Starting phenix.real_space_refine on Thu Sep 26 06:38:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rjg_4904/09_2024/6rjg_4904.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rjg_4904/09_2024/6rjg_4904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rjg_4904/09_2024/6rjg_4904.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rjg_4904/09_2024/6rjg_4904.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rjg_4904/09_2024/6rjg_4904.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rjg_4904/09_2024/6rjg_4904.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 123 5.49 5 S 37 5.16 5 C 7318 2.51 5 N 2103 2.21 5 O 2639 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12220 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1506 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 178} Chain: "B" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1506 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 178} Chain: "C" Number of atoms: 6633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 814, 6633 Classifications: {'peptide': 814} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 794} Chain breaks: 5 Chain: "D" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1656 Classifications: {'RNA': 78} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 6, 'rna3p_pur': 37, 'rna3p_pyr': 32} Link IDs: {'rna2p': 9, 'rna3p': 68} Chain breaks: 2 Chain: "E" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 646 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "G" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 273 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Time building chain proxies: 8.18, per 1000 atoms: 0.67 Number of scatterers: 12220 At special positions: 0 Unit cell: (121.793, 140.462, 111.125, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 37 16.00 P 123 15.00 O 2639 8.00 N 2103 7.00 C 7318 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.07 Conformation dependent library (CDL) restraints added in 1.3 seconds 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2206 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 10 sheets defined 47.7% alpha, 14.4% beta 38 base pairs and 80 stacking pairs defined. Time for finding SS restraints: 4.48 Creating SS restraints... Processing helix chain 'A' and resid 4 through 19 removed outlier: 3.621A pdb=" N LYS A 8 " --> pdb=" O ASN A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 28 removed outlier: 3.836A pdb=" N ASP A 24 " --> pdb=" O PHE A 21 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR A 26 " --> pdb=" O ASN A 23 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS A 27 " --> pdb=" O ASP A 24 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU A 28 " --> pdb=" O PHE A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 43 Processing helix chain 'A' and resid 52 through 64 removed outlier: 3.675A pdb=" N LEU A 63 " --> pdb=" O MET A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 81 removed outlier: 3.896A pdb=" N ASN A 81 " --> pdb=" O THR A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 89 removed outlier: 4.163A pdb=" N LYS A 86 " --> pdb=" O ASP A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 110 Processing helix chain 'A' and resid 143 through 147 removed outlier: 3.935A pdb=" N GLY A 146 " --> pdb=" O LEU A 143 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER A 147 " --> pdb=" O GLY A 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 143 through 147' Processing helix chain 'A' and resid 167 through 178 removed outlier: 3.559A pdb=" N GLU A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN A 177 " --> pdb=" O GLU A 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 19 removed outlier: 3.617A pdb=" N LYS B 8 " --> pdb=" O ASN B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 27 removed outlier: 3.833A pdb=" N TYR B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 43 removed outlier: 3.554A pdb=" N ASN B 43 " --> pdb=" O GLN B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 64 removed outlier: 3.688A pdb=" N LEU B 63 " --> pdb=" O MET B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 80 Processing helix chain 'B' and resid 82 through 89 removed outlier: 4.128A pdb=" N LYS B 86 " --> pdb=" O ASP B 82 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET B 87 " --> pdb=" O ASN B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 110 removed outlier: 3.716A pdb=" N TYR B 94 " --> pdb=" O PRO B 90 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN B 110 " --> pdb=" O TRP B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 142 No H-bonds generated for 'chain 'B' and resid 140 through 142' Processing helix chain 'B' and resid 167 through 178 removed outlier: 3.759A pdb=" N ARG B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 73 removed outlier: 3.757A pdb=" N VAL C 45 " --> pdb=" O GLU C 41 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG C 54 " --> pdb=" O ARG C 50 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU C 55 " --> pdb=" O GLN C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 98 Processing helix chain 'C' and resid 101 through 115 Processing helix chain 'C' and resid 134 through 145 removed outlier: 3.674A pdb=" N GLN C 145 " --> pdb=" O GLU C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 163 Processing helix chain 'C' and resid 185 through 204 removed outlier: 3.748A pdb=" N TYR C 189 " --> pdb=" O PRO C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 220 Processing helix chain 'C' and resid 250 through 255 removed outlier: 4.346A pdb=" N ILE C 254 " --> pdb=" O ASN C 250 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU C 255 " --> pdb=" O ILE C 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 250 through 255' Processing helix chain 'C' and resid 272 through 285 removed outlier: 3.922A pdb=" N GLN C 276 " --> pdb=" O SER C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 311 Processing helix chain 'C' and resid 315 through 328 removed outlier: 3.949A pdb=" N LEU C 319 " --> pdb=" O GLY C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 358 removed outlier: 3.755A pdb=" N THR C 358 " --> pdb=" O ARG C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 382 removed outlier: 3.521A pdb=" N ASN C 382 " --> pdb=" O VAL C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 396 removed outlier: 3.737A pdb=" N PHE C 396 " --> pdb=" O LEU C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 416 removed outlier: 3.644A pdb=" N ASN C 416 " --> pdb=" O PHE C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 removed outlier: 3.832A pdb=" N PHE C 420 " --> pdb=" O ASN C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 436 Processing helix chain 'C' and resid 445 through 453 Processing helix chain 'C' and resid 469 through 474 removed outlier: 3.801A pdb=" N LEU C 473 " --> pdb=" O ASP C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 500 removed outlier: 3.568A pdb=" N ALA C 483 " --> pdb=" O ASN C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 705 Processing helix chain 'C' and resid 854 through 868 Processing helix chain 'C' and resid 869 through 872 removed outlier: 3.687A pdb=" N PHE C 872 " --> pdb=" O LYS C 869 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 869 through 872' Processing helix chain 'C' and resid 873 through 878 Processing helix chain 'C' and resid 878 through 892 removed outlier: 3.594A pdb=" N PHE C 882 " --> pdb=" O ASP C 878 " (cutoff:3.500A) Proline residue: C 888 - end of helix Processing helix chain 'C' and resid 910 through 918 Processing helix chain 'C' and resid 986 through 988 No H-bonds generated for 'chain 'C' and resid 986 through 988' Processing helix chain 'C' and resid 1000 through 1011 Processing sheet with id=AA1, first strand: chain 'A' and resid 114 through 122 removed outlier: 6.776A pdb=" N ILE A 115 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL A 136 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLY A 117 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LEU A 134 " --> pdb=" O GLY A 117 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY A 119 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N MET A 121 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ALA A 130 " --> pdb=" O MET A 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 114 through 122 removed outlier: 6.776A pdb=" N ILE A 115 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL A 136 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLY A 117 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LEU A 134 " --> pdb=" O GLY A 117 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY A 119 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N MET A 121 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ALA A 130 " --> pdb=" O MET A 121 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N TYR A 128 " --> pdb=" O ASP C 947 " (cutoff:3.500A) removed outlier: 11.901A pdb=" N ILE C 827 " --> pdb=" O LYS C 848 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N LYS C 848 " --> pdb=" O ILE C 827 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ALA C 829 " --> pdb=" O LEU C 846 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N THR C 843 " --> pdb=" O LYS C 941 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LYS C 941 " --> pdb=" O THR C 843 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL C 845 " --> pdb=" O ASP C 939 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 114 through 122 removed outlier: 7.535A pdb=" N MET B 121 " --> pdb=" O ASN B 131 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASN B 131 " --> pdb=" O MET B 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 710 through 713 removed outlier: 3.919A pdb=" N HIS C 29 " --> pdb=" O ILE C 19 " (cutoff:3.500A) removed outlier: 9.229A pdb=" N LEU C 809 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LYS C 30 " --> pdb=" O LEU C 809 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N SER C 811 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N SER C 32 " --> pdb=" O SER C 811 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 268 through 269 removed outlier: 3.586A pdb=" N ALA C 268 " --> pdb=" O HIS C 425 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 338 through 339 removed outlier: 3.805A pdb=" N ARG C 338 " --> pdb=" O GLU C 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 978 through 980 removed outlier: 7.039A pdb=" N LEU C 983 " --> pdb=" O TRP C 965 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 978 through 980 removed outlier: 3.561A pdb=" N PHE C1021 " --> pdb=" O VAL C 969 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N PHE C 971 " --> pdb=" O PHE C1019 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N PHE C1019 " --> pdb=" O PHE C 971 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 989 through 990 Processing sheet with id=AB1, first strand: chain 'C' and resid 1085 through 1088 removed outlier: 4.515A pdb=" N CYS C1085 " --> pdb=" O LEU C1058 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLU C1057 " --> pdb=" O LEU C1045 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU C1028 " --> pdb=" O VAL C1099 " (cutoff:3.500A) 419 hydrogen bonds defined for protein. 1242 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 90 hydrogen bonds 172 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 80 stacking parallelities Total time for adding SS restraints: 5.25 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2561 1.33 - 1.45: 3525 1.45 - 1.57: 6301 1.57 - 1.70: 241 1.70 - 1.82: 69 Bond restraints: 12697 Sorted by residual: bond pdb=" CA ASN B 83 " pdb=" C ASN B 83 " ideal model delta sigma weight residual 1.522 1.558 -0.036 1.72e-02 3.38e+03 4.44e+00 bond pdb=" CB ARG C 267 " pdb=" CG ARG C 267 " ideal model delta sigma weight residual 1.520 1.457 0.063 3.00e-02 1.11e+03 4.37e+00 bond pdb=" CG LEU C 959 " pdb=" CD1 LEU C 959 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.34e+00 bond pdb=" CB LYS C1010 " pdb=" CG LYS C1010 " ideal model delta sigma weight residual 1.520 1.466 0.054 3.00e-02 1.11e+03 3.29e+00 bond pdb=" CA GLU C 887 " pdb=" C GLU C 887 " ideal model delta sigma weight residual 1.520 1.540 -0.020 1.23e-02 6.61e+03 2.59e+00 ... (remaining 12692 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 17144 2.45 - 4.91: 427 4.91 - 7.36: 44 7.36 - 9.81: 8 9.81 - 12.26: 3 Bond angle restraints: 17626 Sorted by residual: angle pdb=" CA TYR A 26 " pdb=" CB TYR A 26 " pdb=" CG TYR A 26 " ideal model delta sigma weight residual 113.90 122.15 -8.25 1.80e+00 3.09e-01 2.10e+01 angle pdb=" CA ILE C 436 " pdb=" C ILE C 436 " pdb=" N PRO C 437 " ideal model delta sigma weight residual 118.88 124.84 -5.96 1.54e+00 4.22e-01 1.50e+01 angle pdb=" C HIS C 705 " pdb=" N LYS C 706 " pdb=" CA LYS C 706 " ideal model delta sigma weight residual 122.36 127.36 -5.00 1.42e+00 4.96e-01 1.24e+01 angle pdb=" CA LYS C 706 " pdb=" CB LYS C 706 " pdb=" CG LYS C 706 " ideal model delta sigma weight residual 114.10 121.09 -6.99 2.00e+00 2.50e-01 1.22e+01 angle pdb=" CA GLU C1113 " pdb=" CB GLU C1113 " pdb=" CG GLU C1113 " ideal model delta sigma weight residual 114.10 120.97 -6.87 2.00e+00 2.50e-01 1.18e+01 ... (remaining 17621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 6371 17.72 - 35.44: 859 35.44 - 53.16: 300 53.16 - 70.88: 115 70.88 - 88.60: 29 Dihedral angle restraints: 7674 sinusoidal: 4227 harmonic: 3447 Sorted by residual: dihedral pdb=" CA ILE C 334 " pdb=" C ILE C 334 " pdb=" N LYS C 335 " pdb=" CA LYS C 335 " ideal model delta harmonic sigma weight residual 180.00 -152.80 -27.20 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA HIS C 348 " pdb=" C HIS C 348 " pdb=" N THR C 349 " pdb=" CA THR C 349 " ideal model delta harmonic sigma weight residual 180.00 157.64 22.36 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA MET A 87 " pdb=" C MET A 87 " pdb=" N ASN A 88 " pdb=" CA ASN A 88 " ideal model delta harmonic sigma weight residual -180.00 -157.66 -22.34 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 7671 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1707 0.082 - 0.165: 236 0.165 - 0.247: 21 0.247 - 0.330: 3 0.330 - 0.412: 2 Chirality restraints: 1969 Sorted by residual: chirality pdb=" CB ILE B 48 " pdb=" CA ILE B 48 " pdb=" CG1 ILE B 48 " pdb=" CG2 ILE B 48 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" CB ILE A 48 " pdb=" CA ILE A 48 " pdb=" CG1 ILE A 48 " pdb=" CG2 ILE A 48 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" CB ILE C 999 " pdb=" CA ILE C 999 " pdb=" CG1 ILE C 999 " pdb=" CG2 ILE C 999 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 1966 not shown) Planarity restraints: 1818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 260 " -0.015 2.00e-02 2.50e+03 3.07e-02 9.44e+00 pdb=" C THR C 260 " 0.053 2.00e-02 2.50e+03 pdb=" O THR C 260 " -0.020 2.00e-02 2.50e+03 pdb=" N PHE C 261 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U D 7 " 0.034 2.00e-02 2.50e+03 2.05e-02 9.42e+00 pdb=" N1 U D 7 " -0.049 2.00e-02 2.50e+03 pdb=" C2 U D 7 " 0.007 2.00e-02 2.50e+03 pdb=" O2 U D 7 " -0.002 2.00e-02 2.50e+03 pdb=" N3 U D 7 " 0.000 2.00e-02 2.50e+03 pdb=" C4 U D 7 " 0.003 2.00e-02 2.50e+03 pdb=" O4 U D 7 " 0.010 2.00e-02 2.50e+03 pdb=" C5 U D 7 " -0.000 2.00e-02 2.50e+03 pdb=" C6 U D 7 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 26 " -0.025 2.00e-02 2.50e+03 1.83e-02 6.72e+00 pdb=" CG TYR B 26 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR B 26 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR B 26 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 26 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 26 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR B 26 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 26 " -0.001 2.00e-02 2.50e+03 ... (remaining 1815 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3439 2.82 - 3.34: 9580 3.34 - 3.86: 19773 3.86 - 4.38: 23494 4.38 - 4.90: 38482 Nonbonded interactions: 94768 Sorted by model distance: nonbonded pdb=" OD2 ASP C 878 " pdb=" OG1 THR C 881 " model vdw 2.297 3.040 nonbonded pdb=" OE2 GLU A 68 " pdb=" NZ LYS A 99 " model vdw 2.339 3.120 nonbonded pdb=" OE1 GLU B 135 " pdb=" NE2 GLN B 151 " model vdw 2.341 3.120 nonbonded pdb=" OG1 THR C 830 " pdb=" O LYS C 956 " model vdw 2.362 3.040 nonbonded pdb=" O ALA C 376 " pdb=" OG1 THR C 380 " model vdw 2.377 3.040 ... (remaining 94763 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 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: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 34.610 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 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 : 0.008 0.071 12697 Z= 0.511 Angle : 0.955 12.264 17626 Z= 0.526 Chirality : 0.059 0.412 1969 Planarity : 0.006 0.063 1818 Dihedral : 18.835 88.602 5468 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.10 % Allowed : 6.79 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.18), residues: 1164 helix: -2.16 (0.17), residues: 504 sheet: -1.79 (0.34), residues: 143 loop : -2.74 (0.21), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 38 HIS 0.010 0.002 HIS C 425 PHE 0.023 0.003 PHE C 818 TYR 0.043 0.003 TYR B 26 ARG 0.013 0.001 ARG C 921 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 200 time to evaluate : 1.169 Fit side-chains revert: symmetry clash REVERT: B 15 MET cc_start: 0.7669 (tmm) cc_final: 0.7324 (tmm) REVERT: B 155 LYS cc_start: 0.7389 (tptt) cc_final: 0.7167 (tptt) REVERT: B 156 ASP cc_start: 0.7732 (p0) cc_final: 0.7448 (t0) REVERT: C 273 TYR cc_start: 0.8173 (t80) cc_final: 0.7966 (t80) REVERT: C 447 MET cc_start: 0.6645 (ttt) cc_final: 0.6324 (ttp) REVERT: C 869 LYS cc_start: 0.8728 (ttmt) cc_final: 0.8398 (tttt) REVERT: C 877 HIS cc_start: 0.6938 (m170) cc_final: 0.6612 (t-90) outliers start: 1 outliers final: 1 residues processed: 200 average time/residue: 0.2902 time to fit residues: 78.6827 Evaluate side-chains 150 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 0.0470 chunk 61 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN B 88 ASN B 177 ASN B 178 ASN C 85 ASN C 142 ASN C 227 HIS C 276 GLN C 456 GLN C 505 ASN C 832 GLN C 855 GLN ** C 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1001 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12697 Z= 0.177 Angle : 0.568 8.515 17626 Z= 0.314 Chirality : 0.038 0.166 1969 Planarity : 0.004 0.034 1818 Dihedral : 18.737 79.552 2992 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.24 % Allowed : 12.05 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.21), residues: 1164 helix: -0.00 (0.21), residues: 508 sheet: -1.44 (0.36), residues: 140 loop : -2.47 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 174 HIS 0.005 0.001 HIS C 178 PHE 0.013 0.001 PHE A 67 TYR 0.021 0.001 TYR B 26 ARG 0.008 0.000 ARG C 369 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 169 time to evaluate : 1.335 Fit side-chains REVERT: B 15 MET cc_start: 0.7786 (tmm) cc_final: 0.7557 (tmm) REVERT: B 155 LYS cc_start: 0.7227 (tptt) cc_final: 0.7022 (tptt) REVERT: B 156 ASP cc_start: 0.7576 (p0) cc_final: 0.7309 (t0) REVERT: C 32 SER cc_start: 0.8209 (m) cc_final: 0.7981 (p) REVERT: C 447 MET cc_start: 0.6580 (ttt) cc_final: 0.6305 (ttp) REVERT: C 862 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7570 (tpp) REVERT: C 877 HIS cc_start: 0.6995 (m170) cc_final: 0.6660 (t-90) REVERT: C 1011 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7290 (mm-30) outliers start: 13 outliers final: 9 residues processed: 178 average time/residue: 0.2632 time to fit residues: 65.4901 Evaluate side-chains 161 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 151 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 440 TYR Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 862 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 39 optimal weight: 0.0870 chunk 93 optimal weight: 5.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12697 Z= 0.318 Angle : 0.616 10.763 17626 Z= 0.333 Chirality : 0.041 0.163 1969 Planarity : 0.004 0.037 1818 Dihedral : 18.663 79.779 2989 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.77 % Allowed : 13.00 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.22), residues: 1164 helix: 0.66 (0.22), residues: 511 sheet: -1.12 (0.39), residues: 141 loop : -2.37 (0.22), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 174 HIS 0.003 0.001 HIS C 178 PHE 0.013 0.002 PHE C1044 TYR 0.021 0.002 TYR B 26 ARG 0.003 0.001 ARG B 111 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 149 time to evaluate : 1.195 Fit side-chains REVERT: B 15 MET cc_start: 0.7830 (tmm) cc_final: 0.7601 (tmm) REVERT: B 139 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7863 (mm-30) REVERT: B 155 LYS cc_start: 0.7390 (tptt) cc_final: 0.7167 (tptt) REVERT: C 869 LYS cc_start: 0.8751 (ttmt) cc_final: 0.8370 (ttmt) REVERT: C 877 HIS cc_start: 0.7020 (m170) cc_final: 0.6629 (t-90) REVERT: C 1011 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7375 (mm-30) REVERT: C 1055 TYR cc_start: 0.9057 (OUTLIER) cc_final: 0.8386 (m-10) outliers start: 29 outliers final: 18 residues processed: 171 average time/residue: 0.2667 time to fit residues: 63.9167 Evaluate side-chains 165 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 146 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 440 TYR Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 891 GLU Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1055 TYR Chi-restraints excluded: chain C residue 1070 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 6.9990 chunk 87 optimal weight: 0.0970 chunk 60 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 116 optimal weight: 0.1980 chunk 123 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 ASN B 181 ASN C 348 HIS ** C 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1001 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12697 Z= 0.135 Angle : 0.491 6.939 17626 Z= 0.271 Chirality : 0.036 0.153 1969 Planarity : 0.003 0.033 1818 Dihedral : 18.480 79.676 2989 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.68 % Allowed : 13.67 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.23), residues: 1164 helix: 1.27 (0.23), residues: 513 sheet: -0.73 (0.41), residues: 144 loop : -2.12 (0.24), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 174 HIS 0.001 0.001 HIS C 705 PHE 0.011 0.001 PHE C 261 TYR 0.018 0.001 TYR B 26 ARG 0.008 0.000 ARG B 111 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 172 time to evaluate : 1.155 Fit side-chains revert: symmetry clash REVERT: A 101 GLN cc_start: 0.7778 (pt0) cc_final: 0.7515 (mt0) REVERT: A 149 MET cc_start: 0.9062 (tpt) cc_final: 0.8723 (tpt) REVERT: B 15 MET cc_start: 0.7763 (tmm) cc_final: 0.7495 (tmm) REVERT: B 155 LYS cc_start: 0.7206 (tptt) cc_final: 0.6910 (tptt) REVERT: B 156 ASP cc_start: 0.7599 (p0) cc_final: 0.7267 (t0) REVERT: C 447 MET cc_start: 0.6283 (ttt) cc_final: 0.5936 (ttp) REVERT: C 877 HIS cc_start: 0.6799 (m170) cc_final: 0.6442 (t-90) REVERT: C 991 GLU cc_start: 0.7593 (tt0) cc_final: 0.7305 (tt0) REVERT: C 1011 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7323 (mm-30) REVERT: C 1055 TYR cc_start: 0.8936 (OUTLIER) cc_final: 0.8651 (m-80) outliers start: 28 outliers final: 15 residues processed: 195 average time/residue: 0.2641 time to fit residues: 72.8434 Evaluate side-chains 163 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 147 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 348 HIS Chi-restraints excluded: chain C residue 440 TYR Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 889 ILE Chi-restraints excluded: chain C residue 891 GLU Chi-restraints excluded: chain C residue 1055 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 chunk 111 optimal weight: 0.7980 chunk 31 optimal weight: 9.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN B 178 ASN C 137 GLN ** C 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12697 Z= 0.253 Angle : 0.562 10.679 17626 Z= 0.304 Chirality : 0.039 0.153 1969 Planarity : 0.003 0.036 1818 Dihedral : 18.469 79.274 2989 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.25 % Allowed : 14.53 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.23), residues: 1164 helix: 1.36 (0.22), residues: 514 sheet: -0.74 (0.41), residues: 141 loop : -2.13 (0.23), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 174 HIS 0.018 0.001 HIS C 348 PHE 0.012 0.002 PHE C 412 TYR 0.020 0.002 TYR B 133 ARG 0.006 0.000 ARG C 452 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 150 time to evaluate : 1.212 Fit side-chains REVERT: A 101 GLN cc_start: 0.7816 (pt0) cc_final: 0.7531 (mt0) REVERT: A 149 MET cc_start: 0.9088 (tpt) cc_final: 0.8750 (tpt) REVERT: B 15 MET cc_start: 0.7808 (tmm) cc_final: 0.7544 (tmm) REVERT: B 111 ARG cc_start: 0.7470 (tpt-90) cc_final: 0.7248 (tpt-90) REVERT: B 155 LYS cc_start: 0.7430 (tptt) cc_final: 0.7186 (tptt) REVERT: C 39 GLN cc_start: 0.8202 (pm20) cc_final: 0.7437 (pm20) REVERT: C 157 GLU cc_start: 0.7338 (mt-10) cc_final: 0.7028 (mt-10) REVERT: C 447 MET cc_start: 0.6450 (ttt) cc_final: 0.6164 (ttp) REVERT: C 869 LYS cc_start: 0.8707 (ttmt) cc_final: 0.8271 (ttmt) REVERT: C 877 HIS cc_start: 0.6914 (m170) cc_final: 0.6450 (t-90) REVERT: C 991 GLU cc_start: 0.7668 (tt0) cc_final: 0.7366 (tt0) REVERT: C 1002 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7503 (mt-10) REVERT: C 1011 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7384 (mm-30) REVERT: C 1055 TYR cc_start: 0.9029 (OUTLIER) cc_final: 0.8693 (m-80) outliers start: 34 outliers final: 26 residues processed: 174 average time/residue: 0.2610 time to fit residues: 64.6343 Evaluate side-chains 178 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 150 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 889 ILE Chi-restraints excluded: chain C residue 891 GLU Chi-restraints excluded: chain C residue 962 VAL Chi-restraints excluded: chain C residue 1002 GLU Chi-restraints excluded: chain C residue 1055 TYR Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1070 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 123 optimal weight: 7.9990 chunk 102 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 65 optimal weight: 7.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN C 403 GLN ** C 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12697 Z= 0.217 Angle : 0.538 10.110 17626 Z= 0.292 Chirality : 0.038 0.149 1969 Planarity : 0.003 0.036 1818 Dihedral : 18.428 80.008 2989 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.02 % Allowed : 15.39 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.24), residues: 1164 helix: 1.49 (0.22), residues: 514 sheet: -0.74 (0.41), residues: 141 loop : -2.04 (0.24), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 174 HIS 0.002 0.001 HIS C 348 PHE 0.010 0.001 PHE C 261 TYR 0.014 0.001 TYR B 26 ARG 0.007 0.000 ARG C 385 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 154 time to evaluate : 1.268 Fit side-chains REVERT: A 101 GLN cc_start: 0.7827 (pt0) cc_final: 0.7544 (mt0) REVERT: A 149 MET cc_start: 0.9082 (tpt) cc_final: 0.8751 (tpt) REVERT: A 173 GLU cc_start: 0.7343 (tt0) cc_final: 0.7026 (mt-10) REVERT: B 15 MET cc_start: 0.7781 (tmm) cc_final: 0.7523 (tmm) REVERT: B 155 LYS cc_start: 0.7490 (tptt) cc_final: 0.7240 (tptt) REVERT: C 39 GLN cc_start: 0.8162 (pm20) cc_final: 0.7404 (pm20) REVERT: C 157 GLU cc_start: 0.7389 (mt-10) cc_final: 0.7072 (mt-10) REVERT: C 447 MET cc_start: 0.6476 (ttt) cc_final: 0.6214 (ttp) REVERT: C 869 LYS cc_start: 0.8715 (ttmt) cc_final: 0.8287 (ttmt) REVERT: C 877 HIS cc_start: 0.6893 (m170) cc_final: 0.6442 (t-90) REVERT: C 991 GLU cc_start: 0.7599 (tt0) cc_final: 0.7322 (tt0) REVERT: C 1002 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7519 (mt-10) REVERT: C 1011 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7370 (mm-30) REVERT: C 1055 TYR cc_start: 0.9004 (OUTLIER) cc_final: 0.8562 (m-80) outliers start: 42 outliers final: 33 residues processed: 183 average time/residue: 0.2466 time to fit residues: 64.6228 Evaluate side-chains 184 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 149 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 440 TYR Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 889 ILE Chi-restraints excluded: chain C residue 891 GLU Chi-restraints excluded: chain C residue 962 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1002 GLU Chi-restraints excluded: chain C residue 1055 TYR Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1070 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 chunk 123 optimal weight: 7.9990 chunk 77 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 76 optimal weight: 0.4980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 137 GLN ** C 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12697 Z= 0.170 Angle : 0.508 10.036 17626 Z= 0.277 Chirality : 0.037 0.163 1969 Planarity : 0.003 0.035 1818 Dihedral : 18.370 79.445 2989 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.63 % Allowed : 16.06 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.24), residues: 1164 helix: 1.70 (0.23), residues: 513 sheet: -0.68 (0.41), residues: 144 loop : -1.94 (0.24), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 174 HIS 0.002 0.000 HIS C 425 PHE 0.011 0.001 PHE C 261 TYR 0.014 0.001 TYR B 26 ARG 0.007 0.000 ARG C 385 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 153 time to evaluate : 1.220 Fit side-chains revert: symmetry clash REVERT: A 101 GLN cc_start: 0.7806 (pt0) cc_final: 0.7558 (mt0) REVERT: A 149 MET cc_start: 0.9069 (tpt) cc_final: 0.8726 (tpt) REVERT: B 15 MET cc_start: 0.7751 (tmm) cc_final: 0.7508 (tmm) REVERT: C 39 GLN cc_start: 0.8090 (pm20) cc_final: 0.7378 (pm20) REVERT: C 157 GLU cc_start: 0.7416 (mt-10) cc_final: 0.7105 (mt-10) REVERT: C 447 MET cc_start: 0.6361 (ttt) cc_final: 0.6103 (ttp) REVERT: C 838 ASP cc_start: 0.8224 (t0) cc_final: 0.8020 (t70) REVERT: C 877 HIS cc_start: 0.6864 (m170) cc_final: 0.6490 (t-90) REVERT: C 991 GLU cc_start: 0.7607 (tt0) cc_final: 0.7341 (tt0) REVERT: C 1002 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7482 (mt-10) REVERT: C 1011 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7313 (mm-30) outliers start: 38 outliers final: 29 residues processed: 180 average time/residue: 0.2540 time to fit residues: 64.8819 Evaluate side-chains 177 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 147 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 440 TYR Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 854 THR Chi-restraints excluded: chain C residue 889 ILE Chi-restraints excluded: chain C residue 891 GLU Chi-restraints excluded: chain C residue 924 SER Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1002 GLU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1070 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 0.0870 chunk 23 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 11 optimal weight: 0.0980 chunk 96 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 overall best weight: 1.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12697 Z= 0.193 Angle : 0.530 11.166 17626 Z= 0.288 Chirality : 0.037 0.148 1969 Planarity : 0.003 0.035 1818 Dihedral : 18.341 79.468 2989 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.63 % Allowed : 16.44 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.24), residues: 1164 helix: 1.69 (0.23), residues: 513 sheet: -0.65 (0.41), residues: 144 loop : -1.93 (0.24), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 174 HIS 0.001 0.001 HIS C 348 PHE 0.009 0.001 PHE C 882 TYR 0.014 0.001 TYR B 26 ARG 0.009 0.000 ARG C 452 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 152 time to evaluate : 1.192 Fit side-chains REVERT: A 15 MET cc_start: 0.8657 (tmm) cc_final: 0.8404 (ttp) REVERT: A 101 GLN cc_start: 0.7808 (pt0) cc_final: 0.7565 (mt0) REVERT: A 149 MET cc_start: 0.9074 (tpt) cc_final: 0.8759 (tpt) REVERT: A 173 GLU cc_start: 0.7335 (tt0) cc_final: 0.7009 (mt-10) REVERT: B 15 MET cc_start: 0.7760 (tmm) cc_final: 0.7514 (tmm) REVERT: C 39 GLN cc_start: 0.8113 (pm20) cc_final: 0.7404 (pm20) REVERT: C 157 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7098 (mt-10) REVERT: C 447 MET cc_start: 0.6373 (ttt) cc_final: 0.6110 (ttp) REVERT: C 838 ASP cc_start: 0.8238 (t0) cc_final: 0.8037 (t70) REVERT: C 862 MET cc_start: 0.8047 (tpp) cc_final: 0.7577 (mpp) REVERT: C 869 LYS cc_start: 0.8698 (ttmt) cc_final: 0.8263 (ttmt) REVERT: C 877 HIS cc_start: 0.6874 (m170) cc_final: 0.6442 (t-90) REVERT: C 991 GLU cc_start: 0.7665 (tt0) cc_final: 0.7390 (tt0) REVERT: C 1002 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7484 (mt-10) REVERT: C 1011 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7328 (mm-30) outliers start: 38 outliers final: 35 residues processed: 176 average time/residue: 0.2518 time to fit residues: 63.2219 Evaluate side-chains 186 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 150 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 250 ASN Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 440 TYR Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 854 THR Chi-restraints excluded: chain C residue 889 ILE Chi-restraints excluded: chain C residue 891 GLU Chi-restraints excluded: chain C residue 962 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1002 GLU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1070 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 69 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 90 optimal weight: 0.0870 chunk 35 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 108 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 overall best weight: 2.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 137 GLN C 877 HIS ** C 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12697 Z= 0.274 Angle : 0.583 14.034 17626 Z= 0.314 Chirality : 0.040 0.148 1969 Planarity : 0.003 0.036 1818 Dihedral : 18.390 80.138 2989 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.82 % Allowed : 16.63 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.24), residues: 1164 helix: 1.54 (0.22), residues: 516 sheet: -0.67 (0.41), residues: 141 loop : -1.97 (0.24), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 174 HIS 0.001 0.001 HIS C 917 PHE 0.011 0.002 PHE C1044 TYR 0.017 0.002 TYR A 128 ARG 0.009 0.001 ARG C 452 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 149 time to evaluate : 1.297 Fit side-chains REVERT: A 15 MET cc_start: 0.8707 (tmm) cc_final: 0.8426 (ttp) REVERT: A 101 GLN cc_start: 0.7848 (pt0) cc_final: 0.7560 (mt0) REVERT: A 149 MET cc_start: 0.9091 (tpt) cc_final: 0.8782 (tpt) REVERT: A 173 GLU cc_start: 0.7380 (tt0) cc_final: 0.7068 (mt-10) REVERT: B 15 MET cc_start: 0.7809 (tmm) cc_final: 0.7538 (tmm) REVERT: C 39 GLN cc_start: 0.8192 (pm20) cc_final: 0.7425 (pm20) REVERT: C 157 GLU cc_start: 0.7381 (mt-10) cc_final: 0.7056 (mt-10) REVERT: C 447 MET cc_start: 0.6516 (ttt) cc_final: 0.6266 (ttp) REVERT: C 869 LYS cc_start: 0.8740 (ttmt) cc_final: 0.8332 (ttmt) REVERT: C 877 HIS cc_start: 0.6978 (m-70) cc_final: 0.6337 (t-90) REVERT: C 991 GLU cc_start: 0.7601 (tt0) cc_final: 0.7318 (tt0) REVERT: C 1002 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7534 (mt-10) REVERT: C 1011 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7364 (mm-30) outliers start: 40 outliers final: 35 residues processed: 174 average time/residue: 0.2444 time to fit residues: 61.3914 Evaluate side-chains 181 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 145 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 250 ASN Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 440 TYR Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 854 THR Chi-restraints excluded: chain C residue 889 ILE Chi-restraints excluded: chain C residue 891 GLU Chi-restraints excluded: chain C residue 962 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1002 GLU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1070 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 101 optimal weight: 0.9990 chunk 10 optimal weight: 0.0970 chunk 78 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 108 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12697 Z= 0.190 Angle : 0.535 12.470 17626 Z= 0.290 Chirality : 0.038 0.161 1969 Planarity : 0.003 0.035 1818 Dihedral : 18.351 80.014 2989 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.35 % Allowed : 17.21 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.24), residues: 1164 helix: 1.71 (0.23), residues: 513 sheet: -0.60 (0.41), residues: 144 loop : -1.90 (0.24), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 174 HIS 0.001 0.001 HIS C 115 PHE 0.012 0.001 PHE C 261 TYR 0.015 0.001 TYR B 26 ARG 0.009 0.000 ARG C 452 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 149 time to evaluate : 1.145 Fit side-chains REVERT: A 101 GLN cc_start: 0.7800 (pt0) cc_final: 0.7546 (mt0) REVERT: A 149 MET cc_start: 0.9067 (tpt) cc_final: 0.8759 (tpt) REVERT: A 173 GLU cc_start: 0.7336 (tt0) cc_final: 0.7007 (mt-10) REVERT: B 15 MET cc_start: 0.7766 (tmm) cc_final: 0.7512 (tmm) REVERT: C 39 GLN cc_start: 0.8131 (pm20) cc_final: 0.7404 (pm20) REVERT: C 157 GLU cc_start: 0.7368 (mt-10) cc_final: 0.7049 (mt-10) REVERT: C 181 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.7752 (pt) REVERT: C 447 MET cc_start: 0.6387 (ttt) cc_final: 0.6148 (ttp) REVERT: C 862 MET cc_start: 0.8061 (tpp) cc_final: 0.7579 (tpp) REVERT: C 869 LYS cc_start: 0.8708 (ttmt) cc_final: 0.8301 (ttmt) REVERT: C 877 HIS cc_start: 0.6975 (m-70) cc_final: 0.6342 (t-90) REVERT: C 991 GLU cc_start: 0.7666 (tt0) cc_final: 0.7384 (tt0) REVERT: C 1002 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7470 (mt-10) REVERT: C 1011 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7322 (mm-30) outliers start: 35 outliers final: 31 residues processed: 171 average time/residue: 0.2719 time to fit residues: 66.0514 Evaluate side-chains 174 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 141 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 367 MET Chi-restraints excluded: chain C residue 440 TYR Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 854 THR Chi-restraints excluded: chain C residue 889 ILE Chi-restraints excluded: chain C residue 891 GLU Chi-restraints excluded: chain C residue 924 SER Chi-restraints excluded: chain C residue 962 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1002 GLU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1070 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 9.9990 chunk 93 optimal weight: 0.0070 chunk 14 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 18 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 137 GLN ** C 944 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 = 0.3863 r_free = 0.3863 target = 0.161592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.128510 restraints weight = 16832.421| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.33 r_work: 0.3227 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12697 Z= 0.137 Angle : 0.495 9.619 17626 Z= 0.270 Chirality : 0.036 0.150 1969 Planarity : 0.003 0.035 1818 Dihedral : 18.284 78.587 2989 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.10 % Allowed : 18.83 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.25), residues: 1164 helix: 1.97 (0.23), residues: 517 sheet: -0.40 (0.43), residues: 144 loop : -1.82 (0.25), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP B 174 HIS 0.002 0.000 HIS C 348 PHE 0.008 0.001 PHE C 882 TYR 0.014 0.001 TYR B 26 ARG 0.008 0.000 ARG C 452 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2519.18 seconds wall clock time: 47 minutes 40.62 seconds (2860.62 seconds total)