Starting phenix.real_space_refine on Wed Feb 14 13:01:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rjd_4902/02_2024/6rjd_4902.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rjd_4902/02_2024/6rjd_4902.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rjd_4902/02_2024/6rjd_4902.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rjd_4902/02_2024/6rjd_4902.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rjd_4902/02_2024/6rjd_4902.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rjd_4902/02_2024/6rjd_4902.pdb" } resolution = 3.3 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 123 5.49 5 S 14 5.16 5 C 5476 2.51 5 N 1626 2.21 5 O 2093 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 26": "OE1" <-> "OE2" Residue "C ARG 46": "NH1" <-> "NH2" Residue "C ARG 47": "NH1" <-> "NH2" Residue "C ARG 57": "NH1" <-> "NH2" Residue "C GLU 72": "OE1" <-> "OE2" Residue "C GLU 104": "OE1" <-> "OE2" Residue "C TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 157": "OE1" <-> "OE2" Residue "C ARG 166": "NH1" <-> "NH2" Residue "C PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 179": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C GLU 217": "OE1" <-> "OE2" Residue "C ARG 223": "NH1" <-> "NH2" Residue "C ARG 235": "NH1" <-> "NH2" Residue "C ARG 240": "NH1" <-> "NH2" Residue "C GLU 246": "OE1" <-> "OE2" Residue "C ARG 267": "NH1" <-> "NH2" Residue "C GLU 277": "OE1" <-> "OE2" Residue "C GLU 299": "OE1" <-> "OE2" Residue "C ASP 333": "OD1" <-> "OD2" Residue "C TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 354": "NH1" <-> "NH2" Residue "C GLU 384": "OE1" <-> "OE2" Residue "C GLU 390": "OE1" <-> "OE2" Residue "C GLU 393": "OE1" <-> "OE2" Residue "C ARG 413": "NH1" <-> "NH2" Residue "C GLU 438": "OE1" <-> "OE2" Residue "C ASP 469": "OD1" <-> "OD2" Residue "C GLU 475": "OE1" <-> "OE2" Residue "C ARG 487": "NH1" <-> "NH2" Residue "C ARG 703": "NH1" <-> "NH2" Residue "C TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 815": "OD1" <-> "OD2" Residue "C TYR 828": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 831": "NH1" <-> "NH2" Residue "C GLU 842": "OE1" <-> "OE2" Residue "C ASP 859": "OD1" <-> "OD2" Residue "C TYR 865": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 875": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 876": "NH1" <-> "NH2" Residue "C GLU 883": "OE1" <-> "OE2" Residue "C ARG 921": "NH1" <-> "NH2" Residue "C TYR 937": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 947": "OD1" <-> "OD2" Residue "C ARG 966": "NH1" <-> "NH2" Residue "C PHE 971": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1002": "OE1" <-> "OE2" Residue "C ASP 1016": "OD1" <-> "OD2" Residue "C PHE 1021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1027": "OD1" <-> "OD2" Residue "C ARG 1047": "NH1" <-> "NH2" Residue "C GLU 1113": "OE1" <-> "OE2" Residue "C ASP 1115": "OD1" <-> "OD2" 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: 9332 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 6757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 831, 6757 Classifications: {'peptide': 831} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 811} Chain breaks: 6 Chain: "D" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1656 Classifications: {'RNA': 78} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 6, 'rna3p_pur': 37, 'rna3p_pyr': 32} Link IDs: {'rna2p': 9, 'rna3p': 68} Chain breaks: 2 Chain: "E" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 646 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "G" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 273 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Time building chain proxies: 7.66, per 1000 atoms: 0.82 Number of scatterers: 9332 At special positions: 0 Unit cell: (100.457, 133.35, 113.792, 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 14 16.00 P 123 15.00 O 2093 8.00 N 1626 7.00 C 5476 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.61 Conformation dependent library (CDL) restraints added in 1.2 seconds 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1560 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 6 sheets defined 43.1% alpha, 11.7% beta 38 base pairs and 83 stacking pairs defined. Time for finding SS restraints: 4.32 Creating SS restraints... Processing helix chain 'C' and resid 40 through 73 removed outlier: 3.725A pdb=" N LEU C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 98 removed outlier: 3.867A pdb=" N THR C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 115 removed outlier: 3.501A pdb=" N HIS C 115 " --> pdb=" O ASN C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 146 removed outlier: 4.257A pdb=" N ILE C 138 " --> pdb=" O ASP C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 163 Processing helix chain 'C' and resid 185 through 204 removed outlier: 3.732A pdb=" N TYR C 189 " --> pdb=" O PRO C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 220 Processing helix chain 'C' and resid 250 through 254 removed outlier: 3.541A pdb=" N GLY C 253 " --> pdb=" O ASN C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 287 removed outlier: 3.685A pdb=" N LEU C 287 " --> pdb=" O ASP C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 311 Processing helix chain 'C' and resid 315 through 328 removed outlier: 3.734A pdb=" N LEU C 319 " --> pdb=" O GLY C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 358 Processing helix chain 'C' and resid 369 through 382 Processing helix chain 'C' and resid 384 through 396 removed outlier: 3.784A pdb=" N ILE C 388 " --> pdb=" O GLU C 384 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE C 396 " --> pdb=" O LEU C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 416 Processing helix chain 'C' and resid 418 through 422 removed outlier: 3.621A pdb=" N GLY C 421 " --> pdb=" O SER C 418 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS C 422 " --> pdb=" O ILE C 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 418 through 422' Processing helix chain 'C' and resid 428 through 436 Processing helix chain 'C' and resid 437 through 439 No H-bonds generated for 'chain 'C' and resid 437 through 439' Processing helix chain 'C' and resid 445 through 453 Processing helix chain 'C' and resid 470 through 475 Processing helix chain 'C' and resid 479 through 501 Processing helix chain 'C' and resid 691 through 705 Processing helix chain 'C' and resid 737 through 748 Processing helix chain 'C' and resid 854 through 868 Processing helix chain 'C' and resid 869 through 872 removed outlier: 3.804A pdb=" N PHE C 872 " --> pdb=" O LYS C 869 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 869 through 872' Processing helix chain 'C' and resid 879 through 892 removed outlier: 3.880A pdb=" N GLU C 883 " --> pdb=" O PRO C 879 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS C 884 " --> pdb=" O GLN C 880 " (cutoff:3.500A) Proline residue: C 888 - end of helix Processing helix chain 'C' and resid 910 through 918 Processing helix chain 'C' and resid 1000 through 1012 removed outlier: 3.518A pdb=" N TYR C1004 " --> pdb=" O SER C1000 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 27 through 34 removed outlier: 6.651A pdb=" N ILE C 19 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LYS C 30 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL C 17 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N SER C 32 " --> pdb=" O VAL C 15 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N VAL C 15 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN C 505 " --> pdb=" O LEU C 4 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE C 508 " --> pdb=" O SER C 712 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 169 through 172 removed outlier: 3.558A pdb=" N HIS C 178 " --> pdb=" O VAL C 171 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 935 through 941 removed outlier: 5.768A pdb=" N LYS C 936 " --> pdb=" O ILE C 849 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE C 849 " --> pdb=" O LYS C 936 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N TYR C 938 " --> pdb=" O GLY C 847 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N GLY C 847 " --> pdb=" O TYR C 938 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER C 940 " --> pdb=" O VAL C 845 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ALA C 829 " --> pdb=" O LEU C 846 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 977 through 984 removed outlier: 3.553A pdb=" N LYS C 977 " --> pdb=" O ASN C 972 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG C 966 " --> pdb=" O LEU C 983 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE C1021 " --> pdb=" O VAL C 969 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N PHE C 971 " --> pdb=" O PHE C1019 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N PHE C1019 " --> pdb=" O PHE C 971 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 989 through 990 removed outlier: 3.878A pdb=" N GLN C 989 " --> pdb=" O LYS C 998 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS C 998 " --> pdb=" O GLN C 989 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 1057 through 1059 removed outlier: 5.516A pdb=" N LYS C1059 " --> pdb=" O PHE C1044 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N PHE C1044 " --> pdb=" O LYS C1059 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU C1028 " --> pdb=" O VAL C1099 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL C1099 " --> pdb=" O LEU C1028 " (cutoff:3.500A) 278 hydrogen bonds defined for protein. 819 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 91 hydrogen bonds 178 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 83 stacking parallelities Total time for adding SS restraints: 4.55 Time building geometry restraints manager: 4.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2012 1.33 - 1.45: 2680 1.45 - 1.57: 4789 1.57 - 1.69: 241 1.69 - 1.81: 25 Bond restraints: 9747 Sorted by residual: bond pdb=" N LYS C 706 " pdb=" CA LYS C 706 " ideal model delta sigma weight residual 1.460 1.485 -0.026 1.54e-02 4.22e+03 2.80e+00 bond pdb=" C3' DT E 11 " pdb=" O3' DT E 11 " ideal model delta sigma weight residual 1.422 1.472 -0.050 3.00e-02 1.11e+03 2.76e+00 bond pdb=" N GLU C 887 " pdb=" CA GLU C 887 " ideal model delta sigma weight residual 1.457 1.479 -0.022 1.41e-02 5.03e+03 2.42e+00 bond pdb=" CB ILE C 827 " pdb=" CG2 ILE C 827 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.36e+00 bond pdb=" C1' DC E 28 " pdb=" N1 DC E 28 " ideal model delta sigma weight residual 1.490 1.536 -0.046 3.00e-02 1.11e+03 2.32e+00 ... (remaining 9742 not shown) Histogram of bond angle deviations from ideal: 98.59 - 105.67: 662 105.67 - 112.74: 5174 112.74 - 119.81: 3469 119.81 - 126.89: 4012 126.89 - 133.96: 352 Bond angle restraints: 13669 Sorted by residual: angle pdb=" C LEU C 248 " pdb=" N ASP C 249 " pdb=" CA ASP C 249 " ideal model delta sigma weight residual 121.54 130.47 -8.93 1.91e+00 2.74e-01 2.19e+01 angle pdb=" C HIS C 705 " pdb=" N LYS C 706 " pdb=" CA LYS C 706 " ideal model delta sigma weight residual 122.46 128.07 -5.61 1.41e+00 5.03e-01 1.58e+01 angle pdb=" C LYS C 457 " pdb=" N THR C 458 " pdb=" CA THR C 458 " ideal model delta sigma weight residual 121.54 129.12 -7.58 1.91e+00 2.74e-01 1.58e+01 angle pdb=" C3' DG G 4 " pdb=" O3' DG G 4 " pdb=" P DA G 5 " ideal model delta sigma weight residual 120.20 125.98 -5.78 1.50e+00 4.44e-01 1.49e+01 angle pdb=" CA LYS C 466 " pdb=" CB LYS C 466 " pdb=" CG LYS C 466 " ideal model delta sigma weight residual 114.10 121.35 -7.25 2.00e+00 2.50e-01 1.31e+01 ... (remaining 13664 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.69: 5465 34.69 - 69.37: 405 69.37 - 104.06: 25 104.06 - 138.74: 0 138.74 - 173.43: 2 Dihedral angle restraints: 5897 sinusoidal: 3470 harmonic: 2427 Sorted by residual: dihedral pdb=" CA ASP C 368 " pdb=" C ASP C 368 " pdb=" N ARG C 369 " pdb=" CA ARG C 369 " ideal model delta harmonic sigma weight residual 180.00 157.77 22.23 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA HIS C 115 " pdb=" C HIS C 115 " pdb=" N ARG C 116 " pdb=" CA ARG C 116 " ideal model delta harmonic sigma weight residual 180.00 160.11 19.89 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" C4' DG G 4 " pdb=" C3' DG G 4 " pdb=" O3' DG G 4 " pdb=" P DA G 5 " ideal model delta sinusoidal sigma weight residual -140.00 33.43 -173.43 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 5894 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1088 0.046 - 0.093: 361 0.093 - 0.139: 106 0.139 - 0.186: 18 0.186 - 0.232: 6 Chirality restraints: 1579 Sorted by residual: chirality pdb=" CB ILE C 339 " pdb=" CA ILE C 339 " pdb=" CG1 ILE C 339 " pdb=" CG2 ILE C 339 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CB ILE C 886 " pdb=" CA ILE C 886 " pdb=" CG1 ILE C 886 " pdb=" CG2 ILE C 886 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" C1' A D 68 " pdb=" O4' A D 68 " pdb=" C2' A D 68 " pdb=" N9 A D 68 " both_signs ideal model delta sigma weight residual False 2.46 2.24 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1576 not shown) Planarity restraints: 1301 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A D 63 " -0.030 2.00e-02 2.50e+03 1.81e-02 8.98e+00 pdb=" N9 A D 63 " 0.049 2.00e-02 2.50e+03 pdb=" C8 A D 63 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A D 63 " -0.000 2.00e-02 2.50e+03 pdb=" C5 A D 63 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A D 63 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A D 63 " -0.005 2.00e-02 2.50e+03 pdb=" N1 A D 63 " 0.000 2.00e-02 2.50e+03 pdb=" C2 A D 63 " 0.004 2.00e-02 2.50e+03 pdb=" N3 A D 63 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A D 63 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 466 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.88e+00 pdb=" C LYS C 466 " -0.045 2.00e-02 2.50e+03 pdb=" O LYS C 466 " 0.017 2.00e-02 2.50e+03 pdb=" N TYR C 467 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 249 " -0.013 2.00e-02 2.50e+03 2.57e-02 6.59e+00 pdb=" C ASP C 249 " 0.044 2.00e-02 2.50e+03 pdb=" O ASP C 249 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN C 250 " -0.015 2.00e-02 2.50e+03 ... (remaining 1298 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2004 2.79 - 3.32: 7363 3.32 - 3.84: 15404 3.84 - 4.37: 18273 4.37 - 4.90: 28971 Nonbonded interactions: 72015 Sorted by model distance: nonbonded pdb=" OH TYR C 89 " pdb=" OP1 A D 63 " model vdw 2.259 2.440 nonbonded pdb=" O ALA C 376 " pdb=" OG1 THR C 380 " model vdw 2.304 2.440 nonbonded pdb=" O SER C 119 " pdb=" OG SER C 119 " model vdw 2.317 2.440 nonbonded pdb=" OG1 THR C 830 " pdb=" O LYS C 956 " model vdw 2.324 2.440 nonbonded pdb=" OD2 ASP C 968 " pdb=" OH TYR C1004 " model vdw 2.346 2.440 ... (remaining 72010 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.010 Check model and map are aligned: 0.150 Set scattering table: 0.080 Process input model: 37.710 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 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 0.051 9747 Z= 0.341 Angle : 0.900 11.110 13669 Z= 0.489 Chirality : 0.052 0.232 1579 Planarity : 0.006 0.041 1301 Dihedral : 20.281 173.426 4337 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 0.27 % Allowed : 10.28 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.23), residues: 817 helix: -2.01 (0.22), residues: 328 sheet: -2.03 (0.50), residues: 100 loop : -2.69 (0.25), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP C 965 HIS 0.006 0.001 HIS C 348 PHE 0.029 0.002 PHE C 169 TYR 0.038 0.002 TYR C1055 ARG 0.015 0.001 ARG C 166 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 112 time to evaluate : 0.832 Fit side-chains revert: symmetry clash REVERT: C 367 MET cc_start: 0.4696 (mmm) cc_final: 0.4342 (mtp) REVERT: C 437 PRO cc_start: 0.8637 (Cg_exo) cc_final: 0.8267 (Cg_endo) REVERT: C 438 GLU cc_start: 0.8051 (mp0) cc_final: 0.7160 (mp0) REVERT: C 465 THR cc_start: 0.7825 (m) cc_final: 0.7375 (p) REVERT: C 487 ARG cc_start: 0.7048 (mtp180) cc_final: 0.6255 (mtm180) REVERT: C 699 GLN cc_start: 0.6582 (mt0) cc_final: 0.6113 (tt0) REVERT: C 869 LYS cc_start: 0.8139 (mttt) cc_final: 0.7669 (ttpt) REVERT: C 921 ARG cc_start: 0.8441 (mtt-85) cc_final: 0.8082 (mtp85) REVERT: C 931 GLU cc_start: 0.7496 (mp0) cc_final: 0.7289 (mp0) REVERT: C 1047 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7516 (tpt-90) outliers start: 2 outliers final: 0 residues processed: 114 average time/residue: 0.2814 time to fit residues: 41.6803 Evaluate side-chains 69 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1047 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 300 GLN C 494 ASN C 928 ASN C1054 HIS C1108 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9747 Z= 0.192 Angle : 0.565 7.146 13669 Z= 0.303 Chirality : 0.036 0.131 1579 Planarity : 0.003 0.031 1301 Dihedral : 20.398 176.540 2601 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.44 % Allowed : 14.48 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.26), residues: 817 helix: 0.04 (0.26), residues: 337 sheet: -1.66 (0.49), residues: 100 loop : -2.50 (0.26), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 965 HIS 0.005 0.001 HIS C 178 PHE 0.011 0.001 PHE C1021 TYR 0.020 0.001 TYR C1055 ARG 0.003 0.000 ARG C 166 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 79 time to evaluate : 0.854 Fit side-chains REVERT: C 339 ILE cc_start: 0.8721 (tt) cc_final: 0.8424 (tp) REVERT: C 346 GLU cc_start: 0.7477 (tm-30) cc_final: 0.7150 (tm-30) REVERT: C 367 MET cc_start: 0.4794 (mmm) cc_final: 0.4352 (mtp) REVERT: C 438 GLU cc_start: 0.8115 (mp0) cc_final: 0.7323 (mp0) REVERT: C 465 THR cc_start: 0.7522 (m) cc_final: 0.7039 (p) REVERT: C 487 ARG cc_start: 0.6984 (mtp180) cc_final: 0.6098 (mtm180) REVERT: C 699 GLN cc_start: 0.6578 (mt0) cc_final: 0.6083 (tt0) REVERT: C 869 LYS cc_start: 0.8107 (mttt) cc_final: 0.7638 (ttpt) REVERT: C 921 ARG cc_start: 0.8453 (mtt-85) cc_final: 0.8158 (mtp85) outliers start: 18 outliers final: 11 residues processed: 94 average time/residue: 0.2557 time to fit residues: 32.6297 Evaluate side-chains 72 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 61 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 877 HIS Chi-restraints excluded: chain C residue 928 ASN Chi-restraints excluded: chain C residue 1066 PHE Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain C residue 1104 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 145 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9747 Z= 0.310 Angle : 0.632 8.350 13669 Z= 0.334 Chirality : 0.039 0.136 1579 Planarity : 0.004 0.036 1301 Dihedral : 20.383 175.252 2597 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 3.65 % Allowed : 16.64 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.27), residues: 817 helix: 0.64 (0.27), residues: 337 sheet: -1.10 (0.53), residues: 87 loop : -2.49 (0.26), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 965 HIS 0.003 0.001 HIS C 61 PHE 0.015 0.002 PHE C1021 TYR 0.024 0.002 TYR C1055 ARG 0.003 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 66 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 157 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6944 (mp0) REVERT: C 337 TYR cc_start: 0.7621 (p90) cc_final: 0.7276 (p90) REVERT: C 339 ILE cc_start: 0.8724 (tt) cc_final: 0.8393 (tp) REVERT: C 346 GLU cc_start: 0.7576 (tm-30) cc_final: 0.7209 (tm-30) REVERT: C 367 MET cc_start: 0.5067 (mmm) cc_final: 0.4256 (mtp) REVERT: C 438 GLU cc_start: 0.8198 (mp0) cc_final: 0.7160 (mp0) REVERT: C 465 THR cc_start: 0.7253 (m) cc_final: 0.6730 (p) REVERT: C 487 ARG cc_start: 0.7071 (mtp180) cc_final: 0.6177 (mtm110) REVERT: C 699 GLN cc_start: 0.6648 (mt0) cc_final: 0.6133 (tt0) REVERT: C 869 LYS cc_start: 0.8112 (mttt) cc_final: 0.7850 (mtmt) REVERT: C 921 ARG cc_start: 0.8546 (mtt-85) cc_final: 0.8325 (mtp85) outliers start: 27 outliers final: 19 residues processed: 89 average time/residue: 0.2476 time to fit residues: 30.4741 Evaluate side-chains 80 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 60 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 877 HIS Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 886 ILE Chi-restraints excluded: chain C residue 928 ASN Chi-restraints excluded: chain C residue 954 ASN Chi-restraints excluded: chain C residue 1047 ARG Chi-restraints excluded: chain C residue 1066 PHE Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain C residue 1104 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 145 GLN C 928 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 9747 Z= 0.340 Angle : 0.654 12.379 13669 Z= 0.342 Chirality : 0.041 0.138 1579 Planarity : 0.004 0.038 1301 Dihedral : 20.481 174.276 2597 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 4.47 % Allowed : 18.13 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.28), residues: 817 helix: 0.84 (0.27), residues: 337 sheet: -1.10 (0.54), residues: 85 loop : -2.47 (0.27), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP C 965 HIS 0.003 0.001 HIS C 61 PHE 0.017 0.002 PHE C 184 TYR 0.023 0.002 TYR C1055 ARG 0.003 0.000 ARG C 413 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 58 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: C 157 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6902 (mp0) REVERT: C 337 TYR cc_start: 0.7714 (p90) cc_final: 0.7312 (p90) REVERT: C 346 GLU cc_start: 0.7555 (tm-30) cc_final: 0.7150 (tm-30) REVERT: C 438 GLU cc_start: 0.8178 (mp0) cc_final: 0.7237 (mp0) REVERT: C 487 ARG cc_start: 0.7102 (mtp180) cc_final: 0.6347 (mtm110) REVERT: C 699 GLN cc_start: 0.6634 (mt0) cc_final: 0.6191 (tt0) REVERT: C 869 LYS cc_start: 0.8102 (mttt) cc_final: 0.7839 (mtmt) outliers start: 33 outliers final: 20 residues processed: 85 average time/residue: 0.2220 time to fit residues: 26.4761 Evaluate side-chains 78 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 57 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 367 MET Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 877 HIS Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 886 ILE Chi-restraints excluded: chain C residue 928 ASN Chi-restraints excluded: chain C residue 1022 THR Chi-restraints excluded: chain C residue 1047 ARG Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain C residue 1104 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 20.0000 chunk 1 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 77 optimal weight: 0.0870 chunk 62 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- 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: 0.8122 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9747 Z= 0.289 Angle : 0.616 11.290 13669 Z= 0.323 Chirality : 0.039 0.138 1579 Planarity : 0.004 0.040 1301 Dihedral : 20.431 174.627 2597 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 4.87 % Allowed : 18.94 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.28), residues: 817 helix: 1.05 (0.28), residues: 337 sheet: -1.04 (0.55), residues: 85 loop : -2.39 (0.27), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 965 HIS 0.003 0.001 HIS C 61 PHE 0.013 0.002 PHE C1021 TYR 0.017 0.002 TYR C1055 ARG 0.003 0.000 ARG C 413 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 62 time to evaluate : 1.070 Fit side-chains revert: symmetry clash REVERT: C 157 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6901 (mp0) REVERT: C 337 TYR cc_start: 0.7790 (p90) cc_final: 0.7385 (p90) REVERT: C 438 GLU cc_start: 0.8141 (mp0) cc_final: 0.7220 (mp0) REVERT: C 487 ARG cc_start: 0.7094 (mtp180) cc_final: 0.6333 (mtm110) REVERT: C 699 GLN cc_start: 0.6600 (mt0) cc_final: 0.6189 (tt0) REVERT: C 869 LYS cc_start: 0.8103 (mttt) cc_final: 0.7846 (mtmt) outliers start: 36 outliers final: 27 residues processed: 93 average time/residue: 0.2367 time to fit residues: 31.0612 Evaluate side-chains 85 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 57 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 367 MET Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain C residue 877 HIS Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 886 ILE Chi-restraints excluded: chain C residue 928 ASN Chi-restraints excluded: chain C residue 954 ASN Chi-restraints excluded: chain C residue 1022 THR Chi-restraints excluded: chain C residue 1047 ARG Chi-restraints excluded: chain C residue 1066 PHE Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain C residue 1104 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 7 optimal weight: 0.0770 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 overall best weight: 1.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 928 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9747 Z= 0.174 Angle : 0.538 10.040 13669 Z= 0.283 Chirality : 0.035 0.131 1579 Planarity : 0.003 0.034 1301 Dihedral : 20.196 176.933 2597 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.92 % Allowed : 19.89 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.29), residues: 817 helix: 1.49 (0.28), residues: 337 sheet: -0.79 (0.56), residues: 87 loop : -2.27 (0.27), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 965 HIS 0.003 0.001 HIS C1108 PHE 0.010 0.001 PHE C1066 TYR 0.011 0.001 TYR C 215 ARG 0.002 0.000 ARG C 413 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 65 time to evaluate : 1.036 Fit side-chains revert: symmetry clash REVERT: C 157 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6853 (mp0) REVERT: C 178 HIS cc_start: 0.6610 (p-80) cc_final: 0.6335 (p90) REVERT: C 337 TYR cc_start: 0.7861 (p90) cc_final: 0.7480 (p90) REVERT: C 339 ILE cc_start: 0.8767 (tt) cc_final: 0.8406 (tp) REVERT: C 367 MET cc_start: 0.4889 (OUTLIER) cc_final: 0.3967 (mtp) REVERT: C 438 GLU cc_start: 0.8113 (mp0) cc_final: 0.7156 (mp0) REVERT: C 487 ARG cc_start: 0.7002 (mtp180) cc_final: 0.6133 (mtm110) REVERT: C 503 PHE cc_start: 0.6141 (m-80) cc_final: 0.5894 (m-80) REVERT: C 699 GLN cc_start: 0.6505 (mt0) cc_final: 0.6072 (tt0) REVERT: C 869 LYS cc_start: 0.8078 (mttt) cc_final: 0.7862 (mtmt) outliers start: 29 outliers final: 21 residues processed: 91 average time/residue: 0.2285 time to fit residues: 28.9770 Evaluate side-chains 83 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 60 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 367 MET Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain C residue 877 HIS Chi-restraints excluded: chain C residue 886 ILE Chi-restraints excluded: chain C residue 887 GLU Chi-restraints excluded: chain C residue 928 ASN Chi-restraints excluded: chain C residue 954 ASN Chi-restraints excluded: chain C residue 1066 PHE Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain C residue 1104 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 55 optimal weight: 0.7980 chunk 41 optimal weight: 0.2980 chunk 36 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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: 0.8043 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9747 Z= 0.164 Angle : 0.533 9.515 13669 Z= 0.278 Chirality : 0.035 0.131 1579 Planarity : 0.003 0.034 1301 Dihedral : 20.096 178.052 2597 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.65 % Allowed : 19.89 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.29), residues: 817 helix: 1.70 (0.28), residues: 337 sheet: -0.71 (0.56), residues: 87 loop : -2.18 (0.28), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 965 HIS 0.002 0.000 HIS C 61 PHE 0.009 0.001 PHE C1066 TYR 0.011 0.001 TYR C 215 ARG 0.002 0.000 ARG C 413 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 67 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: C 157 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6908 (mp0) REVERT: C 337 TYR cc_start: 0.7871 (p90) cc_final: 0.7483 (p90) REVERT: C 339 ILE cc_start: 0.8765 (tt) cc_final: 0.8399 (tp) REVERT: C 367 MET cc_start: 0.4910 (OUTLIER) cc_final: 0.4035 (mtp) REVERT: C 438 GLU cc_start: 0.8077 (mp0) cc_final: 0.7084 (mp0) REVERT: C 487 ARG cc_start: 0.6980 (mtp180) cc_final: 0.6126 (mtm110) REVERT: C 503 PHE cc_start: 0.6154 (m-80) cc_final: 0.5879 (m-80) REVERT: C 699 GLN cc_start: 0.6510 (mt0) cc_final: 0.6094 (tt0) REVERT: C 869 LYS cc_start: 0.8086 (mttt) cc_final: 0.7877 (mtmt) outliers start: 27 outliers final: 24 residues processed: 91 average time/residue: 0.2191 time to fit residues: 27.8861 Evaluate side-chains 83 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 57 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 367 MET Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain C residue 877 HIS Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 886 ILE Chi-restraints excluded: chain C residue 887 GLU Chi-restraints excluded: chain C residue 954 ASN Chi-restraints excluded: chain C residue 1066 PHE Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain C residue 1104 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 57 optimal weight: 0.0970 chunk 61 optimal weight: 0.4980 chunk 44 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 928 ASN C1108 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9747 Z= 0.131 Angle : 0.505 8.915 13669 Z= 0.262 Chirality : 0.034 0.128 1579 Planarity : 0.003 0.033 1301 Dihedral : 19.990 179.012 2597 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.92 % Allowed : 19.62 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.29), residues: 817 helix: 1.95 (0.29), residues: 337 sheet: -0.82 (0.52), residues: 100 loop : -1.92 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 965 HIS 0.004 0.001 HIS C1108 PHE 0.009 0.001 PHE C1066 TYR 0.009 0.001 TYR C 978 ARG 0.002 0.000 ARG C 413 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 73 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 157 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6833 (mp0) REVERT: C 337 TYR cc_start: 0.7871 (p90) cc_final: 0.7482 (p90) REVERT: C 339 ILE cc_start: 0.8760 (tt) cc_final: 0.8401 (tp) REVERT: C 367 MET cc_start: 0.4679 (mmm) cc_final: 0.3885 (mtp) REVERT: C 414 LYS cc_start: 0.7645 (mttm) cc_final: 0.7325 (tttm) REVERT: C 438 GLU cc_start: 0.8031 (mp0) cc_final: 0.7100 (mp0) REVERT: C 487 ARG cc_start: 0.6989 (mtp180) cc_final: 0.6171 (mtm110) REVERT: C 503 PHE cc_start: 0.6055 (m-80) cc_final: 0.5775 (m-80) REVERT: C 699 GLN cc_start: 0.6490 (mt0) cc_final: 0.6095 (tt0) REVERT: C 869 LYS cc_start: 0.8093 (mttt) cc_final: 0.7893 (mtmt) outliers start: 29 outliers final: 22 residues processed: 100 average time/residue: 0.2242 time to fit residues: 31.0398 Evaluate side-chains 87 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 64 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 887 GLU Chi-restraints excluded: chain C residue 928 ASN Chi-restraints excluded: chain C residue 1022 THR Chi-restraints excluded: chain C residue 1047 ARG Chi-restraints excluded: chain C residue 1066 PHE Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain C residue 1104 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 178 HIS C 928 ASN C 954 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9747 Z= 0.289 Angle : 0.603 8.606 13669 Z= 0.314 Chirality : 0.038 0.135 1579 Planarity : 0.004 0.040 1301 Dihedral : 19.975 177.818 2597 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 4.33 % Allowed : 19.22 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.29), residues: 817 helix: 1.60 (0.28), residues: 341 sheet: -0.67 (0.57), residues: 85 loop : -2.12 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 965 HIS 0.005 0.001 HIS C1108 PHE 0.013 0.002 PHE C1021 TYR 0.017 0.002 TYR C1055 ARG 0.003 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 57 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 157 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6883 (mp0) REVERT: C 337 TYR cc_start: 0.7851 (p90) cc_final: 0.7414 (p90) REVERT: C 438 GLU cc_start: 0.8158 (mp0) cc_final: 0.7193 (mp0) REVERT: C 487 ARG cc_start: 0.7106 (mtp180) cc_final: 0.6275 (mtm110) REVERT: C 503 PHE cc_start: 0.6310 (m-80) cc_final: 0.5924 (m-80) REVERT: C 699 GLN cc_start: 0.6545 (mt0) cc_final: 0.6107 (tt0) REVERT: C 869 LYS cc_start: 0.8132 (mttt) cc_final: 0.7921 (mtmt) outliers start: 32 outliers final: 27 residues processed: 88 average time/residue: 0.2319 time to fit residues: 28.2660 Evaluate side-chains 84 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 56 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 477 ILE Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain C residue 877 HIS Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 886 ILE Chi-restraints excluded: chain C residue 887 GLU Chi-restraints excluded: chain C residue 928 ASN Chi-restraints excluded: chain C residue 1022 THR Chi-restraints excluded: chain C residue 1047 ARG Chi-restraints excluded: chain C residue 1066 PHE Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain C residue 1104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 9747 Z= 0.441 Angle : 0.729 9.199 13669 Z= 0.379 Chirality : 0.044 0.157 1579 Planarity : 0.005 0.051 1301 Dihedral : 20.137 172.348 2597 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 4.19 % Allowed : 19.62 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.28), residues: 817 helix: 1.02 (0.28), residues: 346 sheet: -1.03 (0.62), residues: 75 loop : -2.25 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP C 965 HIS 0.007 0.001 HIS C1108 PHE 0.019 0.002 PHE C1021 TYR 0.022 0.002 TYR C1055 ARG 0.004 0.000 ARG C 166 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 59 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: C 157 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6138 (mp0) REVERT: C 438 GLU cc_start: 0.8226 (mp0) cc_final: 0.7410 (mp0) REVERT: C 470 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.6006 (mt-10) REVERT: C 487 ARG cc_start: 0.7123 (mtp180) cc_final: 0.6331 (mtm110) REVERT: C 699 GLN cc_start: 0.6630 (mt0) cc_final: 0.6161 (tt0) REVERT: C 869 LYS cc_start: 0.8057 (mttt) cc_final: 0.7840 (mtmt) outliers start: 31 outliers final: 25 residues processed: 87 average time/residue: 0.2418 time to fit residues: 29.0231 Evaluate side-chains 84 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 57 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 877 HIS Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 886 ILE Chi-restraints excluded: chain C residue 928 ASN Chi-restraints excluded: chain C residue 1022 THR Chi-restraints excluded: chain C residue 1047 ARG Chi-restraints excluded: chain C residue 1066 PHE Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain C residue 1104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 74 optimal weight: 0.3980 chunk 31 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 53 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 928 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.160044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.128116 restraints weight = 14144.856| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.01 r_work: 0.3313 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9747 Z= 0.144 Angle : 0.543 8.353 13669 Z= 0.281 Chirality : 0.035 0.134 1579 Planarity : 0.003 0.033 1301 Dihedral : 19.971 175.860 2597 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.25 % Allowed : 21.11 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.29), residues: 817 helix: 1.68 (0.28), residues: 337 sheet: -0.75 (0.57), residues: 85 loop : -2.01 (0.28), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 965 HIS 0.002 0.001 HIS C 61 PHE 0.011 0.001 PHE C1066 TYR 0.023 0.001 TYR C 978 ARG 0.002 0.000 ARG C 166 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1886.83 seconds wall clock time: 35 minutes 5.59 seconds (2105.59 seconds total)