Starting phenix.real_space_refine on Tue Feb 13 16:36:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7v_33049/02_2024/7x7v_33049.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7v_33049/02_2024/7x7v_33049.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7v_33049/02_2024/7x7v_33049.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7v_33049/02_2024/7x7v_33049.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7v_33049/02_2024/7x7v_33049.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7v_33049/02_2024/7x7v_33049.pdb" } resolution = 3.83 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 4365 2.51 5 N 1124 2.21 5 O 1361 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 85": "OE1" <-> "OE2" Residue "L GLU 109": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "F GLU 105": "OE1" <-> "OE2" Residue "C ARG 38": "NH1" <-> "NH2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "E GLU 341": "OE1" <-> "OE2" Residue "E PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 6876 Number of models: 1 Model: "" Number of chains: 9 Chain: "L" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 853 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 103} Chain: "H" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 946 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "F" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 827 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 103} Chain: "A" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 929 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "D" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "C" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 921 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "E" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1513 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 175} Chain: "B" 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: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.80, per 1000 atoms: 0.55 Number of scatterers: 6876 At special positions: 0 Unit cell: (98.028, 118.256, 80.134, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 1361 8.00 N 1124 7.00 C 4365 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 323 " - pdb=" SG CYS E 348 " distance=2.03 Simple disulfide: pdb=" SG CYS E 366 " - pdb=" SG CYS E 419 " distance=1.98 Simple disulfide: pdb=" SG CYS E 467 " - pdb=" SG CYS E 474 " distance=2.04 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 B 1 " - " NAG B 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG B 1 " - " ASN E 330 " " NAG G 1 " - " ASN E 357 " Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 1.5 seconds 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1586 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 20 sheets defined 4.5% alpha, 33.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'H' and resid 61 through 65 removed outlier: 3.623A pdb=" N GLU H 65 " --> pdb=" O LEU H 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.758A pdb=" N ASP A 90 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 87 through 91' Processing helix chain 'A' and resid 101 through 105 removed outlier: 3.888A pdb=" N GLY A 105 " --> pdb=" O ASP A 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 removed outlier: 4.086A pdb=" N LYS C 65 " --> pdb=" O GLN C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 65' Processing helix chain 'E' and resid 324 through 329 removed outlier: 4.005A pdb=" N VAL E 328 " --> pdb=" O PRO E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 340 removed outlier: 4.190A pdb=" N TRP E 340 " --> pdb=" O VAL E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 394 No H-bonds generated for 'chain 'E' and resid 392 through 394' Processing helix chain 'E' and resid 425 through 430 removed outlier: 3.899A pdb=" N ALA E 430 " --> pdb=" O ARG E 426 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.604A pdb=" N THR L 76 " --> pdb=" O SER L 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 12 removed outlier: 7.220A pdb=" N LEU L 11 " --> pdb=" O GLU L 109 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 52 through 53 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.511A pdb=" N VAL H 18 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 46 through 47 removed outlier: 4.670A pdb=" N THR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL H 37 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN H 39 " --> pdb=" O VAL H 93 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 4 through 5 removed outlier: 3.609A pdb=" N ARG F 24 " --> pdb=" O THR F 5 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.657A pdb=" N GLU F 105 " --> pdb=" O LEU F 11 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 44 through 48 removed outlier: 6.824A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR F 97 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 3 through 6 removed outlier: 3.544A pdb=" N VAL A 18 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 3 through 6 removed outlier: 3.657A pdb=" N THR A 78 " --> pdb=" O ASP A 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.868A pdb=" N TRP A 36 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.868A pdb=" N TRP A 36 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.779A pdb=" N VAL D 19 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE D 75 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER D 74 " --> pdb=" O SER D 63 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 10 through 11 Processing sheet with id=AB6, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.367A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N SER D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU D 33 " --> pdb=" O SER D 49 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN D 38 " --> pdb=" O THR D 85 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR D 85 " --> pdb=" O GLN D 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.657A pdb=" N THR C 71 " --> pdb=" O TYR C 80 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 58 through 60 removed outlier: 3.500A pdb=" N THR C 59 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N TYR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N MET C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N CYS C 96 " --> pdb=" O TRP C 112 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N TRP C 112 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LYS C 98 " --> pdb=" O ALA C 110 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 58 through 60 removed outlier: 3.500A pdb=" N THR C 59 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N TYR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N MET C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR C 94 " --> pdb=" O THR C 116 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR C 116 " --> pdb=" O TYR C 94 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 341 through 345 removed outlier: 3.804A pdb=" N GLU E 341 " --> pdb=" O SER E 386 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER E 386 " --> pdb=" O GLU E 341 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS E 343 " --> pdb=" O ALA E 384 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA E 384 " --> pdb=" O LYS E 343 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 439 through 441 190 hydrogen bonds defined for protein. 465 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.77 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1592 1.33 - 1.45: 1828 1.45 - 1.58: 3604 1.58 - 1.70: 0 1.70 - 1.82: 32 Bond restraints: 7056 Sorted by residual: bond pdb=" CA CYS E 366 " pdb=" C CYS E 366 " ideal model delta sigma weight residual 1.522 1.463 0.059 1.22e-02 6.72e+03 2.30e+01 bond pdb=" N PRO E 507 " pdb=" CD PRO E 507 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.65e+01 bond pdb=" CA CYS E 366 " pdb=" CB CYS E 366 " ideal model delta sigma weight residual 1.533 1.455 0.078 2.29e-02 1.91e+03 1.16e+01 bond pdb=" C LYS E 365 " pdb=" O LYS E 365 " ideal model delta sigma weight residual 1.236 1.204 0.032 1.22e-02 6.72e+03 6.70e+00 bond pdb=" N CYS E 366 " pdb=" CA CYS E 366 " ideal model delta sigma weight residual 1.455 1.424 0.031 1.23e-02 6.61e+03 6.46e+00 ... (remaining 7051 not shown) Histogram of bond angle deviations from ideal: 98.99 - 106.06: 153 106.06 - 113.13: 3678 113.13 - 120.20: 2531 120.20 - 127.27: 3148 127.27 - 134.33: 87 Bond angle restraints: 9597 Sorted by residual: angle pdb=" CA PRO E 507 " pdb=" N PRO E 507 " pdb=" CD PRO E 507 " ideal model delta sigma weight residual 112.00 98.99 13.01 1.40e+00 5.10e-01 8.63e+01 angle pdb=" N GLY E 418 " pdb=" CA GLY E 418 " pdb=" C GLY E 418 " ideal model delta sigma weight residual 112.54 122.66 -10.12 1.28e+00 6.10e-01 6.25e+01 angle pdb=" N MET E 417 " pdb=" CA MET E 417 " pdb=" C MET E 417 " ideal model delta sigma weight residual 112.92 104.95 7.97 1.23e+00 6.61e-01 4.20e+01 angle pdb=" C ILE L 98 " pdb=" N PRO L 99 " pdb=" CA PRO L 99 " ideal model delta sigma weight residual 119.90 113.52 6.38 1.05e+00 9.07e-01 3.69e+01 angle pdb=" N ASP C 90 " pdb=" CA ASP C 90 " pdb=" C ASP C 90 " ideal model delta sigma weight residual 113.30 105.24 8.06 1.34e+00 5.57e-01 3.62e+01 ... (remaining 9592 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 3661 16.99 - 33.98: 404 33.98 - 50.97: 76 50.97 - 67.96: 11 67.96 - 84.94: 3 Dihedral angle restraints: 4155 sinusoidal: 1639 harmonic: 2516 Sorted by residual: dihedral pdb=" CB CYS E 366 " pdb=" SG CYS E 366 " pdb=" SG CYS E 419 " pdb=" CB CYS E 419 " ideal model delta sinusoidal sigma weight residual 93.00 137.56 -44.56 1 1.00e+01 1.00e-02 2.76e+01 dihedral pdb=" CA CYS E 467 " pdb=" C CYS E 467 " pdb=" N THR E 468 " pdb=" CA THR E 468 " ideal model delta harmonic sigma weight residual 180.00 154.30 25.70 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" N CYS E 366 " pdb=" C CYS E 366 " pdb=" CA CYS E 366 " pdb=" CB CYS E 366 " ideal model delta harmonic sigma weight residual 122.80 135.63 -12.83 0 2.50e+00 1.60e-01 2.63e+01 ... (remaining 4152 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 1010 0.151 - 0.301: 25 0.301 - 0.452: 1 0.452 - 0.602: 0 0.602 - 0.753: 1 Chirality restraints: 1037 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.17e+02 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 3.95e+01 chirality pdb=" CA CYS E 366 " pdb=" N CYS E 366 " pdb=" C CYS E 366 " pdb=" CB CYS E 366 " both_signs ideal model delta sigma weight residual False 2.51 1.76 0.75 2.00e-01 2.50e+01 1.42e+01 ... (remaining 1034 not shown) Planarity restraints: 1226 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " -0.193 2.00e-02 2.50e+03 1.60e-01 3.18e+02 pdb=" C7 NAG G 1 " 0.052 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " -0.139 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " 0.260 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " -0.173 2.00e-02 2.50e+03 1.47e-01 2.70e+02 pdb=" C7 NAG B 1 " 0.046 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " -0.125 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " 0.245 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 2 " 0.092 2.00e-02 2.50e+03 7.60e-02 7.23e+01 pdb=" C7 NAG G 2 " -0.026 2.00e-02 2.50e+03 pdb=" C8 NAG G 2 " 0.070 2.00e-02 2.50e+03 pdb=" N2 NAG G 2 " -0.121 2.00e-02 2.50e+03 pdb=" O7 NAG G 2 " -0.016 2.00e-02 2.50e+03 ... (remaining 1223 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1968 2.80 - 3.32: 5448 3.32 - 3.85: 11089 3.85 - 4.37: 11905 4.37 - 4.90: 21706 Nonbonded interactions: 52116 Sorted by model distance: nonbonded pdb=" OG SER E 336 " pdb=" O LYS E 439 " model vdw 2.274 2.440 nonbonded pdb=" O ILE F 29 " pdb=" OG1 THR F 92 " model vdw 2.276 2.440 nonbonded pdb=" OG SER E 380 " pdb=" O LEU E 503 " model vdw 2.291 2.440 nonbonded pdb=" OG SER E 346 " pdb=" ND2 ASN E 381 " model vdw 2.302 2.520 nonbonded pdb=" OH TYR L 36 " pdb=" O TYR E 436 " model vdw 2.311 2.440 ... (remaining 52111 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 'B' selection = chain 'G' } 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=0.67 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 16.690 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: 0.000 Extract box with map and model: 44.440 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 23.130 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 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 : 0.006 0.078 7056 Z= 0.432 Angle : 0.975 13.009 9597 Z= 0.562 Chirality : 0.064 0.753 1037 Planarity : 0.011 0.160 1224 Dihedral : 13.942 84.945 2542 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.10 % Favored : 92.78 % Rotamer: Outliers : 0.41 % Allowed : 9.09 % Favored : 90.50 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.88 (0.25), residues: 859 helix: -5.12 (0.37), residues: 8 sheet: -2.34 (0.25), residues: 363 loop : -2.76 (0.23), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP E 423 HIS 0.006 0.001 HIS E 445 PHE 0.018 0.002 PHE E 334 TYR 0.021 0.002 TYR D 91 ARG 0.005 0.001 ARG F 53 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 247 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 49 LYS cc_start: 0.7622 (tttt) cc_final: 0.7408 (tttm) REVERT: L 51 LEU cc_start: 0.8456 (mp) cc_final: 0.8136 (mp) REVERT: L 80 HIS cc_start: 0.8060 (t70) cc_final: 0.7779 (t70) REVERT: H 19 LYS cc_start: 0.8290 (tttt) cc_final: 0.7554 (tttp) REVERT: H 32 TYR cc_start: 0.7790 (m-80) cc_final: 0.7557 (m-10) REVERT: H 46 GLU cc_start: 0.8203 (pt0) cc_final: 0.7695 (pt0) REVERT: H 110 PHE cc_start: 0.7898 (m-80) cc_final: 0.7678 (m-10) REVERT: H 113 GLN cc_start: 0.8745 (pt0) cc_final: 0.8345 (pm20) REVERT: F 45 LYS cc_start: 0.7204 (ptmt) cc_final: 0.6782 (ptpp) REVERT: F 80 GLN cc_start: 0.8044 (tm-30) cc_final: 0.7791 (tp40) REVERT: F 90 GLN cc_start: 0.8057 (tm-30) cc_final: 0.7627 (tm-30) REVERT: A 3 GLN cc_start: 0.8187 (pt0) cc_final: 0.7376 (pp30) REVERT: A 5 GLN cc_start: 0.8265 (tp40) cc_final: 0.7670 (tp40) REVERT: A 10 GLU cc_start: 0.6828 (mp0) cc_final: 0.6234 (mp0) REVERT: A 19 LYS cc_start: 0.6978 (tppp) cc_final: 0.6473 (tptm) REVERT: A 23 LYS cc_start: 0.6820 (tptt) cc_final: 0.6197 (ttpp) REVERT: A 43 GLN cc_start: 0.7777 (mp10) cc_final: 0.7043 (mp10) REVERT: A 113 THR cc_start: 0.7766 (t) cc_final: 0.6780 (t) REVERT: D 79 GLN cc_start: 0.7315 (mp10) cc_final: 0.6456 (mp10) REVERT: C 2 ILE cc_start: 0.8039 (mm) cc_final: 0.7816 (mm) REVERT: C 23 LYS cc_start: 0.7499 (tmmt) cc_final: 0.7251 (tppp) REVERT: C 43 LYS cc_start: 0.8973 (mmmt) cc_final: 0.8692 (mmmm) REVERT: C 109 LEU cc_start: 0.8533 (mt) cc_final: 0.8333 (mt) REVERT: C 114 GLN cc_start: 0.8912 (mt0) cc_final: 0.8621 (mt0) REVERT: E 426 ARG cc_start: 0.8401 (tmm-80) cc_final: 0.7970 (ttt-90) REVERT: E 447 LYS cc_start: 0.8723 (mppt) cc_final: 0.8041 (mtpt) REVERT: E 505 ASN cc_start: 0.8627 (t0) cc_final: 0.8344 (t0) outliers start: 3 outliers final: 2 residues processed: 250 average time/residue: 0.2361 time to fit residues: 74.1244 Evaluate side-chains 207 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 205 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain E residue 363 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 0.0980 chunk 42 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 75 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 35 ASN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN A 39 GLN C 33 ASN E 457 ASN E 473 ASN E 479 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7056 Z= 0.232 Angle : 0.638 9.119 9597 Z= 0.329 Chirality : 0.045 0.263 1037 Planarity : 0.006 0.065 1224 Dihedral : 6.434 62.953 1049 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.66 % Allowed : 17.64 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.26), residues: 859 helix: -5.17 (0.30), residues: 14 sheet: -1.78 (0.26), residues: 341 loop : -2.38 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 423 HIS 0.003 0.001 HIS C 82 PHE 0.019 0.001 PHE E 416 TYR 0.015 0.001 TYR E 442 ARG 0.009 0.001 ARG L 65 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 218 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 80 HIS cc_start: 0.7944 (t70) cc_final: 0.7631 (t70) REVERT: H 10 GLU cc_start: 0.7206 (tp30) cc_final: 0.6663 (pm20) REVERT: H 19 LYS cc_start: 0.8205 (tttt) cc_final: 0.7625 (tttp) REVERT: H 87 THR cc_start: 0.7679 (OUTLIER) cc_final: 0.7448 (p) REVERT: H 113 GLN cc_start: 0.8887 (pt0) cc_final: 0.8364 (pm20) REVERT: F 24 ARG cc_start: 0.7472 (mtp-110) cc_final: 0.7055 (mtp-110) REVERT: F 78 LEU cc_start: 0.7620 (mm) cc_final: 0.7311 (mm) REVERT: F 80 GLN cc_start: 0.7982 (tm-30) cc_final: 0.7675 (tp40) REVERT: A 10 GLU cc_start: 0.6767 (mp0) cc_final: 0.6193 (mp0) REVERT: A 23 LYS cc_start: 0.6902 (tptt) cc_final: 0.6545 (ttpp) REVERT: A 32 TYR cc_start: 0.8292 (m-80) cc_final: 0.8047 (m-80) REVERT: A 43 GLN cc_start: 0.7681 (mp10) cc_final: 0.7302 (mp10) REVERT: A 57 ASP cc_start: 0.7842 (t0) cc_final: 0.7585 (t0) REVERT: A 113 THR cc_start: 0.7806 (t) cc_final: 0.6955 (t) REVERT: D 79 GLN cc_start: 0.7206 (mp10) cc_final: 0.6398 (mp-120) REVERT: C 43 LYS cc_start: 0.8951 (mmmt) cc_final: 0.8441 (mmmt) REVERT: C 65 LYS cc_start: 0.7625 (mmtm) cc_final: 0.7403 (mmtt) REVERT: C 109 LEU cc_start: 0.8485 (mt) cc_final: 0.8192 (mt) REVERT: C 114 GLN cc_start: 0.8891 (mt0) cc_final: 0.8552 (mp10) REVERT: E 426 ARG cc_start: 0.8289 (tmm-80) cc_final: 0.7812 (ttt-90) REVERT: E 447 LYS cc_start: 0.8636 (mppt) cc_final: 0.8043 (mtpt) outliers start: 27 outliers final: 18 residues processed: 227 average time/residue: 0.2139 time to fit residues: 61.6528 Evaluate side-chains 213 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 194 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 445 HIS Chi-restraints excluded: chain E residue 449 ARG Chi-restraints excluded: chain E residue 468 THR Chi-restraints excluded: chain E residue 475 TYR Chi-restraints excluded: chain E residue 497 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 41 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 90 GLN D 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7056 Z= 0.264 Angle : 0.629 9.439 9597 Z= 0.324 Chirality : 0.044 0.228 1037 Planarity : 0.005 0.058 1224 Dihedral : 6.087 57.801 1048 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 5.02 % Allowed : 18.32 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.27), residues: 859 helix: -5.13 (0.32), residues: 14 sheet: -1.40 (0.27), residues: 341 loop : -2.14 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 109 HIS 0.004 0.001 HIS L 94 PHE 0.016 0.001 PHE D 94 TYR 0.016 0.001 TYR C 50 ARG 0.011 0.001 ARG L 65 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 193 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 10 GLU cc_start: 0.7205 (tp30) cc_final: 0.6672 (pm20) REVERT: H 19 LYS cc_start: 0.8244 (tttt) cc_final: 0.7629 (tttp) REVERT: H 87 THR cc_start: 0.7645 (OUTLIER) cc_final: 0.7364 (p) REVERT: H 113 GLN cc_start: 0.8800 (pt0) cc_final: 0.8262 (pm20) REVERT: F 4 MET cc_start: 0.7939 (mtp) cc_final: 0.7128 (mmm) REVERT: F 78 LEU cc_start: 0.7692 (mm) cc_final: 0.7364 (mm) REVERT: F 80 GLN cc_start: 0.7983 (tm-30) cc_final: 0.7643 (tp40) REVERT: A 10 GLU cc_start: 0.6832 (mp0) cc_final: 0.6230 (mp0) REVERT: A 23 LYS cc_start: 0.6998 (tptt) cc_final: 0.6663 (ttpp) REVERT: A 43 GLN cc_start: 0.7685 (mp10) cc_final: 0.7281 (mp10) REVERT: A 57 ASP cc_start: 0.7833 (t0) cc_final: 0.7477 (t0) REVERT: A 64 PHE cc_start: 0.8749 (m-80) cc_final: 0.8515 (m-80) REVERT: C 43 LYS cc_start: 0.8937 (mmmt) cc_final: 0.8412 (mmmt) REVERT: C 67 LYS cc_start: 0.6962 (mtpt) cc_final: 0.6740 (ttmt) REVERT: C 114 GLN cc_start: 0.8876 (mt0) cc_final: 0.8473 (mp10) REVERT: E 426 ARG cc_start: 0.8264 (tmm-80) cc_final: 0.7742 (ttt-90) REVERT: E 447 LYS cc_start: 0.8588 (mppt) cc_final: 0.8063 (mtpt) outliers start: 37 outliers final: 25 residues processed: 205 average time/residue: 0.2349 time to fit residues: 60.7028 Evaluate side-chains 209 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 183 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 475 TYR Chi-restraints excluded: chain E residue 480 ASP Chi-restraints excluded: chain E residue 497 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 75 optimal weight: 0.3980 chunk 80 optimal weight: 0.0980 chunk 71 optimal weight: 0.4980 chunk 21 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 113 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 90 GLN D 30 ASN C 82 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7056 Z= 0.189 Angle : 0.582 8.732 9597 Z= 0.300 Chirality : 0.042 0.212 1037 Planarity : 0.005 0.055 1224 Dihedral : 5.836 54.446 1048 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 4.75 % Allowed : 21.30 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.27), residues: 859 helix: -5.13 (0.32), residues: 14 sheet: -1.23 (0.27), residues: 353 loop : -1.95 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 423 HIS 0.003 0.001 HIS L 94 PHE 0.011 0.001 PHE D 94 TYR 0.013 0.001 TYR F 49 ARG 0.012 0.001 ARG L 65 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 188 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 10 GLU cc_start: 0.7212 (tp30) cc_final: 0.6653 (pm20) REVERT: H 19 LYS cc_start: 0.8301 (tttt) cc_final: 0.7769 (tttp) REVERT: H 71 THR cc_start: 0.7406 (m) cc_final: 0.6832 (p) REVERT: H 87 THR cc_start: 0.7594 (OUTLIER) cc_final: 0.7317 (p) REVERT: H 113 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8213 (pm20) REVERT: F 4 MET cc_start: 0.7707 (mtp) cc_final: 0.6943 (mmm) REVERT: F 78 LEU cc_start: 0.7635 (mm) cc_final: 0.7317 (mm) REVERT: F 80 GLN cc_start: 0.7930 (tm-30) cc_final: 0.7584 (tp40) REVERT: F 105 GLU cc_start: 0.5288 (tt0) cc_final: 0.4907 (tt0) REVERT: A 10 GLU cc_start: 0.6870 (mp0) cc_final: 0.6318 (mp0) REVERT: A 19 LYS cc_start: 0.7621 (tptt) cc_final: 0.7367 (tttp) REVERT: A 23 LYS cc_start: 0.6949 (tttt) cc_final: 0.6650 (ttpp) REVERT: A 43 GLN cc_start: 0.7701 (mp10) cc_final: 0.6852 (mp10) REVERT: A 81 ILE cc_start: 0.7499 (OUTLIER) cc_final: 0.7098 (tt) REVERT: A 82 GLN cc_start: 0.7370 (tp40) cc_final: 0.7134 (mm110) REVERT: C 38 ARG cc_start: 0.7524 (ttp80) cc_final: 0.6754 (ttm-80) REVERT: C 43 LYS cc_start: 0.8863 (mmmt) cc_final: 0.8328 (mmmt) REVERT: C 67 LYS cc_start: 0.6967 (mtpt) cc_final: 0.6712 (ttmt) REVERT: C 114 GLN cc_start: 0.8842 (mt0) cc_final: 0.8402 (mp10) REVERT: E 426 ARG cc_start: 0.8214 (tmm-80) cc_final: 0.7705 (ttt-90) REVERT: E 447 LYS cc_start: 0.8539 (mppt) cc_final: 0.8046 (mtpt) REVERT: E 455 ILE cc_start: 0.8637 (tt) cc_final: 0.8408 (tp) outliers start: 35 outliers final: 21 residues processed: 206 average time/residue: 0.2206 time to fit residues: 57.5782 Evaluate side-chains 206 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 182 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 113 GLN Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain E residue 392 ASP Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 445 HIS Chi-restraints excluded: chain E residue 475 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 45 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN D 30 ASN C 82 HIS ** E 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 7056 Z= 0.388 Angle : 0.650 8.674 9597 Z= 0.340 Chirality : 0.044 0.298 1037 Planarity : 0.005 0.052 1224 Dihedral : 5.919 52.489 1048 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 6.38 % Allowed : 21.03 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.28), residues: 859 helix: -5.08 (0.33), residues: 14 sheet: -1.24 (0.27), residues: 368 loop : -2.02 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 423 HIS 0.006 0.001 HIS L 94 PHE 0.021 0.002 PHE D 94 TYR 0.020 0.002 TYR F 49 ARG 0.013 0.001 ARG L 65 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 183 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 10 GLU cc_start: 0.7288 (tp30) cc_final: 0.6734 (pm20) REVERT: H 19 LYS cc_start: 0.8287 (tttt) cc_final: 0.7748 (tttp) REVERT: H 87 THR cc_start: 0.7549 (OUTLIER) cc_final: 0.7274 (p) REVERT: H 113 GLN cc_start: 0.8753 (pt0) cc_final: 0.8240 (pm20) REVERT: F 4 MET cc_start: 0.7891 (mtp) cc_final: 0.6979 (mmm) REVERT: F 78 LEU cc_start: 0.7631 (mm) cc_final: 0.7320 (mm) REVERT: F 80 GLN cc_start: 0.7965 (tm-30) cc_final: 0.7588 (tp40) REVERT: F 90 GLN cc_start: 0.8190 (tm130) cc_final: 0.7963 (tm-30) REVERT: F 105 GLU cc_start: 0.5462 (tt0) cc_final: 0.5066 (tt0) REVERT: A 19 LYS cc_start: 0.7743 (tptt) cc_final: 0.7437 (tttp) REVERT: A 23 LYS cc_start: 0.6901 (tttt) cc_final: 0.6595 (ttpp) REVERT: A 43 GLN cc_start: 0.7671 (mp10) cc_final: 0.6851 (mp10) REVERT: A 82 GLN cc_start: 0.7569 (tp40) cc_final: 0.7302 (mm110) REVERT: C 43 LYS cc_start: 0.8862 (mmmt) cc_final: 0.8545 (mmmm) REVERT: C 114 GLN cc_start: 0.8808 (mt0) cc_final: 0.8368 (mt0) REVERT: E 423 TRP cc_start: 0.7408 (OUTLIER) cc_final: 0.6870 (p-90) REVERT: E 426 ARG cc_start: 0.8257 (tmm-80) cc_final: 0.7958 (ttp80) REVERT: E 447 LYS cc_start: 0.8498 (mppt) cc_final: 0.8001 (mtpt) outliers start: 47 outliers final: 34 residues processed: 205 average time/residue: 0.2328 time to fit residues: 60.0950 Evaluate side-chains 214 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 178 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain E residue 423 TRP Chi-restraints excluded: chain E residue 445 HIS Chi-restraints excluded: chain E residue 475 TYR Chi-restraints excluded: chain E residue 480 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 72 optimal weight: 0.0270 chunk 15 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 80 optimal weight: 0.0020 chunk 66 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 HIS E 381 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7056 Z= 0.176 Angle : 0.580 8.773 9597 Z= 0.296 Chirality : 0.043 0.283 1037 Planarity : 0.005 0.059 1224 Dihedral : 5.630 53.115 1048 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 4.48 % Allowed : 24.97 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.28), residues: 859 helix: -4.53 (0.67), residues: 20 sheet: -1.09 (0.27), residues: 369 loop : -1.86 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 423 HIS 0.002 0.001 HIS L 34 PHE 0.013 0.001 PHE E 460 TYR 0.014 0.001 TYR F 49 ARG 0.007 0.001 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 193 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 58 LEU cc_start: 0.7110 (OUTLIER) cc_final: 0.6838 (pp) REVERT: H 10 GLU cc_start: 0.7271 (tp30) cc_final: 0.6661 (pm20) REVERT: H 19 LYS cc_start: 0.8309 (tttt) cc_final: 0.7760 (tttp) REVERT: H 87 THR cc_start: 0.7557 (OUTLIER) cc_final: 0.7298 (p) REVERT: H 113 GLN cc_start: 0.8641 (pt0) cc_final: 0.8129 (pm20) REVERT: F 4 MET cc_start: 0.7715 (mtp) cc_final: 0.6952 (mmm) REVERT: F 24 ARG cc_start: 0.7422 (mtp-110) cc_final: 0.7163 (ttt90) REVERT: F 27 GLN cc_start: 0.7500 (pp30) cc_final: 0.7005 (pp30) REVERT: F 78 LEU cc_start: 0.7517 (mm) cc_final: 0.7193 (mm) REVERT: F 90 GLN cc_start: 0.8160 (tm130) cc_final: 0.6967 (tm130) REVERT: F 105 GLU cc_start: 0.5567 (tt0) cc_final: 0.5215 (tt0) REVERT: A 19 LYS cc_start: 0.7724 (tptt) cc_final: 0.7447 (tttp) REVERT: A 23 LYS cc_start: 0.6906 (tttt) cc_final: 0.6571 (ttpp) REVERT: A 38 LYS cc_start: 0.7309 (tttm) cc_final: 0.7104 (tttm) REVERT: A 43 GLN cc_start: 0.7784 (mp10) cc_final: 0.6970 (mp10) REVERT: A 81 ILE cc_start: 0.7558 (OUTLIER) cc_final: 0.7308 (tt) REVERT: C 38 ARG cc_start: 0.7441 (ttp80) cc_final: 0.6662 (ttm-80) REVERT: C 43 LYS cc_start: 0.8867 (mmmt) cc_final: 0.8338 (mmmt) REVERT: C 114 GLN cc_start: 0.8776 (mt0) cc_final: 0.8321 (mp10) REVERT: E 426 ARG cc_start: 0.8186 (tmm-80) cc_final: 0.7882 (ttp80) REVERT: E 447 LYS cc_start: 0.8537 (mppt) cc_final: 0.8067 (mtpt) outliers start: 33 outliers final: 22 residues processed: 211 average time/residue: 0.2217 time to fit residues: 59.4116 Evaluate side-chains 208 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 183 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 41 GLN Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 98 ILE Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 445 HIS Chi-restraints excluded: chain E residue 475 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 3.9990 chunk 45 optimal weight: 0.0770 chunk 58 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 48 optimal weight: 0.0770 chunk 36 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 GLN D 30 ASN C 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7056 Z= 0.203 Angle : 0.582 8.811 9597 Z= 0.298 Chirality : 0.043 0.279 1037 Planarity : 0.005 0.051 1224 Dihedral : 5.456 51.397 1048 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.61 % Allowed : 24.83 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.28), residues: 859 helix: -5.07 (0.33), residues: 14 sheet: -0.92 (0.27), residues: 359 loop : -1.74 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 109 HIS 0.003 0.001 HIS L 94 PHE 0.015 0.001 PHE A 64 TYR 0.013 0.001 TYR F 49 ARG 0.005 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 186 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 58 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6820 (pp) REVERT: H 10 GLU cc_start: 0.7284 (tp30) cc_final: 0.6649 (pm20) REVERT: H 19 LYS cc_start: 0.8310 (tttt) cc_final: 0.7740 (tttp) REVERT: H 87 THR cc_start: 0.7544 (OUTLIER) cc_final: 0.7282 (p) REVERT: H 113 GLN cc_start: 0.8613 (pt0) cc_final: 0.8171 (pm20) REVERT: F 4 MET cc_start: 0.7725 (mtp) cc_final: 0.6941 (mmm) REVERT: F 24 ARG cc_start: 0.7436 (mtp-110) cc_final: 0.7195 (ttt90) REVERT: F 78 LEU cc_start: 0.7570 (mm) cc_final: 0.7246 (mm) REVERT: F 90 GLN cc_start: 0.8119 (tm130) cc_final: 0.6899 (tm130) REVERT: F 105 GLU cc_start: 0.5735 (tt0) cc_final: 0.5373 (tt0) REVERT: A 10 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7869 (mm-30) REVERT: A 23 LYS cc_start: 0.6913 (tttt) cc_final: 0.6575 (ttpp) REVERT: A 43 GLN cc_start: 0.7751 (mp10) cc_final: 0.6923 (mp10) REVERT: A 57 ASP cc_start: 0.7815 (t0) cc_final: 0.7223 (t0) REVERT: C 38 ARG cc_start: 0.7454 (ttp80) cc_final: 0.6813 (ttm-80) REVERT: C 43 LYS cc_start: 0.8880 (mmmt) cc_final: 0.8357 (mmmt) REVERT: C 114 GLN cc_start: 0.8759 (mt0) cc_final: 0.8281 (mp10) REVERT: E 426 ARG cc_start: 0.8147 (tmm-80) cc_final: 0.7838 (ttp80) REVERT: E 447 LYS cc_start: 0.8537 (mppt) cc_final: 0.7990 (mtpt) outliers start: 34 outliers final: 25 residues processed: 202 average time/residue: 0.2271 time to fit residues: 58.5658 Evaluate side-chains 210 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 183 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 41 GLN Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 98 ILE Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 445 HIS Chi-restraints excluded: chain E residue 467 CYS Chi-restraints excluded: chain E residue 475 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 47 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 15 optimal weight: 0.4980 chunk 50 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 HIS A 39 GLN A 111 GLN D 30 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7056 Z= 0.254 Angle : 0.604 8.796 9597 Z= 0.309 Chirality : 0.043 0.282 1037 Planarity : 0.005 0.051 1224 Dihedral : 5.447 50.618 1048 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 5.29 % Allowed : 24.29 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.28), residues: 859 helix: -5.05 (0.34), residues: 14 sheet: -0.95 (0.27), residues: 367 loop : -1.73 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 109 HIS 0.004 0.001 HIS L 94 PHE 0.015 0.001 PHE A 64 TYR 0.015 0.001 TYR F 49 ARG 0.005 0.000 ARG E 449 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 179 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 58 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6821 (pp) REVERT: H 10 GLU cc_start: 0.7332 (tp30) cc_final: 0.6681 (pm20) REVERT: H 19 LYS cc_start: 0.8280 (tttt) cc_final: 0.7645 (tttp) REVERT: H 87 THR cc_start: 0.7570 (OUTLIER) cc_final: 0.7313 (p) REVERT: H 113 GLN cc_start: 0.8545 (pt0) cc_final: 0.8087 (pm20) REVERT: F 4 MET cc_start: 0.7755 (mtp) cc_final: 0.6976 (mmm) REVERT: F 24 ARG cc_start: 0.7416 (mtp-110) cc_final: 0.7175 (ttt90) REVERT: F 78 LEU cc_start: 0.7572 (mm) cc_final: 0.7252 (mm) REVERT: F 105 GLU cc_start: 0.5741 (tt0) cc_final: 0.5403 (tt0) REVERT: A 10 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7988 (mm-30) REVERT: A 19 LYS cc_start: 0.7861 (tttp) cc_final: 0.7393 (tptt) REVERT: A 23 LYS cc_start: 0.6915 (tttt) cc_final: 0.6579 (ttpp) REVERT: A 43 GLN cc_start: 0.7681 (mp10) cc_final: 0.7252 (mp10) REVERT: A 57 ASP cc_start: 0.7856 (t0) cc_final: 0.7265 (t0) REVERT: C 43 LYS cc_start: 0.8870 (mmmt) cc_final: 0.8351 (mmmt) REVERT: C 114 GLN cc_start: 0.8720 (mt0) cc_final: 0.8196 (mp10) REVERT: E 423 TRP cc_start: 0.7399 (OUTLIER) cc_final: 0.6778 (p-90) REVERT: E 426 ARG cc_start: 0.8135 (tmm-80) cc_final: 0.7808 (ttp80) REVERT: E 447 LYS cc_start: 0.8474 (mppt) cc_final: 0.7949 (mtpt) outliers start: 39 outliers final: 28 residues processed: 201 average time/residue: 0.2320 time to fit residues: 60.3157 Evaluate side-chains 206 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 175 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 41 GLN Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 98 ILE Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 423 TRP Chi-restraints excluded: chain E residue 467 CYS Chi-restraints excluded: chain E residue 475 TYR Chi-restraints excluded: chain E residue 480 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 0.6980 chunk 76 optimal weight: 0.3980 chunk 44 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 78 optimal weight: 0.0970 chunk 37 optimal weight: 0.1980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN L 27 GLN H 5 GLN A 111 GLN D 31 ASN C 82 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7056 Z= 0.168 Angle : 0.587 8.643 9597 Z= 0.298 Chirality : 0.043 0.282 1037 Planarity : 0.005 0.053 1224 Dihedral : 5.334 52.755 1048 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.34 % Allowed : 25.37 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.28), residues: 859 helix: -4.49 (0.68), residues: 20 sheet: -0.76 (0.28), residues: 345 loop : -1.67 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP A 109 HIS 0.002 0.001 HIS E 445 PHE 0.015 0.001 PHE A 64 TYR 0.011 0.001 TYR F 49 ARG 0.005 0.001 ARG E 449 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 187 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 10 GLU cc_start: 0.7319 (tp30) cc_final: 0.6643 (pm20) REVERT: H 19 LYS cc_start: 0.8293 (tttt) cc_final: 0.7753 (tttp) REVERT: H 87 THR cc_start: 0.7621 (OUTLIER) cc_final: 0.7366 (p) REVERT: H 113 GLN cc_start: 0.8434 (pt0) cc_final: 0.7920 (pm20) REVERT: F 4 MET cc_start: 0.7702 (mtp) cc_final: 0.6987 (mmm) REVERT: F 24 ARG cc_start: 0.7415 (mtp-110) cc_final: 0.6934 (mtp-110) REVERT: F 78 LEU cc_start: 0.7518 (mm) cc_final: 0.7165 (mm) REVERT: F 105 GLU cc_start: 0.5731 (tt0) cc_final: 0.5423 (tt0) REVERT: A 10 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7965 (mm-30) REVERT: A 23 LYS cc_start: 0.6899 (tttt) cc_final: 0.6559 (ttpp) REVERT: A 35 GLN cc_start: 0.7725 (mp10) cc_final: 0.7262 (mt0) REVERT: A 43 GLN cc_start: 0.7807 (mp10) cc_final: 0.7013 (mp10) REVERT: A 57 ASP cc_start: 0.7857 (t0) cc_final: 0.7245 (t0) REVERT: D 92 TRP cc_start: 0.9054 (t-100) cc_final: 0.8695 (t-100) REVERT: C 43 LYS cc_start: 0.8901 (mmmt) cc_final: 0.8383 (mmmt) REVERT: C 114 GLN cc_start: 0.8742 (mt0) cc_final: 0.8226 (mp10) REVERT: E 426 ARG cc_start: 0.8068 (tmm-80) cc_final: 0.7736 (ttp80) REVERT: E 447 LYS cc_start: 0.8452 (mppt) cc_final: 0.7933 (mtpt) outliers start: 32 outliers final: 26 residues processed: 203 average time/residue: 0.2143 time to fit residues: 55.7128 Evaluate side-chains 208 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 181 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 41 GLN Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 98 ILE Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 445 HIS Chi-restraints excluded: chain E residue 467 CYS Chi-restraints excluded: chain E residue 475 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 54 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 76 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 50 optimal weight: 0.0670 chunk 40 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN H 5 GLN A 111 GLN D 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7056 Z= 0.198 Angle : 0.585 8.318 9597 Z= 0.298 Chirality : 0.043 0.281 1037 Planarity : 0.005 0.052 1224 Dihedral : 5.275 51.528 1048 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.34 % Allowed : 24.83 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.28), residues: 859 helix: -4.96 (0.39), residues: 14 sheet: -0.78 (0.28), residues: 349 loop : -1.61 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 109 HIS 0.003 0.001 HIS L 94 PHE 0.014 0.001 PHE E 460 TYR 0.012 0.001 TYR F 49 ARG 0.005 0.000 ARG C 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 184 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 10 GLU cc_start: 0.7324 (tp30) cc_final: 0.6641 (pm20) REVERT: H 19 LYS cc_start: 0.8315 (tttt) cc_final: 0.7678 (tttp) REVERT: H 87 THR cc_start: 0.7651 (OUTLIER) cc_final: 0.7393 (p) REVERT: H 113 GLN cc_start: 0.8416 (pt0) cc_final: 0.7897 (pm20) REVERT: F 4 MET cc_start: 0.7700 (mtp) cc_final: 0.7020 (mmm) REVERT: F 24 ARG cc_start: 0.7415 (mtp-110) cc_final: 0.6942 (mtp-110) REVERT: F 78 LEU cc_start: 0.7569 (mm) cc_final: 0.7264 (mm) REVERT: F 105 GLU cc_start: 0.5722 (tt0) cc_final: 0.5408 (tt0) REVERT: A 10 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7916 (mm-30) REVERT: A 23 LYS cc_start: 0.6903 (tttt) cc_final: 0.6562 (ttpp) REVERT: A 43 GLN cc_start: 0.7787 (mp10) cc_final: 0.6996 (mp10) REVERT: A 57 ASP cc_start: 0.7869 (t0) cc_final: 0.7281 (t0) REVERT: D 92 TRP cc_start: 0.9044 (t-100) cc_final: 0.8770 (t-100) REVERT: C 43 LYS cc_start: 0.8926 (mmmt) cc_final: 0.8415 (mmmt) REVERT: C 114 GLN cc_start: 0.8727 (mt0) cc_final: 0.8177 (mp10) REVERT: E 423 TRP cc_start: 0.7396 (OUTLIER) cc_final: 0.6755 (p-90) REVERT: E 426 ARG cc_start: 0.8056 (tmm-80) cc_final: 0.7721 (ttp80) REVERT: E 447 LYS cc_start: 0.8441 (mppt) cc_final: 0.7909 (mtpt) outliers start: 32 outliers final: 26 residues processed: 201 average time/residue: 0.2190 time to fit residues: 56.3857 Evaluate side-chains 210 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 182 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 41 GLN Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 98 ILE Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 423 TRP Chi-restraints excluded: chain E residue 445 HIS Chi-restraints excluded: chain E residue 467 CYS Chi-restraints excluded: chain E residue 475 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 0.0050 chunk 57 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.106681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.085212 restraints weight = 12281.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.087740 restraints weight = 7181.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.089381 restraints weight = 5132.755| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2920 r_free = 0.2920 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2920 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7056 Z= 0.225 Angle : 0.592 8.128 9597 Z= 0.302 Chirality : 0.043 0.281 1037 Planarity : 0.005 0.051 1224 Dihedral : 5.254 51.112 1048 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 4.34 % Allowed : 25.24 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.28), residues: 859 helix: -4.98 (0.38), residues: 14 sheet: -0.76 (0.28), residues: 347 loop : -1.62 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 109 HIS 0.003 0.001 HIS L 94 PHE 0.015 0.001 PHE E 460 TYR 0.018 0.001 TYR C 50 ARG 0.004 0.000 ARG C 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2459.27 seconds wall clock time: 45 minutes 35.21 seconds (2735.21 seconds total)