Starting phenix.real_space_refine on Fri Feb 16 19:59:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irn_35680/02_2024/8irn_35680_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irn_35680/02_2024/8irn_35680.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irn_35680/02_2024/8irn_35680.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irn_35680/02_2024/8irn_35680.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irn_35680/02_2024/8irn_35680_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irn_35680/02_2024/8irn_35680_trim_updated.pdb" } resolution = 2.7 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 52 5.16 5 C 5304 2.51 5 N 1316 2.21 5 O 1472 1.98 5 H 8208 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 358": "OD1" <-> "OD2" Residue "A ASP 390": "OD1" <-> "OD2" Residue "A TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 501": "OE1" <-> "OE2" Residue "B TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 358": "OD1" <-> "OD2" Residue "B PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 381": "OE1" <-> "OE2" Residue "B ASP 390": "OD1" <-> "OD2" Residue "B GLU 509": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16352 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 8130 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 516} Chain: "B" Number of atoms: 8130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 8130 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 516} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'EMU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'EMU': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 8.06, per 1000 atoms: 0.49 Number of scatterers: 16352 At special positions: 0 Unit cell: (94.461, 106.375, 101.269, 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 52 16.00 O 1472 8.00 N 1316 7.00 C 5304 6.00 H 8208 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 123 " distance=2.03 Simple disulfide: pdb=" SG CYS A 83 " - pdb=" SG CYS A 111 " distance=2.03 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 254 " - pdb=" SG CYS A 287 " distance=2.03 Simple disulfide: pdb=" SG CYS B 78 " - pdb=" SG CYS B 123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 83 " - pdb=" SG CYS B 111 " distance=2.03 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 254 " - pdb=" SG CYS B 287 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG C 1 " - " ASN A 270 " " NAG D 1 " - " ASN B 270 " Time building additional restraints: 14.60 Conformation dependent library (CDL) restraints added in 1.9 seconds 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1940 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 2 sheets defined 60.6% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.66 Creating SS restraints... Processing helix chain 'A' and resid 20 through 29 Processing helix chain 'A' and resid 32 through 36 Processing helix chain 'A' and resid 39 through 42 No H-bonds generated for 'chain 'A' and resid 39 through 42' Processing helix chain 'A' and resid 47 through 74 removed outlier: 5.194A pdb=" N TYR A 62 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE A 63 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU A 64 " --> pdb=" O MET A 60 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA A 65 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 82 No H-bonds generated for 'chain 'A' and resid 80 through 82' Processing helix chain 'A' and resid 94 through 96 No H-bonds generated for 'chain 'A' and resid 94 through 96' Processing helix chain 'A' and resid 109 through 112 Processing helix chain 'A' and resid 118 through 149 Processing helix chain 'A' and resid 160 through 168 removed outlier: 3.857A pdb=" N ALA A 164 " --> pdb=" O MET A 160 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 200 Processing helix chain 'A' and resid 204 through 210 Processing helix chain 'A' and resid 213 through 232 removed outlier: 4.344A pdb=" N SER A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ALA A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 258 No H-bonds generated for 'chain 'A' and resid 256 through 258' Processing helix chain 'A' and resid 295 through 312 Processing helix chain 'A' and resid 318 through 330 Processing helix chain 'A' and resid 344 through 354 Processing helix chain 'A' and resid 377 through 404 Processing helix chain 'A' and resid 417 through 434 Processing helix chain 'A' and resid 443 through 451 Processing helix chain 'A' and resid 457 through 469 Processing helix chain 'A' and resid 473 through 476 No H-bonds generated for 'chain 'A' and resid 473 through 476' Processing helix chain 'A' and resid 481 through 501 Proline residue: A 486 - end of helix removed outlier: 4.013A pdb=" N LYS A 497 " --> pdb=" O VAL A 493 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N SER A 498 " --> pdb=" O MET A 494 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N VAL A 499 " --> pdb=" O MET A 495 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N THR A 500 " --> pdb=" O MET A 496 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N GLU A 501 " --> pdb=" O LYS A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 522 Proline residue: A 512 - end of helix removed outlier: 3.758A pdb=" N MET A 520 " --> pdb=" O THR A 516 " (cutoff:3.500A) Proline residue: A 521 - end of helix Processing helix chain 'A' and resid 526 through 553 removed outlier: 4.541A pdb=" N TRP A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ASP A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 29 Processing helix chain 'B' and resid 32 through 36 Processing helix chain 'B' and resid 39 through 42 No H-bonds generated for 'chain 'B' and resid 39 through 42' Processing helix chain 'B' and resid 47 through 74 removed outlier: 5.184A pdb=" N TYR B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE B 63 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LEU B 64 " --> pdb=" O MET B 60 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA B 65 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER B 74 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 109 through 112 Processing helix chain 'B' and resid 118 through 149 Processing helix chain 'B' and resid 160 through 168 removed outlier: 3.871A pdb=" N ALA B 164 " --> pdb=" O MET B 160 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR B 165 " --> pdb=" O GLY B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 201 Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 213 through 232 removed outlier: 4.416A pdb=" N SER B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ALA B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 258 No H-bonds generated for 'chain 'B' and resid 256 through 258' Processing helix chain 'B' and resid 295 through 312 Processing helix chain 'B' and resid 318 through 330 Processing helix chain 'B' and resid 344 through 354 Processing helix chain 'B' and resid 377 through 405 Processing helix chain 'B' and resid 417 through 434 Processing helix chain 'B' and resid 443 through 450 Processing helix chain 'B' and resid 457 through 469 Processing helix chain 'B' and resid 473 through 476 No H-bonds generated for 'chain 'B' and resid 473 through 476' Processing helix chain 'B' and resid 481 through 501 Proline residue: B 486 - end of helix removed outlier: 3.982A pdb=" N LYS B 497 " --> pdb=" O VAL B 493 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N SER B 498 " --> pdb=" O MET B 494 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N VAL B 499 " --> pdb=" O MET B 495 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N THR B 500 " --> pdb=" O MET B 496 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N GLU B 501 " --> pdb=" O LYS B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 522 Proline residue: B 512 - end of helix removed outlier: 3.763A pdb=" N MET B 520 " --> pdb=" O THR B 516 " (cutoff:3.500A) Proline residue: B 521 - end of helix Processing helix chain 'B' and resid 526 through 540 Processing helix chain 'B' and resid 542 through 553 Processing sheet with id= A, first strand: chain 'A' and resid 156 through 158 Processing sheet with id= B, first strand: chain 'B' and resid 156 through 158 422 hydrogen bonds defined for protein. 1227 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: 5.62 Time building geometry restraints manager: 15.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8204 1.03 - 1.23: 13 1.23 - 1.42: 3416 1.42 - 1.62: 4823 1.62 - 1.81: 84 Bond restraints: 16540 Sorted by residual: bond pdb=" C6 EMU B 701 " pdb=" N10 EMU B 701 " ideal model delta sigma weight residual 1.338 1.450 -0.112 2.00e-02 2.50e+03 3.12e+01 bond pdb=" C6 EMU A 701 " pdb=" N10 EMU A 701 " ideal model delta sigma weight residual 1.338 1.449 -0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" NZ LYS A 19 " pdb=" HZ2 LYS A 19 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" NZ LYS B 19 " pdb=" HZ3 LYS B 19 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" NZ LYS B 19 " pdb=" HZ1 LYS B 19 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.24e+01 ... (remaining 16535 not shown) Histogram of bond angle deviations from ideal: 98.37 - 105.59: 172 105.59 - 112.81: 19559 112.81 - 120.03: 4918 120.03 - 127.25: 5191 127.25 - 134.47: 88 Bond angle restraints: 29928 Sorted by residual: angle pdb=" N LEU A 248 " pdb=" CA LEU A 248 " pdb=" CB LEU A 248 " ideal model delta sigma weight residual 114.17 110.07 4.10 1.14e+00 7.69e-01 1.29e+01 angle pdb=" N LEU B 248 " pdb=" CA LEU B 248 " pdb=" CB LEU B 248 " ideal model delta sigma weight residual 114.17 110.17 4.00 1.14e+00 7.69e-01 1.23e+01 angle pdb=" C2 EMU A 701 " pdb=" N3 EMU A 701 " pdb=" C4 EMU A 701 " ideal model delta sigma weight residual 111.69 122.00 -10.31 3.00e+00 1.11e-01 1.18e+01 angle pdb=" C2 EMU B 701 " pdb=" N3 EMU B 701 " pdb=" C4 EMU B 701 " ideal model delta sigma weight residual 111.69 121.91 -10.22 3.00e+00 1.11e-01 1.16e+01 angle pdb=" C5 EMU A 701 " pdb=" C4 EMU A 701 " pdb=" N3 EMU A 701 " ideal model delta sigma weight residual 126.32 118.13 8.19 3.00e+00 1.11e-01 7.45e+00 ... (remaining 29923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.81: 7452 24.81 - 49.63: 290 49.63 - 74.44: 133 74.44 - 99.25: 2 99.25 - 124.07: 3 Dihedral angle restraints: 7880 sinusoidal: 4246 harmonic: 3634 Sorted by residual: dihedral pdb=" CB CYS A 78 " pdb=" SG CYS A 78 " pdb=" SG CYS A 123 " pdb=" CB CYS A 123 " ideal model delta sinusoidal sigma weight residual 93.00 164.43 -71.43 1 1.00e+01 1.00e-02 6.54e+01 dihedral pdb=" CB CYS B 78 " pdb=" SG CYS B 78 " pdb=" SG CYS B 123 " pdb=" CB CYS B 123 " ideal model delta sinusoidal sigma weight residual 93.00 163.76 -70.76 1 1.00e+01 1.00e-02 6.44e+01 dihedral pdb=" CA VAL A 484 " pdb=" C VAL A 484 " pdb=" N GLY A 485 " pdb=" CA GLY A 485 " ideal model delta harmonic sigma weight residual 180.00 144.66 35.34 0 5.00e+00 4.00e-02 5.00e+01 ... (remaining 7877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1011 0.041 - 0.082: 266 0.082 - 0.123: 77 0.123 - 0.163: 1 0.163 - 0.204: 1 Chirality restraints: 1356 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN B 270 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ILE B 502 " pdb=" N ILE B 502 " pdb=" C ILE B 502 " pdb=" CB ILE B 502 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.91e-01 chirality pdb=" CA ILE A 105 " pdb=" N ILE A 105 " pdb=" C ILE A 105 " pdb=" CB ILE A 105 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.74e-01 ... (remaining 1353 not shown) Planarity restraints: 2434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 486 " -0.041 5.00e-02 4.00e+02 6.19e-02 6.13e+00 pdb=" N PRO B 487 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 487 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 487 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 486 " -0.041 5.00e-02 4.00e+02 6.17e-02 6.09e+00 pdb=" N PRO A 487 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 487 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 487 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 203 " -0.012 2.00e-02 2.50e+03 7.54e-03 1.70e+00 pdb=" CG PHE A 203 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE A 203 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 203 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 203 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 203 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 203 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE A 203 " 0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE A 203 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE A 203 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 203 " -0.002 2.00e-02 2.50e+03 pdb=" HZ PHE A 203 " -0.000 2.00e-02 2.50e+03 ... (remaining 2431 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 829 2.17 - 2.78: 33024 2.78 - 3.39: 49524 3.39 - 3.99: 63511 3.99 - 4.60: 100143 Nonbonded interactions: 247031 Sorted by model distance: nonbonded pdb="HD22 ASN A 67 " pdb=" OG1 THR A 135 " model vdw 1.565 1.850 nonbonded pdb="HD22 ASN B 67 " pdb=" OG1 THR B 135 " model vdw 1.571 1.850 nonbonded pdb=" O SER A 446 " pdb=" H ARG A 450 " model vdw 1.611 1.850 nonbonded pdb="HG23 THR A 162 " pdb=" HE1 PHE A 386 " model vdw 1.618 2.270 nonbonded pdb="HH22 ARG B 333 " pdb=" OD1 ASP B 347 " model vdw 1.626 1.850 ... (remaining 247026 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.630 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: 0.260 Extract box with map and model: 3.950 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 57.170 Find NCS groups from input model: 0.620 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: 0.010 Load rotamer database and sin/cos tables:13.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 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 0.112 8332 Z= 0.249 Angle : 0.593 10.309 11340 Z= 0.315 Chirality : 0.039 0.204 1356 Planarity : 0.004 0.062 1400 Dihedral : 13.273 124.066 2936 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.23 % Allowed : 0.23 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.26), residues: 1076 helix: 2.11 (0.21), residues: 654 sheet: -5.08 (0.50), residues: 20 loop : -0.42 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 380 HIS 0.002 0.001 HIS A 541 PHE 0.022 0.001 PHE A 203 TYR 0.017 0.001 TYR B 309 ARG 0.006 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 98 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 390 ASP cc_start: 0.7453 (m-30) cc_final: 0.7017 (m-30) REVERT: A 548 GLU cc_start: 0.6584 (mt-10) cc_final: 0.6018 (pt0) REVERT: B 19 LYS cc_start: 0.6145 (OUTLIER) cc_final: 0.5596 (tttt) REVERT: B 548 GLU cc_start: 0.6546 (mt-10) cc_final: 0.6141 (pt0) outliers start: 2 outliers final: 2 residues processed: 100 average time/residue: 2.5490 time to fit residues: 271.9676 Evaluate side-chains 86 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 83 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 393 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 0.0030 chunk 98 optimal weight: 1.9990 overall best weight: 1.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.0759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8332 Z= 0.247 Angle : 0.511 6.567 11340 Z= 0.266 Chirality : 0.039 0.150 1356 Planarity : 0.005 0.063 1400 Dihedral : 8.467 109.913 1242 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.70 % Allowed : 6.18 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.54 (0.26), residues: 1076 helix: 2.16 (0.21), residues: 642 sheet: -4.97 (0.54), residues: 20 loop : -0.47 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 380 HIS 0.002 0.001 HIS B 541 PHE 0.015 0.001 PHE A 442 TYR 0.009 0.001 TYR B 388 ARG 0.004 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 85 time to evaluate : 1.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 GLU cc_start: 0.6599 (mt-10) cc_final: 0.6007 (pt0) REVERT: B 19 LYS cc_start: 0.6268 (OUTLIER) cc_final: 0.5718 (tttt) REVERT: B 548 GLU cc_start: 0.6621 (mt-10) cc_final: 0.6117 (pt0) outliers start: 6 outliers final: 4 residues processed: 88 average time/residue: 2.2282 time to fit residues: 211.3455 Evaluate side-chains 87 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 82 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 413 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8332 Z= 0.311 Angle : 0.540 8.011 11340 Z= 0.281 Chirality : 0.040 0.153 1356 Planarity : 0.005 0.062 1400 Dihedral : 8.109 102.950 1242 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.05 % Allowed : 6.76 % Favored : 92.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.26), residues: 1076 helix: 2.03 (0.21), residues: 642 sheet: -4.84 (0.52), residues: 20 loop : -0.46 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 380 HIS 0.002 0.001 HIS B 541 PHE 0.016 0.001 PHE B 442 TYR 0.011 0.001 TYR B 388 ARG 0.002 0.000 ARG A 508 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 83 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 548 GLU cc_start: 0.6703 (mt-10) cc_final: 0.6042 (pt0) REVERT: B 19 LYS cc_start: 0.6431 (OUTLIER) cc_final: 0.5849 (tttt) REVERT: B 32 ARG cc_start: 0.6674 (OUTLIER) cc_final: 0.4804 (mtm110) REVERT: B 401 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.7613 (mpm) REVERT: B 548 GLU cc_start: 0.6667 (mt-10) cc_final: 0.6143 (pt0) outliers start: 9 outliers final: 6 residues processed: 87 average time/residue: 1.9965 time to fit residues: 188.9976 Evaluate side-chains 90 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 81 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 413 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8332 Z= 0.189 Angle : 0.502 8.740 11340 Z= 0.259 Chirality : 0.038 0.148 1356 Planarity : 0.004 0.061 1400 Dihedral : 7.657 96.650 1242 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.70 % Allowed : 7.23 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.59 (0.26), residues: 1076 helix: 2.16 (0.21), residues: 646 sheet: -4.78 (0.53), residues: 20 loop : -0.43 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 380 HIS 0.002 0.000 HIS B 541 PHE 0.010 0.001 PHE A 189 TYR 0.009 0.001 TYR B 388 ARG 0.004 0.000 ARG A 508 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 520 MET cc_start: 0.9078 (mtt) cc_final: 0.8841 (mtt) REVERT: A 548 GLU cc_start: 0.6672 (mt-10) cc_final: 0.6036 (pt0) REVERT: B 19 LYS cc_start: 0.6452 (OUTLIER) cc_final: 0.5860 (tttt) REVERT: B 32 ARG cc_start: 0.6673 (OUTLIER) cc_final: 0.4832 (mtm110) REVERT: B 401 MET cc_start: 0.8413 (mpm) cc_final: 0.8186 (mpm) REVERT: B 548 GLU cc_start: 0.6673 (mt-10) cc_final: 0.6142 (pt0) outliers start: 6 outliers final: 2 residues processed: 85 average time/residue: 1.9436 time to fit residues: 180.2436 Evaluate side-chains 84 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 413 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.1980 chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 8332 Z= 0.357 Angle : 0.562 9.609 11340 Z= 0.291 Chirality : 0.041 0.154 1356 Planarity : 0.004 0.062 1400 Dihedral : 7.393 89.395 1238 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.16 % Favored : 96.65 % Rotamer: Outliers : 1.52 % Allowed : 8.16 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.40 (0.26), residues: 1076 helix: 1.98 (0.21), residues: 644 sheet: -4.54 (0.61), residues: 20 loop : -0.45 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 380 HIS 0.002 0.001 HIS A 541 PHE 0.013 0.002 PHE B 189 TYR 0.012 0.002 TYR A 388 ARG 0.003 0.000 ARG A 508 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 80 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.6730 (OUTLIER) cc_final: 0.4896 (mtm110) REVERT: A 520 MET cc_start: 0.9084 (mtt) cc_final: 0.8844 (mtt) REVERT: A 548 GLU cc_start: 0.6654 (mt-10) cc_final: 0.6037 (pt0) REVERT: B 19 LYS cc_start: 0.6626 (OUTLIER) cc_final: 0.6013 (tttt) REVERT: B 32 ARG cc_start: 0.6754 (OUTLIER) cc_final: 0.4924 (mtm110) REVERT: B 401 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8279 (mpm) REVERT: B 548 GLU cc_start: 0.6766 (mt-10) cc_final: 0.6207 (pt0) outliers start: 13 outliers final: 6 residues processed: 85 average time/residue: 2.1296 time to fit residues: 196.2497 Evaluate side-chains 90 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 413 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 104 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8332 Z= 0.309 Angle : 0.550 10.276 11340 Z= 0.283 Chirality : 0.040 0.153 1356 Planarity : 0.004 0.061 1400 Dihedral : 7.096 84.701 1238 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.40 % Allowed : 9.09 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.36 (0.26), residues: 1076 helix: 1.95 (0.21), residues: 644 sheet: -4.65 (0.58), residues: 20 loop : -0.47 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 380 HIS 0.002 0.001 HIS A 541 PHE 0.012 0.001 PHE B 189 TYR 0.012 0.001 TYR A 388 ARG 0.002 0.000 ARG A 508 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 81 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.6730 (OUTLIER) cc_final: 0.4912 (mtm110) REVERT: A 494 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7551 (mmt) REVERT: A 548 GLU cc_start: 0.6605 (mt-10) cc_final: 0.5945 (pt0) REVERT: B 19 LYS cc_start: 0.6677 (OUTLIER) cc_final: 0.6076 (tttt) REVERT: B 32 ARG cc_start: 0.6707 (OUTLIER) cc_final: 0.4907 (mtm110) REVERT: B 401 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8269 (mpm) REVERT: B 548 GLU cc_start: 0.6727 (mt-10) cc_final: 0.6061 (pt0) outliers start: 12 outliers final: 4 residues processed: 85 average time/residue: 1.9601 time to fit residues: 181.7485 Evaluate side-chains 89 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 413 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8332 Z= 0.166 Angle : 0.511 10.924 11340 Z= 0.260 Chirality : 0.038 0.144 1356 Planarity : 0.004 0.061 1400 Dihedral : 6.615 78.147 1238 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.70 % Allowed : 9.91 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.60 (0.26), residues: 1076 helix: 2.19 (0.21), residues: 646 sheet: -4.66 (0.57), residues: 20 loop : -0.47 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 482 HIS 0.002 0.000 HIS B 541 PHE 0.010 0.001 PHE B 414 TYR 0.009 0.001 TYR B 388 ARG 0.004 0.000 ARG A 508 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.6700 (OUTLIER) cc_final: 0.4890 (mtm110) REVERT: A 548 GLU cc_start: 0.6578 (mt-10) cc_final: 0.5918 (pt0) REVERT: B 19 LYS cc_start: 0.6612 (OUTLIER) cc_final: 0.6031 (tttt) REVERT: B 32 ARG cc_start: 0.6716 (OUTLIER) cc_final: 0.4919 (mtm110) REVERT: B 401 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8177 (mpm) REVERT: B 548 GLU cc_start: 0.6711 (mt-10) cc_final: 0.6026 (pt0) outliers start: 6 outliers final: 2 residues processed: 84 average time/residue: 2.0674 time to fit residues: 189.1529 Evaluate side-chains 86 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 80 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 413 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8332 Z= 0.201 Angle : 0.516 11.199 11340 Z= 0.262 Chirality : 0.038 0.146 1356 Planarity : 0.004 0.062 1400 Dihedral : 6.136 66.936 1238 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.82 % Allowed : 9.67 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.64 (0.26), residues: 1076 helix: 2.24 (0.21), residues: 646 sheet: -4.61 (0.58), residues: 20 loop : -0.47 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 482 HIS 0.001 0.000 HIS A 541 PHE 0.010 0.001 PHE B 189 TYR 0.009 0.001 TYR A 388 ARG 0.002 0.000 ARG A 508 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.6720 (OUTLIER) cc_final: 0.4909 (mtm110) REVERT: A 548 GLU cc_start: 0.6589 (mt-10) cc_final: 0.5932 (pt0) REVERT: B 19 LYS cc_start: 0.6651 (OUTLIER) cc_final: 0.6067 (tttt) REVERT: B 32 ARG cc_start: 0.6730 (OUTLIER) cc_final: 0.4916 (mtm110) REVERT: B 401 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.8201 (mpm) REVERT: B 548 GLU cc_start: 0.6725 (mt-10) cc_final: 0.6033 (pt0) outliers start: 7 outliers final: 3 residues processed: 82 average time/residue: 1.9778 time to fit residues: 176.2962 Evaluate side-chains 86 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 413 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8332 Z= 0.160 Angle : 0.496 9.063 11340 Z= 0.252 Chirality : 0.038 0.141 1356 Planarity : 0.004 0.062 1400 Dihedral : 5.258 59.509 1238 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.58 % Allowed : 9.91 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.75 (0.26), residues: 1076 helix: 2.32 (0.21), residues: 646 sheet: -4.63 (0.57), residues: 20 loop : -0.42 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 482 HIS 0.001 0.000 HIS B 541 PHE 0.009 0.001 PHE B 189 TYR 0.008 0.001 TYR B 388 ARG 0.003 0.000 ARG A 508 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 83 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.6714 (OUTLIER) cc_final: 0.4893 (mtm110) REVERT: A 548 GLU cc_start: 0.6546 (mt-10) cc_final: 0.5899 (pt0) REVERT: B 19 LYS cc_start: 0.6610 (OUTLIER) cc_final: 0.6015 (tttt) REVERT: B 32 ARG cc_start: 0.6737 (OUTLIER) cc_final: 0.4924 (mtm110) REVERT: B 401 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.8146 (mpm) REVERT: B 548 GLU cc_start: 0.6704 (mt-10) cc_final: 0.6019 (pt0) outliers start: 5 outliers final: 1 residues processed: 85 average time/residue: 2.0841 time to fit residues: 192.1935 Evaluate side-chains 86 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 401 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 99 optimal weight: 0.3980 chunk 85 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8332 Z= 0.234 Angle : 0.517 6.122 11340 Z= 0.264 Chirality : 0.039 0.151 1356 Planarity : 0.004 0.061 1400 Dihedral : 4.983 59.611 1238 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.70 % Allowed : 9.91 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.68 (0.26), residues: 1076 helix: 2.26 (0.21), residues: 646 sheet: -4.55 (0.60), residues: 20 loop : -0.46 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 380 HIS 0.002 0.001 HIS A 541 PHE 0.011 0.001 PHE B 189 TYR 0.009 0.001 TYR B 388 ARG 0.002 0.000 ARG A 508 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.6700 (OUTLIER) cc_final: 0.4886 (mtm110) REVERT: A 548 GLU cc_start: 0.6550 (mt-10) cc_final: 0.5905 (pt0) REVERT: B 19 LYS cc_start: 0.6674 (OUTLIER) cc_final: 0.6088 (tttt) REVERT: B 32 ARG cc_start: 0.6750 (OUTLIER) cc_final: 0.4941 (mtm110) REVERT: B 401 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.8200 (mpm) REVERT: B 548 GLU cc_start: 0.6717 (mt-10) cc_final: 0.6014 (pt0) outliers start: 6 outliers final: 2 residues processed: 84 average time/residue: 2.0103 time to fit residues: 183.1903 Evaluate side-chains 87 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 401 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.106743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.084119 restraints weight = 30988.268| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 1.79 r_work: 0.2826 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8332 Z= 0.253 Angle : 0.518 6.345 11340 Z= 0.269 Chirality : 0.039 0.150 1356 Planarity : 0.004 0.061 1400 Dihedral : 4.848 59.569 1238 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.82 % Allowed : 9.79 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.63 (0.26), residues: 1076 helix: 2.19 (0.21), residues: 646 sheet: -4.58 (0.59), residues: 20 loop : -0.40 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 380 HIS 0.002 0.001 HIS A 541 PHE 0.011 0.001 PHE B 189 TYR 0.010 0.001 TYR A 388 ARG 0.002 0.000 ARG A 508 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5030.31 seconds wall clock time: 89 minutes 24.75 seconds (5364.75 seconds total)