Starting phenix.real_space_refine on Sat Aug 3 11:58:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhr_24467/08_2024/7rhr_24467.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhr_24467/08_2024/7rhr_24467.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhr_24467/08_2024/7rhr_24467.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhr_24467/08_2024/7rhr_24467.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhr_24467/08_2024/7rhr_24467.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhr_24467/08_2024/7rhr_24467.cif" } resolution = 3.0 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= 0.006 sd= 0.137 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 5121 2.51 5 N 1265 2.21 5 O 1394 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 125": "NH1" <-> "NH2" Residue "A TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 155": "OD1" <-> "OD2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 211": "OD1" <-> "OD2" Residue "A TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 291": "OD1" <-> "OD2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 380": "OD1" <-> "OD2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "A TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 451": "OD1" <-> "OD2" Residue "A PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 524": "OE1" <-> "OE2" Residue "A ARG 533": "NH1" <-> "NH2" Residue "A ARG 762": "NH1" <-> "NH2" Residue "A ASP 766": "OD1" <-> "OD2" Residue "A GLU 774": "OE1" <-> "OE2" Residue "A TYR 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 790": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 791": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 821": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 825": "OE1" <-> "OE2" Residue "A PHE 838": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 862": "OD1" <-> "OD2" Residue "A ASP 899": "OD1" <-> "OD2" Residue "A ASP 901": "OD1" <-> "OD2" Residue "A PHE 909": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 944": "OD1" <-> "OD2" Residue "A GLU 948": "OE1" <-> "OE2" Residue "A TYR 960": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 966": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 971": "NH1" <-> "NH2" Residue "A TYR 990": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1002": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1084": "OE1" <-> "OE2" Residue "A PHE 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1093": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1102": "NH1" <-> "NH2" Residue "A ARG 1103": "NH1" <-> "NH2" Residue "A PHE 1112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1139": "NH1" <-> "NH2" Residue "A PHE 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1167": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 7820 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 974, 7680 Classifications: {'peptide': 974} Link IDs: {'PTRANS': 41, 'TRANS': 932} Chain breaks: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 112 Unusual residues: {'CLR': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.00, per 1000 atoms: 0.64 Number of scatterers: 7820 At special positions: 0 Unit cell: (79.5, 81.62, 138.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1394 8.00 N 1265 7.00 C 5121 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 193 " - pdb=" SG CYS A 216 " distance=2.04 Simple disulfide: pdb=" SG CYS A 224 " - pdb=" SG CYS A 317 " distance=2.03 Simple disulfide: pdb=" SG CYS A 286 " - pdb=" SG CYS A 294 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A1503 " - " ASN A 302 " " NAG A1504 " - " ASN A 339 " " NAG B 1 " - " ASN A 989 " Time building additional restraints: 3.57 Conformation dependent library (CDL) restraints added in 1.6 seconds 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1828 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 7 sheets defined 63.6% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 69 through 87 Processing helix chain 'A' and resid 89 through 106 removed outlier: 3.879A pdb=" N VAL A 93 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N PHE A 102 " --> pdb=" O ILE A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 118 Processing helix chain 'A' and resid 124 through 137 removed outlier: 3.755A pdb=" N ARG A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 137 " --> pdb=" O THR A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 188 through 193 removed outlier: 3.601A pdb=" N LEU A 192 " --> pdb=" O LYS A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 214 removed outlier: 3.607A pdb=" N GLN A 208 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 229 removed outlier: 5.935A pdb=" N TRP A 226 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLU A 227 " --> pdb=" O CYS A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 261 removed outlier: 3.988A pdb=" N GLY A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 276 Processing helix chain 'A' and resid 308 through 314 Processing helix chain 'A' and resid 328 through 332 removed outlier: 3.668A pdb=" N ILE A 332 " --> pdb=" O GLN A 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 328 through 332' Processing helix chain 'A' and resid 358 through 366 Processing helix chain 'A' and resid 378 through 400 Processing helix chain 'A' and resid 413 through 423 removed outlier: 3.596A pdb=" N LEU A 417 " --> pdb=" O THR A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 448 Processing helix chain 'A' and resid 456 through 481 Processing helix chain 'A' and resid 492 through 518 removed outlier: 4.180A pdb=" N ASP A 503 " --> pdb=" O GLY A 499 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASP A 504 " --> pdb=" O VAL A 500 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL A 505 " --> pdb=" O GLY A 501 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR A 515 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN A 517 " --> pdb=" O SER A 513 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASN A 518 " --> pdb=" O GLU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 553 removed outlier: 5.490A pdb=" N ALA A 536 " --> pdb=" O LYS A 532 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N SER A 537 " --> pdb=" O ARG A 533 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N MET A 551 " --> pdb=" O THR A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 581 Processing helix chain 'A' and resid 581 through 595 removed outlier: 3.507A pdb=" N ILE A 585 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU A 594 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N VAL A 595 " --> pdb=" O TYR A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 735 removed outlier: 3.995A pdb=" N LYS A 728 " --> pdb=" O SER A 724 " (cutoff:3.500A) Proline residue: A 732 - end of helix removed outlier: 3.737A pdb=" N LEU A 735 " --> pdb=" O ALA A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 758 removed outlier: 4.295A pdb=" N VAL A 741 " --> pdb=" O PRO A 737 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA A 742 " --> pdb=" O LYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 770 removed outlier: 3.552A pdb=" N ASP A 769 " --> pdb=" O ASP A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 788 removed outlier: 3.706A pdb=" N ASP A 779 " --> pdb=" O THR A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 815 removed outlier: 3.610A pdb=" N LEU A 809 " --> pdb=" O ALA A 805 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR A 810 " --> pdb=" O GLN A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 855 removed outlier: 3.647A pdb=" N TYR A 837 " --> pdb=" O MET A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 879 removed outlier: 3.892A pdb=" N GLN A 879 " --> pdb=" O LYS A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 891 removed outlier: 3.916A pdb=" N ASN A 890 " --> pdb=" O ILE A 887 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLN A 891 " --> pdb=" O ASN A 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 887 through 891' Processing helix chain 'A' and resid 908 through 920 Processing helix chain 'A' and resid 920 through 927 Processing helix chain 'A' and resid 972 through 992 removed outlier: 3.586A pdb=" N SER A 992 " --> pdb=" O ASN A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1006 Processing helix chain 'A' and resid 1008 through 1011 removed outlier: 3.635A pdb=" N ILE A1011 " --> pdb=" O GLU A1008 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1008 through 1011' Processing helix chain 'A' and resid 1012 through 1037 removed outlier: 3.656A pdb=" N TRP A1016 " --> pdb=" O SER A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1064 Processing helix chain 'A' and resid 1068 through 1096 removed outlier: 3.950A pdb=" N VAL A1079 " --> pdb=" O LEU A1075 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLY A1080 " --> pdb=" O ILE A1076 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLU A1084 " --> pdb=" O GLY A1080 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N PHE A1085 " --> pdb=" O ILE A1081 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR A1086 " --> pdb=" O GLY A1082 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N HIS A1088 " --> pdb=" O GLU A1084 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL A1089 " --> pdb=" O PHE A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1112 Processing helix chain 'A' and resid 1112 through 1126 removed outlier: 3.537A pdb=" N VAL A1126 " --> pdb=" O THR A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1130 Processing helix chain 'A' and resid 1141 through 1159 Processing helix chain 'A' and resid 1159 through 1167 removed outlier: 3.619A pdb=" N PHE A1166 " --> pdb=" O VAL A1162 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 218 through 219 Processing sheet with id=AA2, first strand: chain 'A' and resid 218 through 219 removed outlier: 3.669A pdb=" N ASN A 144 " --> pdb=" O LEU A 356 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 180 through 182 Processing sheet with id=AA4, first strand: chain 'A' and resid 236 through 237 Processing sheet with id=AA5, first strand: chain 'A' and resid 317 through 318 Processing sheet with id=AA6, first strand: chain 'A' and resid 337 through 338 removed outlier: 6.972A pdb=" N VAL A 337 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 961 through 968 446 hydrogen bonds defined for protein. 1293 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: 2.26 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2384 1.34 - 1.46: 1327 1.46 - 1.58: 4236 1.58 - 1.70: 1 1.70 - 1.82: 65 Bond restraints: 8013 Sorted by residual: bond pdb=" CA ASP A 223 " pdb=" C ASP A 223 " ideal model delta sigma weight residual 1.522 1.488 0.034 1.38e-02 5.25e+03 6.06e+00 bond pdb=" CB PRO A 732 " pdb=" CG PRO A 732 " ideal model delta sigma weight residual 1.492 1.614 -0.122 5.00e-02 4.00e+02 5.91e+00 bond pdb=" CA ASN A 144 " pdb=" CB ASN A 144 " ideal model delta sigma weight residual 1.526 1.543 -0.016 9.30e-03 1.16e+04 3.12e+00 bond pdb=" CB VAL A 159 " pdb=" CG2 VAL A 159 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.75e+00 bond pdb=" C10 CLR A1502 " pdb=" C9 CLR A1502 " ideal model delta sigma weight residual 1.551 1.520 0.031 2.00e-02 2.50e+03 2.44e+00 ... (remaining 8008 not shown) Histogram of bond angle deviations from ideal: 98.77 - 105.85: 172 105.85 - 112.92: 4397 112.92 - 120.00: 2816 120.00 - 127.08: 3439 127.08 - 134.15: 92 Bond angle restraints: 10916 Sorted by residual: angle pdb=" CA PRO A 732 " pdb=" N PRO A 732 " pdb=" CD PRO A 732 " ideal model delta sigma weight residual 112.00 103.07 8.93 1.40e+00 5.10e-01 4.07e+01 angle pdb=" N PHE A1004 " pdb=" CA PHE A1004 " pdb=" C PHE A1004 " ideal model delta sigma weight residual 114.75 107.40 7.35 1.26e+00 6.30e-01 3.41e+01 angle pdb=" N ASN A 907 " pdb=" CA ASN A 907 " pdb=" C ASN A 907 " ideal model delta sigma weight residual 114.04 108.06 5.98 1.24e+00 6.50e-01 2.32e+01 angle pdb=" C TYR A 237 " pdb=" N LEU A 238 " pdb=" CA LEU A 238 " ideal model delta sigma weight residual 120.49 114.92 5.57 1.42e+00 4.96e-01 1.54e+01 angle pdb=" CA ARG A 932 " pdb=" CB ARG A 932 " pdb=" CG ARG A 932 " ideal model delta sigma weight residual 114.10 107.41 6.69 2.00e+00 2.50e-01 1.12e+01 ... (remaining 10911 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 4606 17.76 - 35.52: 272 35.52 - 53.28: 37 53.28 - 71.04: 13 71.04 - 88.80: 7 Dihedral angle restraints: 4935 sinusoidal: 2097 harmonic: 2838 Sorted by residual: dihedral pdb=" CA ARG A 932 " pdb=" C ARG A 932 " pdb=" N PRO A 933 " pdb=" CA PRO A 933 " ideal model delta harmonic sigma weight residual -180.00 -103.48 -76.52 0 5.00e+00 4.00e-02 2.34e+02 dihedral pdb=" CA LYS A 828 " pdb=" C LYS A 828 " pdb=" N GLN A 829 " pdb=" CA GLN A 829 " ideal model delta harmonic sigma weight residual -180.00 -150.91 -29.09 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA ASN A 882 " pdb=" C ASN A 882 " pdb=" N SER A 883 " pdb=" CA SER A 883 " ideal model delta harmonic sigma weight residual -180.00 -157.54 -22.46 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 4932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 920 0.050 - 0.101: 296 0.101 - 0.151: 52 0.151 - 0.201: 6 0.201 - 0.252: 3 Chirality restraints: 1277 Sorted by residual: chirality pdb=" C13 CLR A1502 " pdb=" C12 CLR A1502 " pdb=" C14 CLR A1502 " pdb=" C17 CLR A1502 " both_signs ideal model delta sigma weight residual False -2.93 -2.68 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" C13 CLR A1505 " pdb=" C12 CLR A1505 " pdb=" C14 CLR A1505 " pdb=" C17 CLR A1505 " both_signs ideal model delta sigma weight residual False -2.93 -2.72 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" C13 CLR A1501 " pdb=" C12 CLR A1501 " pdb=" C14 CLR A1501 " pdb=" C17 CLR A1501 " both_signs ideal model delta sigma weight residual False -2.93 -2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 1274 not shown) Planarity restraints: 1350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 932 " 0.067 5.00e-02 4.00e+02 1.01e-01 1.62e+01 pdb=" N PRO A 933 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO A 933 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 933 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 731 " 0.039 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO A 732 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 732 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 732 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 912 " 0.014 2.00e-02 2.50e+03 1.26e-02 3.15e+00 pdb=" CG TYR A 912 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR A 912 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A 912 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 912 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 912 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 912 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 912 " 0.000 2.00e-02 2.50e+03 ... (remaining 1347 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 113 2.69 - 3.24: 7635 3.24 - 3.79: 11802 3.79 - 4.35: 16297 4.35 - 4.90: 27294 Nonbonded interactions: 63141 Sorted by model distance: nonbonded pdb=" OH TYR A 442 " pdb=" OD1 ASP A1117 " model vdw 2.131 3.040 nonbonded pdb=" NE2 GLN A 150 " pdb=" OE1 GLN A 407 " model vdw 2.172 3.120 nonbonded pdb=" NH2 ARG A 134 " pdb=" OE2 GLU A 140 " model vdw 2.191 3.120 nonbonded pdb=" NH2 ARG A 431 " pdb=" O MET A1128 " model vdw 2.235 3.120 nonbonded pdb=" OG1 THR A 880 " pdb=" O ASP A 884 " model vdw 2.315 3.040 ... (remaining 63136 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.560 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 24.900 Find NCS groups from input model: 0.070 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:12.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 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 0.122 8013 Z= 0.396 Angle : 0.838 8.980 10916 Z= 0.480 Chirality : 0.050 0.252 1277 Planarity : 0.005 0.101 1347 Dihedral : 11.889 88.803 3098 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.05 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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: -0.44 (0.27), residues: 970 helix: 0.41 (0.22), residues: 563 sheet: 0.63 (0.77), residues: 47 loop : -1.49 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 268 HIS 0.006 0.001 HIS A 813 PHE 0.029 0.003 PHE A 249 TYR 0.031 0.002 TYR A 912 ARG 0.011 0.001 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.837 Fit side-chains REVERT: A 107 ARG cc_start: 0.7263 (pmt170) cc_final: 0.6571 (mmt180) REVERT: A 395 GLN cc_start: 0.7629 (mt0) cc_final: 0.7238 (tt0) REVERT: A 738 LYS cc_start: 0.7101 (mttt) cc_final: 0.6386 (tmtt) REVERT: A 785 PHE cc_start: 0.7810 (m-10) cc_final: 0.7451 (t80) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 1.1891 time to fit residues: 147.5599 Evaluate side-chains 93 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 25 optimal weight: 0.0670 chunk 49 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 245 GLN A 846 GLN ** A1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1009 GLN ** A1038 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8013 Z= 0.204 Angle : 0.601 6.384 10916 Z= 0.309 Chirality : 0.042 0.149 1277 Planarity : 0.005 0.087 1347 Dihedral : 6.476 70.825 1326 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.33 % Favored : 95.57 % Rotamer: Outliers : 1.57 % Allowed : 7.97 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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: 0.40 (0.27), residues: 970 helix: 1.07 (0.22), residues: 568 sheet: 0.95 (0.80), residues: 46 loop : -1.11 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 246 HIS 0.004 0.001 HIS A 168 PHE 0.022 0.002 PHE A 78 TYR 0.016 0.002 TYR A 912 ARG 0.006 0.000 ARG A 762 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 109 time to evaluate : 0.824 Fit side-chains REVERT: A 107 ARG cc_start: 0.7354 (pmt170) cc_final: 0.6570 (mmt180) REVERT: A 395 GLN cc_start: 0.7557 (mt0) cc_final: 0.7184 (tt0) REVERT: A 738 LYS cc_start: 0.7108 (mttt) cc_final: 0.6520 (tmtt) REVERT: A 785 PHE cc_start: 0.7624 (m-10) cc_final: 0.7275 (t80) outliers start: 13 outliers final: 8 residues processed: 116 average time/residue: 0.9915 time to fit residues: 123.2700 Evaluate side-chains 104 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 1000 ASN Chi-restraints excluded: chain A residue 1110 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 0.0980 chunk 95 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 846 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8013 Z= 0.214 Angle : 0.569 5.899 10916 Z= 0.292 Chirality : 0.041 0.140 1277 Planarity : 0.005 0.087 1347 Dihedral : 5.869 68.964 1326 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.43 % Favored : 95.46 % Rotamer: Outliers : 2.05 % Allowed : 11.71 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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: 0.67 (0.28), residues: 970 helix: 1.25 (0.22), residues: 569 sheet: 1.11 (0.80), residues: 46 loop : -0.92 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 327 HIS 0.003 0.001 HIS A 398 PHE 0.014 0.002 PHE A 963 TYR 0.016 0.002 TYR A 990 ARG 0.004 0.000 ARG A 762 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 0.902 Fit side-chains REVERT: A 107 ARG cc_start: 0.7558 (pmt170) cc_final: 0.6749 (mmt-90) REVERT: A 395 GLN cc_start: 0.7525 (mt0) cc_final: 0.7152 (tt0) REVERT: A 407 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7776 (mt0) REVERT: A 738 LYS cc_start: 0.7098 (mttt) cc_final: 0.6523 (tmtt) REVERT: A 785 PHE cc_start: 0.7646 (m-10) cc_final: 0.7313 (t80) outliers start: 17 outliers final: 7 residues processed: 103 average time/residue: 1.1208 time to fit residues: 123.3632 Evaluate side-chains 103 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1000 ASN Chi-restraints excluded: chain A residue 1110 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 0.0170 chunk 66 optimal weight: 0.0060 chunk 45 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 846 GLN A1000 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8013 Z= 0.179 Angle : 0.532 6.282 10916 Z= 0.275 Chirality : 0.040 0.143 1277 Planarity : 0.004 0.083 1347 Dihedral : 5.501 66.596 1326 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.02 % Favored : 95.88 % Rotamer: Outliers : 2.42 % Allowed : 12.92 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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: 0.93 (0.28), residues: 970 helix: 1.46 (0.22), residues: 570 sheet: 1.10 (0.80), residues: 46 loop : -0.82 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 327 HIS 0.002 0.001 HIS A 934 PHE 0.021 0.001 PHE A 78 TYR 0.017 0.001 TYR A 363 ARG 0.002 0.000 ARG A 762 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 109 time to evaluate : 0.766 Fit side-chains REVERT: A 235 MET cc_start: 0.8151 (tpp) cc_final: 0.7921 (mmm) REVERT: A 395 GLN cc_start: 0.7468 (mt0) cc_final: 0.7098 (tt0) REVERT: A 407 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7750 (mt0) REVERT: A 738 LYS cc_start: 0.7117 (mttt) cc_final: 0.6544 (tmtt) REVERT: A 785 PHE cc_start: 0.7659 (m-10) cc_final: 0.7409 (t80) REVERT: A 953 ARG cc_start: 0.7975 (ptm160) cc_final: 0.7678 (ptm-80) REVERT: A 1062 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7630 (mp) outliers start: 20 outliers final: 9 residues processed: 118 average time/residue: 1.0340 time to fit residues: 130.8532 Evaluate side-chains 115 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 1000 ASN Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1110 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 47 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 846 GLN A1101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 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 : 0.004 0.039 8013 Z= 0.288 Angle : 0.595 7.354 10916 Z= 0.305 Chirality : 0.043 0.147 1277 Planarity : 0.005 0.092 1347 Dihedral : 5.566 68.510 1326 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.33 % Favored : 95.57 % Rotamer: Outliers : 3.02 % Allowed : 13.29 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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: 0.73 (0.27), residues: 970 helix: 1.26 (0.22), residues: 577 sheet: 1.11 (0.79), residues: 46 loop : -0.89 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 327 HIS 0.004 0.001 HIS A 398 PHE 0.025 0.002 PHE A 78 TYR 0.021 0.002 TYR A 990 ARG 0.005 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 103 time to evaluate : 0.855 Fit side-chains REVERT: A 235 MET cc_start: 0.8187 (tpp) cc_final: 0.7943 (mmm) REVERT: A 360 LYS cc_start: 0.7791 (tttm) cc_final: 0.7419 (ttpp) REVERT: A 395 GLN cc_start: 0.7544 (mt0) cc_final: 0.7175 (tt0) REVERT: A 407 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7769 (mm-40) REVERT: A 738 LYS cc_start: 0.7124 (mttt) cc_final: 0.6531 (tmtt) REVERT: A 785 PHE cc_start: 0.7681 (m-10) cc_final: 0.7338 (t80) REVERT: A 905 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7675 (tm-30) REVERT: A 1062 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7695 (mp) outliers start: 25 outliers final: 13 residues processed: 115 average time/residue: 1.0063 time to fit residues: 123.9727 Evaluate side-chains 118 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 905 GLN Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1110 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 0.9980 chunk 84 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 0.0370 chunk 49 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 ASN A 846 GLN A1101 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8013 Z= 0.201 Angle : 0.546 7.767 10916 Z= 0.281 Chirality : 0.041 0.149 1277 Planarity : 0.004 0.086 1347 Dihedral : 5.402 67.139 1326 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.43 % Favored : 95.46 % Rotamer: Outliers : 2.66 % Allowed : 14.13 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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: 0.93 (0.28), residues: 970 helix: 1.44 (0.22), residues: 575 sheet: 1.14 (0.81), residues: 46 loop : -0.83 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 327 HIS 0.002 0.001 HIS A 374 PHE 0.015 0.001 PHE A 963 TYR 0.020 0.001 TYR A 363 ARG 0.002 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 106 time to evaluate : 0.824 Fit side-chains REVERT: A 235 MET cc_start: 0.8177 (tpp) cc_final: 0.7940 (mmm) REVERT: A 360 LYS cc_start: 0.7775 (tttm) cc_final: 0.7402 (ttpp) REVERT: A 395 GLN cc_start: 0.7524 (mt0) cc_final: 0.7147 (tt0) REVERT: A 407 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7819 (mt0) REVERT: A 422 LYS cc_start: 0.7646 (ttpt) cc_final: 0.7106 (mtpp) REVERT: A 738 LYS cc_start: 0.7126 (mttt) cc_final: 0.6497 (tmtt) REVERT: A 785 PHE cc_start: 0.7659 (m-10) cc_final: 0.7339 (t80) REVERT: A 905 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7709 (tm-30) REVERT: A 1062 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7652 (mp) outliers start: 22 outliers final: 14 residues processed: 117 average time/residue: 0.9054 time to fit residues: 114.2443 Evaluate side-chains 119 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 905 GLN Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1110 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.0702 > 50: distance: 21 - 23: 5.288 distance: 23 - 24: 5.238 distance: 24 - 27: 5.194 distance: 25 - 26: 3.230 distance: 25 - 31: 3.220 distance: 27 - 28: 5.284 distance: 28 - 29: 4.802 distance: 28 - 30: 3.037 distance: 31 - 32: 4.564 distance: 32 - 33: 6.417 distance: 32 - 35: 6.886 distance: 33 - 34: 4.734 distance: 35 - 36: 4.595 distance: 36 - 37: 5.191 distance: 36 - 38: 3.388 distance: 39 - 40: 3.471 distance: 40 - 41: 3.908 distance: 42 - 62: 4.612 distance: 43 - 44: 3.272 distance: 44 - 45: 3.355 distance: 47 - 48: 4.606 distance: 48 - 49: 3.962 distance: 51 - 53: 4.280 distance: 54 - 55: 4.807 distance: 55 - 58: 4.195 distance: 56 - 57: 3.209 distance: 56 - 62: 4.845 distance: 59 - 60: 3.042 distance: 59 - 61: 4.451 distance: 62 - 63: 7.211 distance: 63 - 64: 6.732 distance: 64 - 65: 6.949 distance: 66 - 67: 4.540 distance: 67 - 69: 3.107 distance: 70 - 71: 3.387 distance: 71 - 72: 9.007 distance: 71 - 74: 7.883 distance: 72 - 73: 5.934 distance: 72 - 77: 9.612 distance: 74 - 75: 5.034 distance: 74 - 76: 9.615 distance: 77 - 78: 9.492 distance: 77 - 83: 6.733 distance: 78 - 79: 13.078 distance: 78 - 81: 7.560 distance: 79 - 80: 10.772 distance: 79 - 84: 45.775 distance: 81 - 82: 3.458 distance: 82 - 83: 8.514 distance: 84 - 85: 52.070 distance: 85 - 86: 20.858 distance: 85 - 88: 15.395 distance: 86 - 87: 6.418 distance: 86 - 95: 6.997 distance: 88 - 89: 9.480 distance: 91 - 92: 3.267 distance: 95 - 96: 6.597 distance: 96 - 97: 4.416 distance: 97 - 98: 9.960 distance: 99 - 100: 4.643 distance: 100 - 101: 3.950 distance: 101 - 103: 5.267