Starting phenix.real_space_refine on Thu Feb 15 06:10:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kcm_22816/02_2024/7kcm_22816_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kcm_22816/02_2024/7kcm_22816.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kcm_22816/02_2024/7kcm_22816.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kcm_22816/02_2024/7kcm_22816.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kcm_22816/02_2024/7kcm_22816_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kcm_22816/02_2024/7kcm_22816_updated.pdb" } resolution = 3.43 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 522 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians K 2 8.98 5 Fe 2 7.16 5 P 6 5.49 5 Mg 2 5.21 5 S 55 5.16 5 C 6845 2.51 5 N 1883 2.21 5 O 2043 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 79": "OE1" <-> "OE2" Residue "A GLU 108": "OE1" <-> "OE2" Residue "A GLU 115": "OE1" <-> "OE2" Residue "A GLU 125": "OE1" <-> "OE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A ASP 213": "OD1" <-> "OD2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A ARG 291": "NH1" <-> "NH2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A ASP 323": "OD1" <-> "OD2" Residue "A TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A ASP 392": "OD1" <-> "OD2" Residue "A GLU 394": "OE1" <-> "OE2" Residue "A ARG 402": "NH1" <-> "NH2" Residue "A GLU 442": "OE1" <-> "OE2" Residue "A TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 449": "NH1" <-> "NH2" Residue "A ASP 463": "OD1" <-> "OD2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 523": "OE1" <-> "OE2" Residue "A GLU 529": "OE1" <-> "OE2" Residue "A PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 533": "OE1" <-> "OE2" Residue "A GLU 578": "OE1" <-> "OE2" Residue "A GLU 581": "OE1" <-> "OE2" Residue "A ARG 658": "NH1" <-> "NH2" Residue "A GLU 674": "OE1" <-> "OE2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B GLU 115": "OE1" <-> "OE2" Residue "B GLU 125": "OE1" <-> "OE2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B ASP 158": "OD1" <-> "OD2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 291": "NH1" <-> "NH2" Residue "B ASP 305": "OD1" <-> "OD2" Residue "B GLU 312": "OE1" <-> "OE2" Residue "B TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B GLU 403": "OE1" <-> "OE2" Residue "B ASP 416": "OD1" <-> "OD2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B ARG 449": "NH1" <-> "NH2" Residue "B GLU 523": "OE1" <-> "OE2" Residue "B GLU 541": "OE1" <-> "OE2" Residue "B ASP 557": "OD1" <-> "OD2" Residue "B ASP 604": "OD1" <-> "OD2" Residue "B GLU 632": "OE1" <-> "OE2" Residue "B GLU 633": "OE1" <-> "OE2" Residue "B ARG 634": "NH1" <-> "NH2" Residue "B GLU 643": "OE1" <-> "OE2" Residue "B ARG 658": "NH1" <-> "NH2" Residue "B GLU 695": "OE1" <-> "OE2" Residue "C ASP 48": "OD1" <-> "OD2" Residue "C ASP 50": "OD1" <-> "OD2" Residue "C ASP 54": "OD1" <-> "OD2" Residue "C TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 154": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10838 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4890 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 18, 'TRANS': 593} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 4915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4915 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 18, 'TRANS': 595} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 963 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 113} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10324 SG CYS C 101 61.372 22.904 42.313 1.00137.29 S ATOM 10403 SG CYS C 113 61.826 21.691 38.704 1.00144.04 S ATOM 10270 SG CYS C 93 58.230 17.757 41.308 1.00147.05 S ATOM 10308 SG CYS C 98 57.052 20.959 43.032 1.00140.48 S Time building chain proxies: 6.31, per 1000 atoms: 0.58 Number of scatterers: 10838 At special positions: 0 Unit cell: (96.866, 91.982, 130.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Fe 2 26.01 K 2 19.00 S 55 16.00 P 6 15.00 Mg 2 11.99 O 2043 8.00 N 1883 7.00 C 6845 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: 4.63 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES C 201 " pdb="FE2 FES C 201 " - pdb=" SG CYS C 98 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 113 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 101 " pdb="FE2 FES C 201 " - pdb=" SG CYS C 93 " Number of angles added : 6 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2568 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 10 sheets defined 38.8% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.54 Creating SS restraints... Processing helix chain 'A' and resid 94 through 103 Processing helix chain 'A' and resid 109 through 134 removed outlier: 4.255A pdb=" N PHE A 112 " --> pdb=" O LYS A 109 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE A 113 " --> pdb=" O GLU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 171 Processing helix chain 'A' and resid 179 through 186 Processing helix chain 'A' and resid 205 through 210 Processing helix chain 'A' and resid 262 through 265 Processing helix chain 'A' and resid 267 through 277 Processing helix chain 'A' and resid 308 through 318 Processing helix chain 'A' and resid 383 through 385 No H-bonds generated for 'chain 'A' and resid 383 through 385' Processing helix chain 'A' and resid 409 through 432 Processing helix chain 'A' and resid 434 through 454 removed outlier: 6.712A pdb=" N LEU A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N PHE A 447 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET A 448 " --> pdb=" O TYR A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 467 removed outlier: 4.015A pdb=" N LEU A 467 " --> pdb=" O ASP A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 489 removed outlier: 3.579A pdb=" N ARG A 489 " --> pdb=" O GLU A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 512 through 519 removed outlier: 4.334A pdb=" N LYS A 519 " --> pdb=" O GLU A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 550 through 556 Processing helix chain 'A' and resid 576 through 589 Processing helix chain 'A' and resid 615 through 627 Processing helix chain 'A' and resid 649 through 657 removed outlier: 3.743A pdb=" N LEU A 654 " --> pdb=" O LEU A 650 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASN A 655 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLN A 656 " --> pdb=" O LYS A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 680 Processing helix chain 'A' and resid 687 through 699 removed outlier: 4.450A pdb=" N GLY A 691 " --> pdb=" O ARG A 687 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 109 through 133 removed outlier: 4.176A pdb=" N PHE B 112 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE B 113 " --> pdb=" O GLU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 171 Processing helix chain 'B' and resid 179 through 185 Processing helix chain 'B' and resid 205 through 210 Processing helix chain 'B' and resid 262 through 265 Processing helix chain 'B' and resid 267 through 277 Processing helix chain 'B' and resid 303 through 305 No H-bonds generated for 'chain 'B' and resid 303 through 305' Processing helix chain 'B' and resid 308 through 319 Processing helix chain 'B' and resid 382 through 386 removed outlier: 4.344A pdb=" N PHE B 386 " --> pdb=" O TRP B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 432 Processing helix chain 'B' and resid 435 through 454 removed outlier: 6.858A pdb=" N LEU B 446 " --> pdb=" O GLU B 442 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHE B 447 " --> pdb=" O ASP B 443 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N MET B 448 " --> pdb=" O TYR B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 467 removed outlier: 4.080A pdb=" N LEU B 467 " --> pdb=" O ASP B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 489 Processing helix chain 'B' and resid 505 through 509 Processing helix chain 'B' and resid 512 through 519 removed outlier: 4.486A pdb=" N LYS B 519 " --> pdb=" O GLU B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 539 Processing helix chain 'B' and resid 550 through 556 Processing helix chain 'B' and resid 576 through 589 Processing helix chain 'B' and resid 615 through 622 removed outlier: 3.584A pdb=" N HIS B 620 " --> pdb=" O GLY B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 638 Processing helix chain 'B' and resid 649 through 660 removed outlier: 3.721A pdb=" N GLN B 656 " --> pdb=" O LYS B 652 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ALA B 659 " --> pdb=" O ASN B 655 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER B 660 " --> pdb=" O GLN B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 679 Processing helix chain 'B' and resid 688 through 703 removed outlier: 4.488A pdb=" N ARG B 692 " --> pdb=" O ALA B 688 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLU B 702 " --> pdb=" O VAL B 698 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ARG B 703 " --> pdb=" O LYS B 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 67 No H-bonds generated for 'chain 'C' and resid 65 through 67' Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 135 through 139 Processing helix chain 'C' and resid 146 through 151 Processing sheet with id= A, first strand: chain 'A' and resid 284 through 287 removed outlier: 4.233A pdb=" N ARG A 214 " --> pdb=" O HIS A 256 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 387 through 390 removed outlier: 3.840A pdb=" N TYR A 327 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 546 through 549 removed outlier: 3.567A pdb=" N TYR A 499 " --> pdb=" O ILE A 548 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 596 through 599 Processing sheet with id= E, first strand: chain 'B' and resid 284 through 287 removed outlier: 4.005A pdb=" N ARG B 214 " --> pdb=" O HIS B 256 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 363 through 366 removed outlier: 7.536A pdb=" N ALA B 364 " --> pdb=" O ILE B 387 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLY B 389 " --> pdb=" O ALA B 364 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N TYR B 366 " --> pdb=" O GLY B 389 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL B 391 " --> pdb=" O TYR B 366 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR B 327 " --> pdb=" O VAL B 345 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 546 through 549 removed outlier: 3.515A pdb=" N TYR B 499 " --> pdb=" O ILE B 548 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 597 through 599 removed outlier: 7.035A pdb=" N LEU B 642 " --> pdb=" O LYS B 598 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR B 641 " --> pdb=" O THR B 611 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 57 through 64 removed outlier: 4.306A pdb=" N HIS C 57 " --> pdb=" O ARG C 46 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ARG C 46 " --> pdb=" O HIS C 57 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN C 59 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER C 125 " --> pdb=" O ALA C 43 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N TYR C 45 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N ILE C 127 " --> pdb=" O TYR C 45 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 102 through 105 422 hydrogen bonds defined for protein. 1080 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: 3.01 Time building geometry restraints manager: 4.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.42: 4537 1.42 - 1.62: 6393 1.62 - 1.81: 96 1.81 - 2.01: 1 2.01 - 2.20: 4 Bond restraints: 11031 Sorted by residual: bond pdb=" O3A ANP A 801 " pdb=" PB ANP A 801 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" O3A ANP B 801 " pdb=" PB ANP B 801 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.11e+01 bond pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 1.795 1.691 0.104 2.00e-02 2.50e+03 2.73e+01 bond pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 1.795 1.691 0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" O5' ANP A 801 " pdb=" PA ANP A 801 " ideal model delta sigma weight residual 1.655 1.579 0.076 2.00e-02 2.50e+03 1.44e+01 ... (remaining 11026 not shown) Histogram of bond angle deviations from ideal: 75.05 - 86.85: 2 86.85 - 98.64: 1 98.64 - 110.44: 2633 110.44 - 122.23: 10461 122.23 - 134.03: 1789 Bond angle restraints: 14886 Sorted by residual: angle pdb=" PB ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 126.95 110.12 16.83 3.00e+00 1.11e-01 3.15e+01 angle pdb=" PB ANP B 801 " pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 126.95 110.27 16.68 3.00e+00 1.11e-01 3.09e+01 angle pdb=" O1B ANP B 801 " pdb=" PB ANP B 801 " pdb=" O2B ANP B 801 " ideal model delta sigma weight residual 120.08 108.91 11.17 3.00e+00 1.11e-01 1.39e+01 angle pdb=" O1B ANP A 801 " pdb=" PB ANP A 801 " pdb=" O2B ANP A 801 " ideal model delta sigma weight residual 120.08 108.95 11.13 3.00e+00 1.11e-01 1.38e+01 angle pdb=" CA ARG C 94 " pdb=" CB ARG C 94 " pdb=" CG ARG C 94 " ideal model delta sigma weight residual 114.10 120.88 -6.78 2.00e+00 2.50e-01 1.15e+01 ... (remaining 14881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 6005 17.88 - 35.75: 612 35.75 - 53.62: 126 53.62 - 71.50: 35 71.50 - 89.37: 16 Dihedral angle restraints: 6794 sinusoidal: 2839 harmonic: 3955 Sorted by residual: dihedral pdb=" CA LEU C 130 " pdb=" C LEU C 130 " pdb=" N PRO C 131 " pdb=" CA PRO C 131 " ideal model delta harmonic sigma weight residual -180.00 -156.16 -23.84 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA TYR B 277 " pdb=" C TYR B 277 " pdb=" N SER B 278 " pdb=" CA SER B 278 " ideal model delta harmonic sigma weight residual -180.00 -162.36 -17.64 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA ASP B 158 " pdb=" CB ASP B 158 " pdb=" CG ASP B 158 " pdb=" OD1 ASP B 158 " ideal model delta sinusoidal sigma weight residual -30.00 -88.78 58.78 1 2.00e+01 2.50e-03 1.16e+01 ... (remaining 6791 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1432 0.055 - 0.109: 207 0.109 - 0.164: 32 0.164 - 0.219: 1 0.219 - 0.273: 2 Chirality restraints: 1674 Sorted by residual: chirality pdb=" C3' ANP B 801 " pdb=" C2' ANP B 801 " pdb=" C4' ANP B 801 " pdb=" O3' ANP B 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C3' ANP A 801 " pdb=" C2' ANP A 801 " pdb=" C4' ANP A 801 " pdb=" O3' ANP A 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA GLU C 154 " pdb=" N GLU C 154 " pdb=" C GLU C 154 " pdb=" CB GLU C 154 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.81e-01 ... (remaining 1671 not shown) Planarity restraints: 1889 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 661 " 0.068 5.00e-02 4.00e+02 1.03e-01 1.69e+01 pdb=" N PRO A 662 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO A 662 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 662 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 585 " -0.012 2.00e-02 2.50e+03 1.20e-02 3.62e+00 pdb=" CG TRP B 585 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP B 585 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP B 585 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 585 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 585 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 585 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 585 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 585 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 585 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 585 " 0.011 2.00e-02 2.50e+03 9.12e-03 2.08e+00 pdb=" CG TRP A 585 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP A 585 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP A 585 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 585 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 585 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 585 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 585 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 585 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 585 " 0.002 2.00e-02 2.50e+03 ... (remaining 1886 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.62: 154 2.62 - 3.25: 10957 3.25 - 3.88: 22221 3.88 - 4.51: 29487 4.51 - 5.14: 46205 Nonbonded interactions: 109024 Sorted by model distance: nonbonded pdb=" O3G ANP A 801 " pdb="MG MG A 802 " model vdw 1.994 2.170 nonbonded pdb=" OD1 ASN A 119 " pdb="MG MG A 802 " model vdw 2.010 2.170 nonbonded pdb=" O3G ANP B 801 " pdb="MG MG B 802 " model vdw 2.042 2.170 nonbonded pdb=" OD1 ASN B 119 " pdb="MG MG B 802 " model vdw 2.048 2.170 nonbonded pdb=" O1B ANP B 801 " pdb="MG MG B 802 " model vdw 2.068 2.170 ... (remaining 109019 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 70 through 355 or resid 361 through 626 or resid 631 throu \ gh 704 or resid 801 through 803)) selection = (chain 'B' and (resid 70 through 355 or resid 361 through 625 or resid 631 or re \ sid 636 through 704 or resid 801 through 803)) } 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: 2.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 7.710 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 35.120 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.050 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 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 0.144 11031 Z= 0.274 Angle : 0.643 16.828 14886 Z= 0.322 Chirality : 0.041 0.273 1674 Planarity : 0.003 0.103 1889 Dihedral : 15.796 89.374 4226 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: 0.75 (0.25), residues: 1329 helix: 1.26 (0.24), residues: 543 sheet: 1.47 (0.40), residues: 200 loop : -0.55 (0.28), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 585 HIS 0.007 0.001 HIS A 311 PHE 0.012 0.001 PHE A 112 TYR 0.014 0.001 TYR C 150 ARG 0.006 0.000 ARG B 540 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.275 Fit side-chains revert: symmetry clash REVERT: A 586 MET cc_start: 0.8787 (mpp) cc_final: 0.7777 (mpp) REVERT: B 292 MET cc_start: 0.7199 (ppp) cc_final: 0.6933 (ppp) REVERT: B 517 MET cc_start: 0.6882 (tmm) cc_final: 0.6580 (tmm) REVERT: B 576 GLU cc_start: 0.7480 (tp30) cc_final: 0.7231 (tp30) REVERT: C 44 ILE cc_start: 0.8049 (mt) cc_final: 0.7838 (mm) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.2406 time to fit residues: 48.5670 Evaluate side-chains 112 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 78 optimal weight: 8.9990 chunk 121 optimal weight: 7.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN A 506 HIS ** A 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 704 HIS ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 GLN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 HIS ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 11031 Z= 0.540 Angle : 0.698 8.973 14886 Z= 0.361 Chirality : 0.047 0.175 1674 Planarity : 0.005 0.072 1889 Dihedral : 6.132 56.292 1540 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.02 % Allowed : 11.29 % Favored : 87.69 % 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: -0.07 (0.23), residues: 1329 helix: 0.44 (0.22), residues: 547 sheet: 0.87 (0.39), residues: 198 loop : -0.78 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 585 HIS 0.013 0.002 HIS B 620 PHE 0.024 0.002 PHE C 146 TYR 0.018 0.002 TYR A 315 ARG 0.005 0.001 ARG B 421 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 116 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 583 MET cc_start: 0.7826 (mtm) cc_final: 0.7520 (mtm) REVERT: A 586 MET cc_start: 0.8911 (mpp) cc_final: 0.8510 (mpp) REVERT: C 47 TRP cc_start: 0.7195 (t60) cc_final: 0.6470 (t60) REVERT: C 58 MET cc_start: 0.6098 (mmm) cc_final: 0.5626 (mmm) outliers start: 12 outliers final: 8 residues processed: 124 average time/residue: 0.2409 time to fit residues: 43.0993 Evaluate side-chains 110 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 102 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 672 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 chunk 108 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 GLN A 620 HIS ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 GLN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11031 Z= 0.186 Angle : 0.510 7.220 14886 Z= 0.265 Chirality : 0.040 0.152 1674 Planarity : 0.004 0.059 1889 Dihedral : 5.660 59.348 1540 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.36 % Allowed : 12.56 % Favored : 86.08 % 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: -0.10 (0.23), residues: 1329 helix: 0.47 (0.22), residues: 552 sheet: 0.70 (0.39), residues: 193 loop : -0.77 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 585 HIS 0.005 0.001 HIS B 620 PHE 0.010 0.001 PHE C 146 TYR 0.014 0.001 TYR A 206 ARG 0.007 0.000 ARG B 692 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 122 time to evaluate : 1.391 Fit side-chains revert: symmetry clash REVERT: A 583 MET cc_start: 0.7842 (mtm) cc_final: 0.7512 (mtm) REVERT: A 586 MET cc_start: 0.8839 (mpp) cc_final: 0.8447 (mpp) REVERT: B 586 MET cc_start: 0.8378 (mtm) cc_final: 0.8106 (mtt) REVERT: C 47 TRP cc_start: 0.7224 (t60) cc_final: 0.6399 (t60) REVERT: C 72 VAL cc_start: 0.5762 (t) cc_final: 0.5533 (t) outliers start: 16 outliers final: 9 residues processed: 134 average time/residue: 0.2684 time to fit residues: 50.2220 Evaluate side-chains 123 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 114 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 481 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 122 optimal weight: 20.0000 chunk 129 optimal weight: 8.9990 chunk 115 optimal weight: 0.4980 chunk 34 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 HIS ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 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 0.038 11031 Z= 0.250 Angle : 0.528 9.826 14886 Z= 0.271 Chirality : 0.041 0.156 1674 Planarity : 0.004 0.052 1889 Dihedral : 5.611 59.433 1540 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.46 % Allowed : 13.75 % Favored : 83.79 % 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: -0.17 (0.24), residues: 1329 helix: 0.36 (0.22), residues: 559 sheet: 0.65 (0.39), residues: 194 loop : -0.77 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 585 HIS 0.006 0.001 HIS B 620 PHE 0.009 0.001 PHE C 146 TYR 0.018 0.002 TYR A 315 ARG 0.005 0.000 ARG B 692 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 114 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 462 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7142 (mp0) REVERT: A 586 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8449 (mpp) REVERT: B 583 MET cc_start: 0.7579 (mmm) cc_final: 0.7305 (mmm) REVERT: B 586 MET cc_start: 0.8387 (mtm) cc_final: 0.8141 (mtt) REVERT: C 47 TRP cc_start: 0.7194 (t60) cc_final: 0.6432 (t60) REVERT: C 72 VAL cc_start: 0.5835 (t) cc_final: 0.5582 (t) outliers start: 29 outliers final: 19 residues processed: 135 average time/residue: 0.2441 time to fit residues: 47.1788 Evaluate side-chains 131 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 110 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain C residue 146 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 0.0000 chunk 1 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 0.6980 chunk 116 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 43 optimal weight: 6.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11031 Z= 0.143 Angle : 0.482 9.757 14886 Z= 0.248 Chirality : 0.040 0.161 1674 Planarity : 0.003 0.048 1889 Dihedral : 5.271 56.497 1540 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.95 % Allowed : 15.53 % Favored : 82.51 % 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 (0.24), residues: 1329 helix: 0.56 (0.22), residues: 549 sheet: 0.71 (0.40), residues: 195 loop : -0.77 (0.27), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 585 HIS 0.004 0.001 HIS A 311 PHE 0.007 0.001 PHE C 146 TYR 0.013 0.001 TYR A 315 ARG 0.007 0.000 ARG B 692 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 119 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 462 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7150 (mp0) REVERT: A 586 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8458 (mpp) REVERT: B 98 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8983 (mm) REVERT: B 586 MET cc_start: 0.8393 (mtm) cc_final: 0.8153 (mtt) REVERT: C 47 TRP cc_start: 0.7210 (t60) cc_final: 0.6391 (t60) outliers start: 23 outliers final: 12 residues processed: 135 average time/residue: 0.2474 time to fit residues: 47.2762 Evaluate side-chains 129 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 114 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain C residue 146 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 76 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 129 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 124 optimal weight: 20.0000 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11031 Z= 0.318 Angle : 0.563 11.707 14886 Z= 0.286 Chirality : 0.042 0.161 1674 Planarity : 0.004 0.046 1889 Dihedral : 5.491 53.443 1540 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.63 % Allowed : 16.13 % Favored : 81.24 % 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: -0.16 (0.24), residues: 1329 helix: 0.42 (0.22), residues: 557 sheet: 0.56 (0.39), residues: 195 loop : -0.77 (0.27), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 585 HIS 0.004 0.001 HIS A 330 PHE 0.012 0.001 PHE C 146 TYR 0.020 0.002 TYR A 315 ARG 0.008 0.000 ARG B 692 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 114 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.7498 (OUTLIER) cc_final: 0.7130 (ptm) REVERT: A 462 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7049 (mp0) REVERT: A 586 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8353 (mpp) REVERT: B 98 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.8976 (mm) REVERT: B 586 MET cc_start: 0.8411 (mtm) cc_final: 0.8165 (mtt) REVERT: C 47 TRP cc_start: 0.7261 (t60) cc_final: 0.6471 (t60) REVERT: C 58 MET cc_start: 0.6182 (mmm) cc_final: 0.5870 (mmm) outliers start: 31 outliers final: 21 residues processed: 138 average time/residue: 0.2328 time to fit residues: 45.8985 Evaluate side-chains 134 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 109 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain C residue 146 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 109 optimal weight: 9.9990 chunk 72 optimal weight: 0.6980 chunk 129 optimal weight: 8.9990 chunk 80 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 51 optimal weight: 8.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11031 Z= 0.273 Angle : 0.546 11.255 14886 Z= 0.278 Chirality : 0.041 0.161 1674 Planarity : 0.004 0.044 1889 Dihedral : 5.484 53.266 1540 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.38 % Allowed : 16.81 % Favored : 80.81 % 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: -0.21 (0.23), residues: 1329 helix: 0.46 (0.22), residues: 551 sheet: 0.44 (0.39), residues: 194 loop : -0.85 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 585 HIS 0.004 0.001 HIS A 330 PHE 0.011 0.001 PHE C 146 TYR 0.019 0.002 TYR A 315 ARG 0.007 0.000 ARG B 692 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 112 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.7537 (OUTLIER) cc_final: 0.7183 (ptm) REVERT: A 462 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7044 (mp0) REVERT: A 586 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8339 (mpp) REVERT: B 98 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8976 (mm) REVERT: B 586 MET cc_start: 0.8425 (mtm) cc_final: 0.8173 (mtt) REVERT: C 47 TRP cc_start: 0.7263 (t60) cc_final: 0.6507 (t60) REVERT: C 58 MET cc_start: 0.6207 (mmm) cc_final: 0.5931 (mmm) outliers start: 28 outliers final: 22 residues processed: 135 average time/residue: 0.2330 time to fit residues: 45.3148 Evaluate side-chains 134 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 108 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain C residue 146 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 112 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11031 Z= 0.171 Angle : 0.515 10.724 14886 Z= 0.262 Chirality : 0.040 0.189 1674 Planarity : 0.004 0.049 1889 Dihedral : 5.244 50.827 1540 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.21 % Allowed : 17.91 % Favored : 79.88 % 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: -0.11 (0.24), residues: 1329 helix: 0.55 (0.22), residues: 554 sheet: 0.49 (0.39), residues: 194 loop : -0.82 (0.27), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 585 HIS 0.004 0.001 HIS A 311 PHE 0.009 0.001 PHE C 146 TYR 0.016 0.001 TYR A 315 ARG 0.006 0.000 ARG B 692 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 117 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7086 (mp0) REVERT: A 582 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.7591 (tp) REVERT: A 586 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8371 (mpp) REVERT: B 98 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8961 (mm) REVERT: B 586 MET cc_start: 0.8391 (mtm) cc_final: 0.8151 (mtt) REVERT: B 668 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9040 (tt) REVERT: C 47 TRP cc_start: 0.7235 (t60) cc_final: 0.6488 (t60) REVERT: C 58 MET cc_start: 0.6187 (mmm) cc_final: 0.5915 (mmm) outliers start: 26 outliers final: 19 residues processed: 136 average time/residue: 0.2480 time to fit residues: 47.8253 Evaluate side-chains 136 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 112 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain C residue 146 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 94 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 119 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 704 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11031 Z= 0.269 Angle : 0.563 11.795 14886 Z= 0.283 Chirality : 0.041 0.192 1674 Planarity : 0.004 0.044 1889 Dihedral : 5.360 52.567 1540 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.38 % Allowed : 18.08 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.23), residues: 1329 helix: 0.43 (0.22), residues: 558 sheet: 0.42 (0.39), residues: 193 loop : -0.86 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 585 HIS 0.004 0.001 HIS A 330 PHE 0.011 0.001 PHE C 146 TYR 0.020 0.002 TYR A 315 ARG 0.008 0.000 ARG B 692 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 113 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.7182 (ptm) REVERT: A 462 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7037 (mp0) REVERT: A 582 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.7551 (tp) REVERT: A 586 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8365 (mpp) REVERT: B 98 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.8975 (mm) REVERT: B 586 MET cc_start: 0.8416 (mtm) cc_final: 0.8169 (mtt) REVERT: B 668 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9030 (tt) REVERT: C 47 TRP cc_start: 0.7212 (t60) cc_final: 0.6518 (t60) REVERT: C 58 MET cc_start: 0.6262 (mmm) cc_final: 0.6016 (mmm) outliers start: 28 outliers final: 20 residues processed: 135 average time/residue: 0.2306 time to fit residues: 45.1172 Evaluate side-chains 137 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 111 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain C residue 146 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 133 optimal weight: 8.9990 chunk 122 optimal weight: 20.0000 chunk 106 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 113 optimal weight: 6.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11031 Z= 0.259 Angle : 0.774 44.588 14886 Z= 0.442 Chirality : 0.041 0.196 1674 Planarity : 0.004 0.080 1889 Dihedral : 5.366 52.296 1540 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.63 % Allowed : 17.74 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.23), residues: 1329 helix: 0.42 (0.22), residues: 558 sheet: 0.38 (0.39), residues: 193 loop : -0.88 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 585 HIS 0.004 0.001 HIS A 330 PHE 0.042 0.001 PHE B 280 TYR 0.022 0.002 TYR A 315 ARG 0.009 0.000 ARG B 692 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 111 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.7176 (ptm) REVERT: A 462 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7036 (mp0) REVERT: A 582 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.7554 (tp) REVERT: A 586 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8357 (mpp) REVERT: B 98 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8973 (mm) REVERT: B 586 MET cc_start: 0.8414 (mtm) cc_final: 0.8161 (mtt) REVERT: B 668 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9030 (tt) REVERT: C 47 TRP cc_start: 0.7210 (t60) cc_final: 0.6523 (t60) REVERT: C 58 MET cc_start: 0.6194 (mmm) cc_final: 0.5944 (mmm) outliers start: 31 outliers final: 21 residues processed: 136 average time/residue: 0.2305 time to fit residues: 45.8002 Evaluate side-chains 137 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 110 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain C residue 146 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 0.6980 chunk 98 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 29 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 chunk 44 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 overall best weight: 1.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.111049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.087336 restraints weight = 20759.871| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.70 r_work: 0.2981 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11031 Z= 0.259 Angle : 0.555 12.012 14886 Z= 0.282 Chirality : 0.041 0.194 1674 Planarity : 0.004 0.041 1889 Dihedral : 5.387 52.104 1540 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.55 % Allowed : 18.25 % Favored : 79.20 % 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: -0.26 (0.23), residues: 1329 helix: 0.45 (0.22), residues: 555 sheet: 0.42 (0.39), residues: 193 loop : -0.92 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 585 HIS 0.004 0.001 HIS A 330 PHE 0.011 0.001 PHE C 146 TYR 0.020 0.002 TYR A 315 ARG 0.007 0.000 ARG B 692 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2319.92 seconds wall clock time: 43 minutes 16.74 seconds (2596.74 seconds total)