " pdb=" C2' PCG B1301 " pdb=" C4' PCG B1301 " pdb=" O3' PCG B1301 " both_signs ideal model delta sigma weight residual False -2.10 -2.57 0.46 2.00e-01 2.50e+01 5.35e+00 ... (remaining 2279 not shown) Planarity restraints: 2521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 763 " 0.048 5.00e-02 4.00e+02 7.28e-02 8.48e+00 pdb=" N PRO B 764 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 764 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 764 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET C 281 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.53e+00 pdb=" C MET C 281 " -0.041 2.00e-02 2.50e+03 pdb=" O MET C 281 " 0.015 2.00e-02 2.50e+03 pdb=" N PHE C 282 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE D 254 " -0.039 5.00e-02 4.00e+02 5.74e-02 5.26e+00 pdb=" N PRO D 255 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 255 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 255 " -0.032 5.00e-02 4.00e+02 ... (remaining 2518 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3555 2.79 - 3.32: 14567 3.32 - 3.84: 26637 3.84 - 4.37: 30547 4.37 - 4.90: 51452 Nonbonded interactions: 126758 Sorted by model distance: nonbonded pdb=" O LEU C 169 " pdb=" OG1 THR C 173 " model vdw 2.261 2.440 nonbonded pdb=" OD1 ASN B 776 " pdb=" OH TYR B 789 " model vdw 2.262 2.440 nonbonded pdb=" O LEU D 169 " pdb=" OG1 THR D 173 " model vdw 2.262 2.440 nonbonded pdb=" OE2 GLU A 515 " pdb=" OH TYR A 517 " model vdw 2.269 2.440 nonbonded pdb=" O LEU A 169 " pdb=" OG1 THR A 173 " model vdw 2.271 2.440 ... (remaining 126753 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 156 through 605) selection = (chain 'C' and resid 156 through 605) selection = (chain 'D' and resid 156 through 605) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.060 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: 0.020 Extract box with map and model: 5.940 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 42.840 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 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 : 0.012 0.314 15099 Z= 0.717 Angle : 0.756 11.378 20478 Z= 0.383 Chirality : 0.052 0.469 2282 Planarity : 0.005 0.073 2521 Dihedral : 13.241 89.886 5576 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.12 % Allowed : 0.62 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.19), residues: 1773 helix: 0.38 (0.15), residues: 1087 sheet: -1.36 (0.66), residues: 54 loop : -0.39 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 442 HIS 0.006 0.001 HIS C 422 PHE 0.018 0.002 PHE C 285 TYR 0.019 0.001 TYR B 865 ARG 0.005 0.000 ARG C 407 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 214 time to evaluate : 1.752 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "VAL C 156 " (corrupted residue). Skipping it. REVERT: B 970 MET cc_start: 0.6197 (ttt) cc_final: 0.5979 (ttt) REVERT: D 451 LYS cc_start: 0.6809 (mmtt) cc_final: 0.6596 (mmmt) REVERT: D 498 GLN cc_start: 0.6527 (tt0) cc_final: 0.6185 (tp40) outliers start: 2 outliers final: 1 residues processed: 216 average time/residue: 1.1788 time to fit residues: 282.6449 Evaluate side-chains 162 residues out of total 1605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 161 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 547 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 0.0670 chunk 134 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 72 optimal weight: 0.0000 chunk 139 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 161 optimal weight: 0.0980 overall best weight: 0.3722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 496 GLN B 689 HIS B1003 GLN D 243 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.0870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 15099 Z= 0.125 Angle : 0.460 12.431 20478 Z= 0.234 Chirality : 0.037 0.168 2282 Planarity : 0.004 0.058 2521 Dihedral : 4.514 37.957 2051 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.50 % Allowed : 8.93 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.19), residues: 1773 helix: 1.04 (0.15), residues: 1096 sheet: -1.41 (0.67), residues: 54 loop : -0.26 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 442 HIS 0.004 0.001 HIS B 803 PHE 0.022 0.001 PHE D 410 TYR 0.021 0.001 TYR C 543 ARG 0.005 0.000 ARG D 407 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 173 time to evaluate : 1.839 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "VAL C 156 " (corrupted residue). Skipping it. REVERT: A 234 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8188 (tm) REVERT: B 665 MET cc_start: 0.7409 (OUTLIER) cc_final: 0.6759 (mmm) REVERT: B 851 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.7443 (p0) REVERT: B 970 MET cc_start: 0.6333 (ttt) cc_final: 0.6101 (ttt) REVERT: B 974 MET cc_start: 0.6907 (ppp) cc_final: 0.6443 (ptp) REVERT: B 1078 LYS cc_start: 0.5867 (tttt) cc_final: 0.5545 (pptt) outliers start: 24 outliers final: 8 residues processed: 184 average time/residue: 1.0683 time to fit residues: 220.7213 Evaluate side-chains 167 residues out of total 1605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 156 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 851 ASP Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 473 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 134 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 161 optimal weight: 4.9990 chunk 174 optimal weight: 0.8980 chunk 144 optimal weight: 0.9990 chunk 160 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 129 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 496 GLN ** B 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1003 GLN C 498 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15099 Z= 0.248 Angle : 0.510 8.602 20478 Z= 0.267 Chirality : 0.040 0.155 2282 Planarity : 0.004 0.059 2521 Dihedral : 4.383 37.424 2049 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.37 % Allowed : 10.30 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.19), residues: 1773 helix: 1.14 (0.15), residues: 1097 sheet: -1.48 (0.67), residues: 54 loop : -0.21 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 168 HIS 0.006 0.001 HIS B 803 PHE 0.019 0.002 PHE D 410 TYR 0.022 0.002 TYR C 351 ARG 0.006 0.000 ARG D 407 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 178 time to evaluate : 1.947 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "VAL C 156 " (corrupted residue). Skipping it. REVERT: A 234 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8187 (tm) REVERT: A 286 GLN cc_start: 0.7265 (OUTLIER) cc_final: 0.6978 (mp10) REVERT: B 665 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.7024 (mmm) REVERT: B 851 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7465 (p0) REVERT: B 947 ASP cc_start: 0.6614 (OUTLIER) cc_final: 0.5861 (m-30) REVERT: B 1078 LYS cc_start: 0.6005 (tttt) cc_final: 0.5597 (pptt) REVERT: C 430 MET cc_start: 0.7642 (tpp) cc_final: 0.7394 (tpp) REVERT: D 451 LYS cc_start: 0.7019 (mmtt) cc_final: 0.6686 (mmmt) REVERT: D 580 ASP cc_start: 0.6492 (m-30) cc_final: 0.5959 (t0) outliers start: 38 outliers final: 12 residues processed: 198 average time/residue: 1.1784 time to fit residues: 259.5472 Evaluate side-chains 183 residues out of total 1605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 166 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 851 ASP Chi-restraints excluded: chain B residue 947 ASP Chi-restraints excluded: chain B residue 980 SER Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 473 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 172 optimal weight: 0.0040 chunk 154 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 143 optimal weight: 0.7980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN ** B 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1003 GLN C 226 GLN C 498 GLN ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 15099 Z= 0.139 Angle : 0.449 7.431 20478 Z= 0.232 Chirality : 0.037 0.171 2282 Planarity : 0.003 0.052 2521 Dihedral : 4.157 36.837 2049 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.25 % Allowed : 12.73 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.20), residues: 1773 helix: 1.36 (0.15), residues: 1100 sheet: -1.49 (0.66), residues: 54 loop : -0.16 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 168 HIS 0.003 0.001 HIS B 803 PHE 0.013 0.001 PHE D 410 TYR 0.017 0.001 TYR C 543 ARG 0.006 0.000 ARG D 413 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 173 time to evaluate : 1.826 Fit side-chains TARDY: cannot create tardy model for: "VAL C 156 " (corrupted residue). Skipping it. REVERT: A 234 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8189 (tm) REVERT: A 286 GLN cc_start: 0.7186 (OUTLIER) cc_final: 0.6862 (mp10) REVERT: A 415 ASP cc_start: 0.7612 (m-30) cc_final: 0.7345 (m-30) REVERT: A 433 ARG cc_start: 0.7800 (ttp80) cc_final: 0.7527 (mtm180) REVERT: A 579 ASP cc_start: 0.7145 (OUTLIER) cc_final: 0.6931 (p0) REVERT: A 580 ASP cc_start: 0.6456 (m-30) cc_final: 0.6173 (m-30) REVERT: B 651 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7722 (mm) REVERT: B 665 MET cc_start: 0.7557 (OUTLIER) cc_final: 0.6921 (mmm) REVERT: B 694 MET cc_start: 0.7788 (mmm) cc_final: 0.7545 (tpp) REVERT: B 851 ASP cc_start: 0.7693 (OUTLIER) cc_final: 0.7488 (p0) REVERT: B 998 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6671 (pt0) REVERT: B 1078 LYS cc_start: 0.6080 (tttt) cc_final: 0.5669 (pptt) REVERT: C 430 MET cc_start: 0.7633 (tpp) cc_final: 0.7421 (tpp) REVERT: C 496 GLN cc_start: 0.6141 (OUTLIER) cc_final: 0.5873 (tp-100) REVERT: D 451 LYS cc_start: 0.7035 (mmtt) cc_final: 0.6692 (mmmt) REVERT: D 580 ASP cc_start: 0.6348 (m-30) cc_final: 0.5801 (t0) outliers start: 36 outliers final: 9 residues processed: 192 average time/residue: 1.2732 time to fit residues: 271.9920 Evaluate side-chains 179 residues out of total 1605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 162 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 851 ASP Chi-restraints excluded: chain B residue 998 GLU Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 496 GLN Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 473 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 chunk 128 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 154 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN B 653 ASN B 805 ASN B 864 ASN B 939 GLN B1003 GLN C 226 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15099 Z= 0.244 Angle : 0.504 7.994 20478 Z= 0.261 Chirality : 0.039 0.166 2282 Planarity : 0.004 0.055 2521 Dihedral : 4.278 35.024 2049 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.87 % Allowed : 13.30 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.20), residues: 1773 helix: 1.31 (0.15), residues: 1102 sheet: -1.44 (0.65), residues: 52 loop : -0.17 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 442 HIS 0.005 0.001 HIS B 803 PHE 0.017 0.001 PHE D 298 TYR 0.023 0.002 TYR C 543 ARG 0.003 0.000 ARG D 424 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 173 time to evaluate : 1.716 Fit side-chains TARDY: cannot create tardy model for: "VAL C 156 " (corrupted residue). Skipping it. REVERT: A 234 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8208 (tm) REVERT: A 286 GLN cc_start: 0.7200 (OUTLIER) cc_final: 0.6917 (mp10) REVERT: A 415 ASP cc_start: 0.7656 (m-30) cc_final: 0.7399 (m-30) REVERT: A 423 PHE cc_start: 0.7491 (t80) cc_final: 0.7189 (t80) REVERT: B 651 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7716 (mm) REVERT: B 665 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.7046 (mmm) REVERT: B 851 ASP cc_start: 0.7672 (OUTLIER) cc_final: 0.7457 (p0) REVERT: B 947 ASP cc_start: 0.6695 (OUTLIER) cc_final: 0.5990 (m-30) REVERT: B 994 GLU cc_start: 0.6979 (tt0) cc_final: 0.6511 (pt0) REVERT: B 998 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6702 (pt0) REVERT: B 1078 LYS cc_start: 0.6177 (tttt) cc_final: 0.5723 (pptt) REVERT: C 411 GLN cc_start: 0.8052 (mm-40) cc_final: 0.7584 (tp-100) REVERT: C 496 GLN cc_start: 0.6081 (OUTLIER) cc_final: 0.5776 (tp-100) REVERT: D 426 VAL cc_start: -0.1095 (OUTLIER) cc_final: -0.1299 (t) REVERT: D 451 LYS cc_start: 0.7070 (mmtt) cc_final: 0.6655 (mmmt) REVERT: D 580 ASP cc_start: 0.6496 (m-30) cc_final: 0.5968 (t0) outliers start: 46 outliers final: 10 residues processed: 198 average time/residue: 1.1259 time to fit residues: 248.7765 Evaluate side-chains 186 residues out of total 1605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 167 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 851 ASP Chi-restraints excluded: chain B residue 947 ASP Chi-restraints excluded: chain B residue 998 GLU Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 496 GLN Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 473 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 142 optimal weight: 0.9980 chunk 79 optimal weight: 0.0020 chunk 14 optimal weight: 0.9980 chunk 56 optimal weight: 0.2980 chunk 90 optimal weight: 0.9980 chunk 166 optimal weight: 10.0000 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN B 653 ASN B1003 GLN C 226 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15099 Z= 0.144 Angle : 0.466 10.461 20478 Z= 0.238 Chirality : 0.038 0.257 2282 Planarity : 0.003 0.051 2521 Dihedral : 4.092 34.004 2049 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.25 % Allowed : 14.42 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.20), residues: 1773 helix: 1.43 (0.15), residues: 1102 sheet: -1.41 (0.66), residues: 52 loop : -0.08 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 442 HIS 0.003 0.001 HIS B 803 PHE 0.011 0.001 PHE B 870 TYR 0.022 0.001 TYR C 543 ARG 0.004 0.000 ARG D 407 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 173 time to evaluate : 1.742 Fit side-chains TARDY: cannot create tardy model for: "VAL C 156 " (corrupted residue). Skipping it. REVERT: A 234 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8194 (tm) REVERT: A 286 GLN cc_start: 0.7121 (OUTLIER) cc_final: 0.6840 (mp10) REVERT: A 415 ASP cc_start: 0.7632 (m-30) cc_final: 0.7374 (m-30) REVERT: B 665 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.6958 (mmm) REVERT: B 974 MET cc_start: 0.7115 (ppp) cc_final: 0.6854 (pp-130) REVERT: B 994 GLU cc_start: 0.6921 (tt0) cc_final: 0.6485 (pt0) REVERT: B 998 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6698 (pt0) REVERT: B 1078 LYS cc_start: 0.6133 (tttt) cc_final: 0.5705 (pptt) REVERT: D 426 VAL cc_start: -0.1188 (OUTLIER) cc_final: -0.1418 (t) REVERT: D 580 ASP cc_start: 0.6397 (m-30) cc_final: 0.5844 (t0) outliers start: 36 outliers final: 14 residues processed: 197 average time/residue: 1.1665 time to fit residues: 256.1820 Evaluate side-chains 180 residues out of total 1605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 161 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 934 SER Chi-restraints excluded: chain B residue 980 SER Chi-restraints excluded: chain B residue 998 GLU Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 403 MET Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 564 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 171 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN B1003 GLN C 226 GLN C 411 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15099 Z= 0.243 Angle : 0.509 9.400 20478 Z= 0.262 Chirality : 0.039 0.233 2282 Planarity : 0.004 0.054 2521 Dihedral : 4.224 32.345 2049 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.81 % Allowed : 14.23 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.20), residues: 1773 helix: 1.39 (0.15), residues: 1100 sheet: -1.36 (0.62), residues: 58 loop : -0.06 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 442 HIS 0.006 0.001 HIS B 803 PHE 0.016 0.001 PHE D 298 TYR 0.022 0.001 TYR C 543 ARG 0.002 0.000 ARG D 424 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 168 time to evaluate : 1.957 Fit side-chains TARDY: cannot create tardy model for: "VAL C 156 " (corrupted residue). Skipping it. REVERT: A 234 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8208 (tm) REVERT: A 286 GLN cc_start: 0.7134 (OUTLIER) cc_final: 0.6885 (mp10) REVERT: A 415 ASP cc_start: 0.7662 (m-30) cc_final: 0.7413 (m-30) REVERT: A 423 PHE cc_start: 0.7510 (t80) cc_final: 0.7198 (t80) REVERT: B 665 MET cc_start: 0.7677 (OUTLIER) cc_final: 0.7108 (mmm) REVERT: B 947 ASP cc_start: 0.6657 (OUTLIER) cc_final: 0.6029 (m-30) REVERT: B 974 MET cc_start: 0.7088 (ppp) cc_final: 0.6724 (pp-130) REVERT: B 994 GLU cc_start: 0.7027 (tt0) cc_final: 0.6590 (pt0) REVERT: B 998 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6720 (pt0) REVERT: B 1078 LYS cc_start: 0.6148 (tttt) cc_final: 0.5724 (pptt) REVERT: C 499 VAL cc_start: 0.7003 (OUTLIER) cc_final: 0.6767 (t) REVERT: D 426 VAL cc_start: -0.0984 (OUTLIER) cc_final: -0.1198 (t) REVERT: D 451 LYS cc_start: 0.7086 (mmtt) cc_final: 0.6663 (mmmt) REVERT: D 580 ASP cc_start: 0.6533 (m-30) cc_final: 0.5990 (t0) outliers start: 45 outliers final: 15 residues processed: 196 average time/residue: 1.1912 time to fit residues: 260.7171 Evaluate side-chains 187 residues out of total 1605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 165 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 934 SER Chi-restraints excluded: chain B residue 947 ASP Chi-restraints excluded: chain B residue 980 SER Chi-restraints excluded: chain B residue 998 GLU Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 403 MET Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 564 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 0.0370 chunk 102 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 164 optimal weight: 10.0000 overall best weight: 0.7658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN B1003 GLN C 226 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15099 Z= 0.155 Angle : 0.479 9.314 20478 Z= 0.244 Chirality : 0.038 0.253 2282 Planarity : 0.003 0.051 2521 Dihedral : 4.090 31.323 2049 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.94 % Allowed : 15.54 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.20), residues: 1773 helix: 1.45 (0.15), residues: 1102 sheet: -1.47 (0.66), residues: 52 loop : -0.08 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 442 HIS 0.004 0.001 HIS B 803 PHE 0.012 0.001 PHE B 870 TYR 0.022 0.001 TYR C 543 ARG 0.003 0.000 ARG D 407 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 162 time to evaluate : 1.785 Fit side-chains TARDY: cannot create tardy model for: "VAL C 156 " (corrupted residue). Skipping it. REVERT: A 234 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8209 (tm) REVERT: A 286 GLN cc_start: 0.7048 (OUTLIER) cc_final: 0.6782 (mp10) REVERT: A 415 ASP cc_start: 0.7641 (m-30) cc_final: 0.7388 (m-30) REVERT: B 665 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.6978 (mmm) REVERT: B 1078 LYS cc_start: 0.6101 (tttt) cc_final: 0.5684 (pptt) REVERT: D 426 VAL cc_start: -0.1165 (OUTLIER) cc_final: -0.1410 (t) REVERT: D 451 LYS cc_start: 0.7058 (mmtt) cc_final: 0.6646 (mmmt) REVERT: D 580 ASP cc_start: 0.6441 (OUTLIER) cc_final: 0.5894 (t0) outliers start: 31 outliers final: 15 residues processed: 181 average time/residue: 1.1019 time to fit residues: 223.7048 Evaluate side-chains 178 residues out of total 1605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 158 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 980 SER Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 403 MET Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 564 ASN Chi-restraints excluded: chain D residue 580 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 4.9990 chunk 159 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 96 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 125 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 169 optimal weight: 5.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 496 GLN B1003 GLN ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15099 Z= 0.242 Angle : 0.526 10.142 20478 Z= 0.269 Chirality : 0.040 0.238 2282 Planarity : 0.004 0.054 2521 Dihedral : 4.226 29.788 2049 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.00 % Allowed : 15.67 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.20), residues: 1773 helix: 1.36 (0.15), residues: 1096 sheet: -1.25 (0.63), residues: 56 loop : -0.11 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 442 HIS 0.005 0.001 HIS B 803 PHE 0.016 0.001 PHE D 298 TYR 0.022 0.001 TYR C 543 ARG 0.002 0.000 ARG D 424 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 168 time to evaluate : 1.821 Fit side-chains revert: symmetry clash REVERT: A 234 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8225 (tm) REVERT: A 286 GLN cc_start: 0.7071 (OUTLIER) cc_final: 0.6810 (mp10) REVERT: A 415 ASP cc_start: 0.7667 (m-30) cc_final: 0.7410 (m-30) REVERT: A 423 PHE cc_start: 0.7525 (t80) cc_final: 0.7231 (t80) REVERT: B 665 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.7116 (mmm) REVERT: B 947 ASP cc_start: 0.6641 (OUTLIER) cc_final: 0.5916 (m-30) REVERT: D 426 VAL cc_start: -0.1086 (OUTLIER) cc_final: -0.1322 (t) REVERT: D 451 LYS cc_start: 0.7121 (mmtt) cc_final: 0.6702 (mmmt) REVERT: D 580 ASP cc_start: 0.6666 (OUTLIER) cc_final: 0.6128 (t0) outliers start: 32 outliers final: 13 residues processed: 186 average time/residue: 1.0572 time to fit residues: 220.4760 Evaluate side-chains 182 residues out of total 1605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 163 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 947 ASP Chi-restraints excluded: chain B residue 980 SER Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 564 ASN Chi-restraints excluded: chain D residue 580 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 chunk 177 optimal weight: 0.6980 chunk 163 optimal weight: 0.9980 chunk 141 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 112 optimal weight: 0.6980 chunk 150 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 496 GLN B1003 GLN C 226 GLN D 226 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15099 Z= 0.153 Angle : 0.497 9.692 20478 Z= 0.251 Chirality : 0.038 0.219 2282 Planarity : 0.003 0.051 2521 Dihedral : 4.062 28.860 2049 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.69 % Allowed : 16.17 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.20), residues: 1773 helix: 1.46 (0.16), residues: 1095 sheet: -1.12 (0.64), residues: 56 loop : -0.08 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 442 HIS 0.004 0.001 HIS B 803 PHE 0.012 0.001 PHE B 870 TYR 0.021 0.001 TYR C 543 ARG 0.021 0.000 ARG D 413 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 163 time to evaluate : 1.851 Fit side-chains TARDY: cannot create tardy model for: "VAL C 156 " (corrupted residue). Skipping it. REVERT: A 234 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8209 (tm) REVERT: A 415 ASP cc_start: 0.7639 (m-30) cc_final: 0.7395 (m-30) REVERT: B 665 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.6972 (mmm) REVERT: D 426 VAL cc_start: -0.1177 (OUTLIER) cc_final: -0.1405 (t) REVERT: D 451 LYS cc_start: 0.7120 (mmtt) cc_final: 0.6689 (mmmt) REVERT: D 580 ASP cc_start: 0.6583 (OUTLIER) cc_final: 0.6029 (t0) outliers start: 27 outliers final: 15 residues processed: 183 average time/residue: 1.1408 time to fit residues: 234.2167 Evaluate side-chains 177 residues out of total 1605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 158 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 934 SER Chi-restraints excluded: chain B residue 980 SER Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 564 ASN Chi-restraints excluded: chain D residue 580 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 141 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 17 optimal weight: 0.0060 chunk 26 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 496 GLN B1003 GLN ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 GLN D 226 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.157548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.119653 restraints weight = 17448.950| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.97 r_work: 0.2978 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15099 Z= 0.184 Angle : 0.506 10.308 20478 Z= 0.256 Chirality : 0.039 0.220 2282 Planarity : 0.003 0.052 2521 Dihedral : 4.082 26.976 2049 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.50 % Allowed : 16.42 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.20), residues: 1773 helix: 1.44 (0.15), residues: 1094 sheet: -1.17 (0.63), residues: 56 loop : -0.08 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 442 HIS 0.005 0.001 HIS B 803 PHE 0.013 0.001 PHE B 870 TYR 0.022 0.001 TYR A 543 ARG 0.002 0.000 ARG A 220 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4857.93 seconds wall clock time: 87 minutes 48.94 seconds (5268.94 seconds total)