Starting phenix.real_space_refine on Wed Feb 14 13:55:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsw_30169/02_2024/7bsw_30169_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsw_30169/02_2024/7bsw_30169.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsw_30169/02_2024/7bsw_30169.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsw_30169/02_2024/7bsw_30169.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsw_30169/02_2024/7bsw_30169_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsw_30169/02_2024/7bsw_30169_trim_updated.pdb" } resolution = 3.9 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= 0.001 sd= 0.008 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: 7 Type Number sf(0) Gaussians Al 1 5.89 5 P 1 5.49 5 S 45 5.16 5 C 6078 2.51 5 N 1504 2.21 5 O 1696 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 62": "OE1" <-> "OE2" Residue "A GLU 129": "OE1" <-> "OE2" Residue "A ARG 135": "NH1" <-> "NH2" Residue "A GLU 137": "OE1" <-> "OE2" Residue "A GLU 210": "OE1" <-> "OE2" Residue "A GLU 233": "OE1" <-> "OE2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A GLU 383": "OE1" <-> "OE2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "A GLU 699": "OE1" <-> "OE2" Residue "A GLU 707": "OE1" <-> "OE2" Residue "A GLU 837": "OE1" <-> "OE2" Residue "A ARG 839": "NH1" <-> "NH2" Residue "A GLU 984": "OE1" <-> "OE2" Residue "A PHE 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1052": "NH1" <-> "NH2" Residue "C ARG 76": "NH1" <-> "NH2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "C GLU 164": "OE1" <-> "OE2" Residue "C TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 309": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9329 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 815, 6596 Classifications: {'peptide': 815} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 792} Chain breaks: 3 Chain: "C" Number of atoms: 2613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2613 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 298} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ALF': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "C" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 66 Unusual residues: {'MAN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 5.40, per 1000 atoms: 0.58 Number of scatterers: 9329 At special positions: 0 Unit cell: (97.2, 105.3, 141.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 45 16.00 P 1 15.00 Al 1 13.00 F 4 9.00 O 1696 8.00 N 1504 7.00 C 6078 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 91 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 102 " distance=2.02 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM 9314 O5 NAG C 404 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9314 O5 NAG C 404 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " NAG C 402 " - " MAN C 403 " BETA1-4 " NAG C 401 " - " NAG C 402 " NAG-ASN " NAG C 401 " - " ASN C 180 " " NAG C 404 " - " ASN C 294 " " NAG C 405 " - " ASN C 107 " Time building additional restraints: 3.81 Conformation dependent library (CDL) restraints added in 1.7 seconds 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 9 sheets defined 37.1% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'A' and resid 55 through 63 removed outlier: 4.197A pdb=" N PHE A 61 " --> pdb=" O PRO A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 81 removed outlier: 3.915A pdb=" N LEU A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'A' and resid 94 through 118 removed outlier: 3.686A pdb=" N ILE A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR A 102 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ARG A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 140 No H-bonds generated for 'chain 'A' and resid 138 through 140' Processing helix chain 'A' and resid 287 through 313 removed outlier: 3.752A pdb=" N PHE A 297 " --> pdb=" O ILE A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 333 No H-bonds generated for 'chain 'A' and resid 330 through 333' Processing helix chain 'A' and resid 336 through 350 removed outlier: 3.772A pdb=" N PHE A 341 " --> pdb=" O VAL A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 354 No H-bonds generated for 'chain 'A' and resid 352 through 354' Processing helix chain 'A' and resid 361 through 370 removed outlier: 4.097A pdb=" N MET A 365 " --> pdb=" O VAL A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 376 Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 658 through 665 Processing helix chain 'A' and resid 680 through 687 removed outlier: 3.699A pdb=" N CYS A 685 " --> pdb=" O ALA A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 719 Processing helix chain 'A' and resid 755 through 761 Processing helix chain 'A' and resid 771 through 781 Processing helix chain 'A' and resid 792 through 801 removed outlier: 3.955A pdb=" N ALA A 796 " --> pdb=" O PRO A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 826 No H-bonds generated for 'chain 'A' and resid 823 through 826' Processing helix chain 'A' and resid 854 through 860 removed outlier: 3.766A pdb=" N LEU A 859 " --> pdb=" O LEU A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 893 removed outlier: 4.246A pdb=" N ASN A 881 " --> pdb=" O PHE A 877 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE A 884 " --> pdb=" O LYS A 880 " (cutoff:3.500A) Proline residue: A 887 - end of helix removed outlier: 4.669A pdb=" N GLN A 892 " --> pdb=" O GLN A 888 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE A 893 " --> pdb=" O PHE A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 910 No H-bonds generated for 'chain 'A' and resid 907 through 910' Processing helix chain 'A' and resid 919 through 925 Processing helix chain 'A' and resid 932 through 935 No H-bonds generated for 'chain 'A' and resid 932 through 935' Processing helix chain 'A' and resid 939 through 943 removed outlier: 3.600A pdb=" N TYR A 942 " --> pdb=" O PRO A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 951 No H-bonds generated for 'chain 'A' and resid 949 through 951' Processing helix chain 'A' and resid 953 through 978 removed outlier: 3.715A pdb=" N ALA A 964 " --> pdb=" O THR A 960 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE A 965 " --> pdb=" O PHE A 961 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N THR A 968 " --> pdb=" O ALA A 964 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE A 971 " --> pdb=" O GLY A 967 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 977 " --> pdb=" O GLY A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1014 removed outlier: 3.762A pdb=" N GLY A 996 " --> pdb=" O ASN A 992 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU A1011 " --> pdb=" O VAL A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1040 removed outlier: 3.658A pdb=" N PHE A1024 " --> pdb=" O TRP A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1061 Processing helix chain 'A' and resid 1064 through 1076 removed outlier: 3.648A pdb=" N LEU A1068 " --> pdb=" O VAL A1064 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE A1075 " --> pdb=" O ILE A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1087 Processing helix chain 'C' and resid 47 through 70 Proline residue: C 52 - end of helix removed outlier: 3.631A pdb=" N PHE C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY C 58 " --> pdb=" O PHE C 54 " (cutoff:3.500A) Proline residue: C 63 - end of helix Processing helix chain 'C' and resid 92 through 94 No H-bonds generated for 'chain 'C' and resid 92 through 94' Processing helix chain 'C' and resid 132 through 135 No H-bonds generated for 'chain 'C' and resid 132 through 135' Processing helix chain 'C' and resid 140 through 143 No H-bonds generated for 'chain 'C' and resid 140 through 143' Processing helix chain 'C' and resid 149 through 151 No H-bonds generated for 'chain 'C' and resid 149 through 151' Processing helix chain 'C' and resid 173 through 176 No H-bonds generated for 'chain 'C' and resid 173 through 176' Processing helix chain 'C' and resid 207 through 211 Processing helix chain 'C' and resid 240 through 242 No H-bonds generated for 'chain 'C' and resid 240 through 242' Processing helix chain 'C' and resid 255 through 261 Processing helix chain 'C' and resid 324 through 349 removed outlier: 3.618A pdb=" N LEU C 339 " --> pdb=" O ILE C 335 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 20 through 23 Processing sheet with id= B, first strand: chain 'A' and resid 124 through 128 Processing sheet with id= C, first strand: chain 'A' and resid 146 through 150 removed outlier: 4.123A pdb=" N VAL A 149 " --> pdb=" O ILE A 257 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 172 through 174 removed outlier: 3.814A pdb=" N TYR A 172 " --> pdb=" O LYS A 252 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A 250 " --> pdb=" O THR A 174 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 405 through 408 removed outlier: 6.799A pdb=" N LYS A 669 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N THR A 408 " --> pdb=" O LYS A 669 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N TRP A 671 " --> pdb=" O THR A 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 696 through 699 removed outlier: 3.740A pdb=" N GLY A 748 " --> pdb=" O GLU A 696 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 812 through 815 removed outlier: 6.861A pdb=" N VAL A 829 " --> pdb=" O SER A 813 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N GLY A 815 " --> pdb=" O VAL A 829 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ILE A 831 " --> pdb=" O GLY A 815 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'C' and resid 77 through 81 removed outlier: 3.517A pdb=" N ARG C 309 " --> pdb=" O GLY C 123 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N TYR C 122 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LEU C 272 " --> pdb=" O TYR C 122 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 108 through 110 removed outlier: 3.588A pdb=" N PHE C 108 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ARG C 290 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE C 188 " --> pdb=" O ARG C 290 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR C 182 " --> pdb=" O THR C 296 " (cutoff:3.500A) 264 hydrogen bonds defined for protein. 774 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: 2.51 Time building geometry restraints manager: 4.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1518 1.32 - 1.45: 2643 1.45 - 1.57: 5325 1.57 - 1.69: 2 1.69 - 1.81: 71 Bond restraints: 9559 Sorted by residual: bond pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.684 1.799 -0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" F3 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.685 1.799 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" F4 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.686 1.800 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" F2 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.685 1.797 -0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" N THR C 100 " pdb=" CA THR C 100 " ideal model delta sigma weight residual 1.455 1.487 -0.032 9.60e-03 1.09e+04 1.13e+01 ... (remaining 9554 not shown) Histogram of bond angle deviations from ideal: 89.68 - 107.68: 361 107.68 - 125.68: 12444 125.68 - 143.68: 154 143.68 - 161.68: 0 161.68 - 179.69: 2 Bond angle restraints: 12961 Sorted by residual: angle pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " pdb=" F2 ALF A1101 " ideal model delta sigma weight residual 108.68 179.22 -70.54 3.00e+00 1.11e-01 5.53e+02 angle pdb=" F3 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 109.63 179.69 -70.06 3.00e+00 1.11e-01 5.45e+02 angle pdb=" N LYS A1088 " pdb=" CA LYS A1088 " pdb=" C LYS A1088 " ideal model delta sigma weight residual 112.93 103.39 9.54 1.12e+00 7.97e-01 7.26e+01 angle pdb=" F2 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 110.21 90.20 20.01 3.00e+00 1.11e-01 4.45e+01 angle pdb=" F2 ALF A1101 " pdb="AL ALF A1101 " pdb=" F3 ALF A1101 " ideal model delta sigma weight residual 109.59 89.68 19.91 3.00e+00 1.11e-01 4.41e+01 ... (remaining 12956 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.09: 5428 26.09 - 52.18: 245 52.18 - 78.27: 23 78.27 - 104.35: 17 104.35 - 130.44: 13 Dihedral angle restraints: 5726 sinusoidal: 2383 harmonic: 3343 Sorted by residual: dihedral pdb=" C3 PEE A1102 " pdb=" C1 PEE A1102 " pdb=" C2 PEE A1102 " pdb=" O3P PEE A1102 " ideal model delta sinusoidal sigma weight residual 62.73 -67.71 130.44 1 3.00e+01 1.11e-03 1.76e+01 dihedral pdb=" O2 PEE A1102 " pdb=" C1 PEE A1102 " pdb=" C2 PEE A1102 " pdb=" O3P PEE A1102 " ideal model delta sinusoidal sigma weight residual 300.04 170.89 129.15 1 3.00e+01 1.11e-03 1.74e+01 dihedral pdb=" N PEE A1102 " pdb=" C4 PEE A1102 " pdb=" C5 PEE A1102 " pdb=" O4P PEE A1102 " ideal model delta sinusoidal sigma weight residual -56.97 -178.16 121.19 1 3.00e+01 1.11e-03 1.62e+01 ... (remaining 5723 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.091: 1462 1.091 - 2.182: 0 2.182 - 3.272: 1 3.272 - 4.363: 0 4.363 - 5.454: 2 Chirality restraints: 1465 Sorted by residual: chirality pdb=" C1 NAG C 402 " pdb=" O4 NAG C 401 " pdb=" C2 NAG C 402 " pdb=" O5 NAG C 402 " both_signs ideal model delta sigma weight residual False -2.40 3.05 -5.45 2.00e-02 2.50e+03 7.44e+04 chirality pdb=" C1 MAN C 403 " pdb=" O4 NAG C 402 " pdb=" C2 MAN C 403 " pdb=" O5 MAN C 403 " both_signs ideal model delta sigma weight residual False 2.40 -2.42 4.82 2.00e-02 2.50e+03 5.81e+04 chirality pdb=" C1 NAG C 404 " pdb=" ND2 ASN C 294 " pdb=" C2 NAG C 404 " pdb=" O5 NAG C 404 " both_signs ideal model delta sigma weight residual False -2.40 -0.17 -2.23 2.00e-01 2.50e+01 1.25e+02 ... (remaining 1462 not shown) Planarity restraints: 1614 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 294 " 0.271 2.00e-02 2.50e+03 4.91e-01 3.01e+03 pdb=" CG ASN C 294 " -0.164 2.00e-02 2.50e+03 pdb=" OD1 ASN C 294 " 0.086 2.00e-02 2.50e+03 pdb=" ND2 ASN C 294 " -0.831 2.00e-02 2.50e+03 pdb=" C1 NAG C 404 " 0.639 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 402 " 0.275 2.00e-02 2.50e+03 2.27e-01 6.46e+02 pdb=" C7 NAG C 402 " -0.075 2.00e-02 2.50e+03 pdb=" C8 NAG C 402 " 0.187 2.00e-02 2.50e+03 pdb=" N2 NAG C 402 " -0.377 2.00e-02 2.50e+03 pdb=" O7 NAG C 402 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 401 " 0.130 2.00e-02 2.50e+03 1.10e-01 1.50e+02 pdb=" C7 NAG C 401 " -0.027 2.00e-02 2.50e+03 pdb=" C8 NAG C 401 " -0.032 2.00e-02 2.50e+03 pdb=" N2 NAG C 401 " -0.175 2.00e-02 2.50e+03 pdb=" O7 NAG C 401 " 0.104 2.00e-02 2.50e+03 ... (remaining 1611 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 56 2.36 - 2.99: 5665 2.99 - 3.63: 13000 3.63 - 4.26: 20823 4.26 - 4.90: 34942 Nonbonded interactions: 74486 Sorted by model distance: nonbonded pdb=" CD2 TYR A 876 " pdb=" CD1 ILE A 920 " model vdw 1.719 3.760 nonbonded pdb=" OE2 GLU A 181 " pdb=" OD2 ASP A 676 " model vdw 1.869 3.040 nonbonded pdb=" CG ASN C 294 " pdb=" O5 NAG C 404 " model vdw 1.919 2.616 nonbonded pdb=" OH TYR A 876 " pdb=" O VAL A1007 " model vdw 1.932 2.440 nonbonded pdb=" OD1 ASN C 294 " pdb=" O5 NAG C 404 " model vdw 1.962 3.040 ... (remaining 74481 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 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: 0.190 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: 1.360 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 28.360 Find NCS groups from input model: 0.240 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: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 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 : 0.005 0.115 9559 Z= 0.312 Angle : 1.225 70.538 12961 Z= 0.602 Chirality : 0.206 5.454 1465 Planarity : 0.008 0.227 1611 Dihedral : 16.587 130.443 3561 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 37.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 0.69 % Allowed : 3.74 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -5.22 (0.19), residues: 1129 helix: -2.91 (0.19), residues: 474 sheet: -3.89 (0.33), residues: 151 loop : -3.83 (0.22), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 323 HIS 0.005 0.001 HIS C 348 PHE 0.012 0.001 PHE A 884 TYR 0.015 0.001 TYR C 350 ARG 0.005 0.000 ARG A 723 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 226 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 ASN cc_start: 0.7848 (t0) cc_final: 0.7585 (t0) REVERT: A 381 TYR cc_start: 0.7636 (t80) cc_final: 0.7287 (t80) REVERT: A 399 GLU cc_start: 0.8819 (tt0) cc_final: 0.8579 (mt-10) REVERT: A 826 GLU cc_start: 0.8349 (tp30) cc_final: 0.7988 (tp30) REVERT: A 914 CYS cc_start: 0.8052 (m) cc_final: 0.7751 (m) REVERT: A 1050 GLN cc_start: 0.8516 (pp30) cc_final: 0.8128 (pp30) REVERT: C 106 ILE cc_start: 0.8564 (mm) cc_final: 0.8300 (mm) REVERT: C 122 TYR cc_start: 0.8611 (p90) cc_final: 0.8410 (p90) REVERT: C 310 MET cc_start: 0.8525 (ttp) cc_final: 0.7885 (tmm) outliers start: 7 outliers final: 2 residues processed: 231 average time/residue: 0.2440 time to fit residues: 75.1168 Evaluate side-chains 145 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 143 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 275 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.5980 chunk 85 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 53 optimal weight: 0.2980 chunk 65 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 352 ASN A 392 ASN A 402 GLN A 653 GLN A 716 HIS A 744 HIS A 828 HIS A 862 HIS A 864 HIS C 36 GLN C 129 GLN C 142 GLN C 216 ASN ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9559 Z= 0.310 Angle : 0.701 8.139 12961 Z= 0.348 Chirality : 0.048 0.227 1465 Planarity : 0.004 0.030 1611 Dihedral : 12.558 102.067 1381 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 2.65 % Allowed : 12.78 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -3.91 (0.22), residues: 1129 helix: -1.92 (0.22), residues: 467 sheet: -3.74 (0.32), residues: 158 loop : -2.77 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 260 HIS 0.009 0.002 HIS C 302 PHE 0.022 0.002 PHE A1075 TYR 0.018 0.002 TYR A 108 ARG 0.003 0.000 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 170 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 LYS cc_start: 0.8015 (mtpp) cc_final: 0.7642 (mmmt) REVERT: A 359 MET cc_start: 0.8652 (ttp) cc_final: 0.8292 (ttp) REVERT: A 654 ASP cc_start: 0.7826 (m-30) cc_final: 0.7616 (m-30) REVERT: A 747 TYR cc_start: 0.6988 (m-80) cc_final: 0.6586 (m-80) REVERT: A 826 GLU cc_start: 0.8361 (tp30) cc_final: 0.7991 (tp30) REVERT: A 877 PHE cc_start: 0.8837 (OUTLIER) cc_final: 0.8090 (t80) REVERT: A 910 MET cc_start: 0.8368 (mmm) cc_final: 0.7805 (mmm) REVERT: A 914 CYS cc_start: 0.8487 (m) cc_final: 0.8232 (m) REVERT: A 975 TYR cc_start: 0.9145 (t80) cc_final: 0.8806 (t80) REVERT: A 1050 GLN cc_start: 0.8778 (pp30) cc_final: 0.8291 (pp30) REVERT: C 310 MET cc_start: 0.8752 (ttp) cc_final: 0.8234 (tmm) outliers start: 27 outliers final: 20 residues processed: 183 average time/residue: 0.1929 time to fit residues: 50.4667 Evaluate side-chains 166 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 145 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 341 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 85 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 111 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 ASN A 828 HIS ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9559 Z= 0.255 Angle : 0.629 8.112 12961 Z= 0.312 Chirality : 0.046 0.183 1465 Planarity : 0.004 0.033 1611 Dihedral : 9.417 81.438 1376 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 3.34 % Allowed : 16.03 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -3.22 (0.23), residues: 1129 helix: -1.32 (0.23), residues: 469 sheet: -3.37 (0.33), residues: 158 loop : -2.42 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 323 HIS 0.007 0.002 HIS C 302 PHE 0.015 0.001 PHE A1039 TYR 0.013 0.001 TYR C 299 ARG 0.003 0.000 ARG A 940 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 151 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 LYS cc_start: 0.8060 (mtpp) cc_final: 0.7623 (mmmt) REVERT: A 366 GLN cc_start: 0.8390 (tm-30) cc_final: 0.8076 (tm-30) REVERT: A 877 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.8123 (t80) REVERT: A 910 MET cc_start: 0.8539 (mmm) cc_final: 0.7919 (mmm) REVERT: A 914 CYS cc_start: 0.8387 (m) cc_final: 0.8166 (m) REVERT: A 975 TYR cc_start: 0.9168 (t80) cc_final: 0.8825 (t80) REVERT: A 1050 GLN cc_start: 0.8796 (pp30) cc_final: 0.8433 (pp30) REVERT: C 310 MET cc_start: 0.8764 (ttp) cc_final: 0.8406 (tmm) outliers start: 34 outliers final: 25 residues processed: 173 average time/residue: 0.1876 time to fit residues: 46.9622 Evaluate side-chains 172 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 146 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 341 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 69 optimal weight: 0.3980 chunk 103 optimal weight: 9.9990 chunk 109 optimal weight: 0.6980 chunk 97 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9559 Z= 0.334 Angle : 0.675 9.916 12961 Z= 0.331 Chirality : 0.046 0.202 1465 Planarity : 0.004 0.032 1611 Dihedral : 8.475 82.378 1376 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 5.01 % Allowed : 16.42 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -2.97 (0.24), residues: 1129 helix: -1.15 (0.23), residues: 469 sheet: -2.97 (0.35), residues: 163 loop : -2.34 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 323 HIS 0.007 0.002 HIS C 302 PHE 0.018 0.002 PHE A1039 TYR 0.014 0.002 TYR A 747 ARG 0.003 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 157 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 LYS cc_start: 0.7909 (mtpp) cc_final: 0.7525 (mmmt) REVERT: A 174 THR cc_start: 0.9620 (OUTLIER) cc_final: 0.9308 (p) REVERT: A 366 GLN cc_start: 0.8405 (tm-30) cc_final: 0.8165 (tm-30) REVERT: A 877 PHE cc_start: 0.8918 (OUTLIER) cc_final: 0.8171 (t80) REVERT: A 910 MET cc_start: 0.8647 (mmm) cc_final: 0.8212 (mmm) REVERT: A 914 CYS cc_start: 0.8447 (m) cc_final: 0.8188 (m) REVERT: A 950 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7728 (mtm) REVERT: A 1050 GLN cc_start: 0.8920 (pp30) cc_final: 0.8586 (pp30) REVERT: A 1088 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.7201 (mttt) REVERT: C 310 MET cc_start: 0.8889 (ttp) cc_final: 0.8392 (tmm) REVERT: C 347 ASN cc_start: 0.7584 (OUTLIER) cc_final: 0.7369 (t0) outliers start: 51 outliers final: 37 residues processed: 187 average time/residue: 0.2022 time to fit residues: 54.4203 Evaluate side-chains 183 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 141 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 822 SER Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1088 LYS Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 347 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 81 optimal weight: 0.0270 chunk 45 optimal weight: 7.9990 chunk 93 optimal weight: 0.3980 chunk 75 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 0.0050 overall best weight: 0.4854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 ASN C 142 GLN ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9559 Z= 0.149 Angle : 0.560 8.339 12961 Z= 0.277 Chirality : 0.042 0.177 1465 Planarity : 0.003 0.033 1611 Dihedral : 7.613 83.082 1376 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.34 % Allowed : 18.88 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -2.51 (0.24), residues: 1129 helix: -0.73 (0.24), residues: 467 sheet: -2.70 (0.35), residues: 168 loop : -2.11 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 260 HIS 0.006 0.001 HIS C 302 PHE 0.014 0.001 PHE A1039 TYR 0.011 0.001 TYR A 311 ARG 0.003 0.000 ARG C 290 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 159 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 ASP cc_start: 0.7986 (p0) cc_final: 0.7670 (p0) REVERT: A 183 ASN cc_start: 0.9081 (p0) cc_final: 0.8818 (p0) REVERT: A 402 GLN cc_start: 0.8822 (mm-40) cc_final: 0.8479 (mm-40) REVERT: A 877 PHE cc_start: 0.8958 (OUTLIER) cc_final: 0.8093 (t80) REVERT: A 910 MET cc_start: 0.8588 (mmm) cc_final: 0.8313 (mmm) REVERT: A 914 CYS cc_start: 0.8422 (m) cc_final: 0.8222 (m) REVERT: A 1050 GLN cc_start: 0.8935 (pp30) cc_final: 0.8719 (pp30) REVERT: C 310 MET cc_start: 0.8777 (ttp) cc_final: 0.8391 (tmm) REVERT: C 343 LEU cc_start: 0.7615 (mp) cc_final: 0.7156 (mp) outliers start: 34 outliers final: 24 residues processed: 179 average time/residue: 0.1861 time to fit residues: 48.1323 Evaluate side-chains 176 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 151 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 0.7980 chunk 21 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9559 Z= 0.162 Angle : 0.548 7.437 12961 Z= 0.271 Chirality : 0.042 0.172 1465 Planarity : 0.003 0.031 1611 Dihedral : 7.107 85.198 1376 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.83 % Allowed : 19.86 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -2.15 (0.24), residues: 1129 helix: -0.48 (0.24), residues: 474 sheet: -2.40 (0.38), residues: 163 loop : -1.95 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 260 HIS 0.005 0.001 HIS C 302 PHE 0.013 0.001 PHE A1039 TYR 0.015 0.001 TYR A 71 ARG 0.002 0.000 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 165 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 ASP cc_start: 0.8000 (p0) cc_final: 0.7693 (p0) REVERT: A 183 ASN cc_start: 0.8907 (p0) cc_final: 0.8685 (p0) REVERT: A 218 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8489 (tp) REVERT: A 402 GLN cc_start: 0.8779 (mm-40) cc_final: 0.8421 (mm-40) REVERT: A 403 VAL cc_start: 0.8878 (t) cc_final: 0.8676 (m) REVERT: A 790 MET cc_start: 0.8961 (mmt) cc_final: 0.8354 (mmm) REVERT: A 877 PHE cc_start: 0.8992 (OUTLIER) cc_final: 0.8123 (t80) REVERT: A 910 MET cc_start: 0.8599 (mmm) cc_final: 0.8315 (mmm) REVERT: A 914 CYS cc_start: 0.8457 (m) cc_final: 0.8231 (m) REVERT: A 975 TYR cc_start: 0.9169 (t80) cc_final: 0.8932 (t80) REVERT: A 1088 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.7233 (mttt) REVERT: C 310 MET cc_start: 0.8835 (ttp) cc_final: 0.8461 (tmm) outliers start: 39 outliers final: 29 residues processed: 187 average time/residue: 0.1860 time to fit residues: 50.2051 Evaluate side-chains 184 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 152 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 978 PHE Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1088 LYS Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 66 optimal weight: 0.3980 chunk 50 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9559 Z= 0.216 Angle : 0.593 9.154 12961 Z= 0.292 Chirality : 0.044 0.202 1465 Planarity : 0.003 0.032 1611 Dihedral : 6.978 84.786 1376 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.13 % Allowed : 20.94 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -2.02 (0.25), residues: 1129 helix: -0.40 (0.24), residues: 475 sheet: -2.17 (0.38), residues: 168 loop : -1.91 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 323 HIS 0.005 0.001 HIS C 302 PHE 0.020 0.001 PHE A1039 TYR 0.014 0.001 TYR A 71 ARG 0.003 0.000 ARG A1052 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 164 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 ASP cc_start: 0.8046 (p0) cc_final: 0.7703 (p0) REVERT: A 183 ASN cc_start: 0.9018 (p0) cc_final: 0.8655 (p0) REVERT: A 366 GLN cc_start: 0.8202 (tm-30) cc_final: 0.7910 (tm-30) REVERT: A 402 GLN cc_start: 0.8831 (mm-40) cc_final: 0.8482 (mm-40) REVERT: A 403 VAL cc_start: 0.8894 (t) cc_final: 0.8671 (m) REVERT: A 877 PHE cc_start: 0.9016 (OUTLIER) cc_final: 0.8114 (t80) REVERT: A 910 MET cc_start: 0.8584 (mmm) cc_final: 0.8181 (mmm) REVERT: A 914 CYS cc_start: 0.8434 (m) cc_final: 0.8195 (m) REVERT: A 975 TYR cc_start: 0.9184 (t80) cc_final: 0.8911 (t80) REVERT: A 1088 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7264 (mttt) REVERT: C 310 MET cc_start: 0.8910 (ttp) cc_final: 0.8531 (tmm) REVERT: C 343 LEU cc_start: 0.7645 (mp) cc_final: 0.7125 (mp) outliers start: 42 outliers final: 32 residues processed: 189 average time/residue: 0.2210 time to fit residues: 60.3886 Evaluate side-chains 189 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 155 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 823 MET Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 978 PHE Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1044 ILE Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1088 LYS Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 69 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 chunk 85 optimal weight: 8.9990 chunk 99 optimal weight: 0.0000 chunk 104 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 888 GLN C 129 GLN ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.084 9559 Z= 0.156 Angle : 0.541 7.349 12961 Z= 0.268 Chirality : 0.041 0.174 1465 Planarity : 0.003 0.031 1611 Dihedral : 6.530 82.123 1376 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.44 % Allowed : 20.75 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -1.58 (0.25), residues: 1129 helix: -0.04 (0.25), residues: 471 sheet: -1.79 (0.40), residues: 162 loop : -1.73 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 260 HIS 0.004 0.001 HIS C 302 PHE 0.021 0.001 PHE A1039 TYR 0.015 0.001 TYR C 122 ARG 0.003 0.000 ARG A1052 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 155 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 ASP cc_start: 0.8021 (p0) cc_final: 0.7686 (p0) REVERT: A 402 GLN cc_start: 0.8692 (mm-40) cc_final: 0.8335 (mm-40) REVERT: A 678 MET cc_start: 0.7856 (tpp) cc_final: 0.7347 (tpt) REVERT: A 877 PHE cc_start: 0.8982 (OUTLIER) cc_final: 0.8093 (t80) REVERT: A 882 LEU cc_start: 0.8694 (tp) cc_final: 0.8258 (tt) REVERT: A 910 MET cc_start: 0.8604 (mmm) cc_final: 0.8339 (mmm) REVERT: A 975 TYR cc_start: 0.9160 (t80) cc_final: 0.8915 (t80) REVERT: A 1088 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.7178 (mttt) REVERT: C 310 MET cc_start: 0.8749 (ttp) cc_final: 0.8311 (tmm) REVERT: C 343 LEU cc_start: 0.7542 (mp) cc_final: 0.7077 (mp) REVERT: C 350 TYR cc_start: 0.6450 (m-80) cc_final: 0.6184 (m-80) outliers start: 35 outliers final: 27 residues processed: 178 average time/residue: 0.2021 time to fit residues: 51.2372 Evaluate side-chains 176 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 147 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 978 PHE Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1044 ILE Chi-restraints excluded: chain A residue 1088 LYS Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 131 HIS Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 61 optimal weight: 0.0070 chunk 44 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 65 optimal weight: 0.8980 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9559 Z= 0.190 Angle : 0.570 11.690 12961 Z= 0.279 Chirality : 0.042 0.187 1465 Planarity : 0.003 0.029 1611 Dihedral : 6.467 84.975 1376 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.95 % Allowed : 21.53 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -1.50 (0.25), residues: 1129 helix: 0.02 (0.24), residues: 469 sheet: -1.64 (0.41), residues: 162 loop : -1.70 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 323 HIS 0.004 0.001 HIS C 302 PHE 0.022 0.001 PHE A1039 TYR 0.016 0.001 TYR C 122 ARG 0.002 0.000 ARG A1052 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 156 time to evaluate : 1.060 Fit side-chains revert: symmetry clash REVERT: A 145 ASP cc_start: 0.8057 (p0) cc_final: 0.7679 (p0) REVERT: A 402 GLN cc_start: 0.8827 (mm-40) cc_final: 0.8458 (mm-40) REVERT: A 678 MET cc_start: 0.7844 (tpp) cc_final: 0.7567 (tpt) REVERT: A 790 MET cc_start: 0.8963 (mmm) cc_final: 0.8124 (mmm) REVERT: A 877 PHE cc_start: 0.9012 (OUTLIER) cc_final: 0.8110 (t80) REVERT: A 975 TYR cc_start: 0.9168 (t80) cc_final: 0.8898 (t80) REVERT: A 1088 LYS cc_start: 0.7590 (OUTLIER) cc_final: 0.7205 (mttt) REVERT: C 343 LEU cc_start: 0.7554 (mp) cc_final: 0.7067 (mp) outliers start: 30 outliers final: 26 residues processed: 175 average time/residue: 0.1961 time to fit residues: 49.5755 Evaluate side-chains 179 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 151 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 978 PHE Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1044 ILE Chi-restraints excluded: chain A residue 1088 LYS Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 69 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 9559 Z= 0.266 Angle : 0.607 9.373 12961 Z= 0.301 Chirality : 0.044 0.163 1465 Planarity : 0.003 0.031 1611 Dihedral : 6.587 82.796 1376 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 3.24 % Allowed : 21.34 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -1.67 (0.25), residues: 1129 helix: -0.11 (0.24), residues: 471 sheet: -1.74 (0.40), residues: 167 loop : -1.80 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 323 HIS 0.005 0.001 HIS A1023 PHE 0.023 0.002 PHE A1039 TYR 0.017 0.001 TYR C 122 ARG 0.002 0.000 ARG C 215 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 147 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: A 145 ASP cc_start: 0.8013 (p0) cc_final: 0.7623 (p0) REVERT: A 402 GLN cc_start: 0.8983 (mm-40) cc_final: 0.8595 (mm-40) REVERT: A 678 MET cc_start: 0.7893 (tpp) cc_final: 0.7646 (tpt) REVERT: A 790 MET cc_start: 0.9034 (mmm) cc_final: 0.8109 (mmm) REVERT: A 877 PHE cc_start: 0.9047 (OUTLIER) cc_final: 0.8147 (t80) REVERT: A 1088 LYS cc_start: 0.7560 (OUTLIER) cc_final: 0.7212 (mttt) REVERT: C 310 MET cc_start: 0.9073 (tmm) cc_final: 0.8465 (tmm) REVERT: C 343 LEU cc_start: 0.7629 (mp) cc_final: 0.7111 (mp) outliers start: 33 outliers final: 27 residues processed: 169 average time/residue: 0.2077 time to fit residues: 51.1560 Evaluate side-chains 170 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 141 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 978 PHE Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 1044 ILE Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1088 LYS Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.6980 chunk 13 optimal weight: 0.0270 chunk 24 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 overall best weight: 1.3242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1089 ASN ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.164767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.153981 restraints weight = 10597.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.150632 restraints weight = 17584.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.149328 restraints weight = 21959.504| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 9559 Z= 0.209 Angle : 0.575 9.272 12961 Z= 0.284 Chirality : 0.043 0.167 1465 Planarity : 0.003 0.031 1611 Dihedral : 6.416 81.064 1376 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.75 % Allowed : 22.03 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -1.54 (0.25), residues: 1129 helix: 0.00 (0.25), residues: 466 sheet: -1.58 (0.41), residues: 162 loop : -1.77 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 376 HIS 0.004 0.001 HIS C 302 PHE 0.025 0.001 PHE A 775 TYR 0.017 0.001 TYR C 122 ARG 0.001 0.000 ARG A 113 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1921.58 seconds wall clock time: 36 minutes 2.43 seconds (2162.43 seconds total)