Starting phenix.real_space_refine on Sun Aug 4 10:53:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8se9_40407/08_2024/8se9_40407.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8se9_40407/08_2024/8se9_40407.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/8se9_40407/08_2024/8se9_40407.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8se9_40407/08_2024/8se9_40407.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8se9_40407/08_2024/8se9_40407.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8se9_40407/08_2024/8se9_40407.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= 0.023 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 1 5.49 5 S 38 5.16 5 C 6480 2.51 5 N 1790 2.21 5 O 1886 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 832": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 881": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 10195 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 989, 7693 Classifications: {'peptide': 989} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 65, 'TRANS': 923} Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 633 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "C" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1243 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 133} Chain: "D" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 6.41, per 1000 atoms: 0.63 Number of scatterers: 10195 At special positions: 0 Unit cell: (91.652, 105.816, 117.481, 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 38 16.00 P 1 15.00 O 1886 8.00 N 1790 7.00 C 6480 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 599 " - pdb=" SG CYS C 86 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.05 Conformation dependent library (CDL) restraints added in 1.9 seconds 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2424 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 10 sheets defined 44.3% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 24 through 31 removed outlier: 3.533A pdb=" N ARG A 29 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN A 31 " --> pdb=" O MET A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 55 Processing helix chain 'A' and resid 68 through 72 removed outlier: 3.909A pdb=" N ASP A 71 " --> pdb=" O CYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 86 through 99 removed outlier: 3.919A pdb=" N GLU A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASN A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 119 removed outlier: 3.837A pdb=" N ASP A 118 " --> pdb=" O ASP A 114 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 142 Processing helix chain 'A' and resid 197 through 203 removed outlier: 4.268A pdb=" N HIS A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 Processing helix chain 'A' and resid 280 through 305 Processing helix chain 'A' and resid 312 through 326 Processing helix chain 'A' and resid 327 through 331 Processing helix chain 'A' and resid 342 through 352 Processing helix chain 'A' and resid 357 through 378 Processing helix chain 'A' and resid 391 through 395 removed outlier: 3.528A pdb=" N CYS A 394 " --> pdb=" O ALA A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 423 through 432 Processing helix chain 'A' and resid 441 through 455 Processing helix chain 'A' and resid 476 through 480 removed outlier: 3.921A pdb=" N ARG A 479 " --> pdb=" O ASN A 476 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN A 480 " --> pdb=" O LEU A 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 476 through 480' Processing helix chain 'A' and resid 484 through 488 removed outlier: 3.557A pdb=" N ASP A 487 " --> pdb=" O ARG A 484 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL A 488 " --> pdb=" O SER A 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 484 through 488' Processing helix chain 'A' and resid 491 through 504 Processing helix chain 'A' and resid 517 through 521 removed outlier: 3.835A pdb=" N GLU A 521 " --> pdb=" O PRO A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 530 Processing helix chain 'A' and resid 541 through 556 Processing helix chain 'A' and resid 585 through 593 removed outlier: 4.359A pdb=" N ASP A 593 " --> pdb=" O ALA A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 601 removed outlier: 3.602A pdb=" N THR A 600 " --> pdb=" O PRO A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 624 Processing helix chain 'A' and resid 624 through 631 removed outlier: 4.043A pdb=" N GLU A 628 " --> pdb=" O ARG A 624 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ASN A 631 " --> pdb=" O ALA A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 637 Processing helix chain 'A' and resid 644 through 653 removed outlier: 4.302A pdb=" N THR A 648 " --> pdb=" O ASP A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 682 removed outlier: 4.771A pdb=" N HIS A 676 " --> pdb=" O TRP A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 Processing helix chain 'A' and resid 722 through 740 removed outlier: 3.638A pdb=" N TYR A 727 " --> pdb=" O THR A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 756 Processing helix chain 'A' and resid 760 through 763 removed outlier: 3.512A pdb=" N GLN A 763 " --> pdb=" O PRO A 760 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 760 through 763' Processing helix chain 'A' and resid 764 through 770 removed outlier: 3.611A pdb=" N ILE A 768 " --> pdb=" O GLN A 764 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 798 Processing helix chain 'A' and resid 816 through 832 removed outlier: 3.553A pdb=" N PHE A 820 " --> pdb=" O PHE A 816 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 821 " --> pdb=" O HIS A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 844 Processing helix chain 'A' and resid 853 through 874 removed outlier: 3.678A pdb=" N LYS A 870 " --> pdb=" O LEU A 866 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY A 874 " --> pdb=" O LYS A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 881 Processing helix chain 'A' and resid 889 through 891 No H-bonds generated for 'chain 'A' and resid 889 through 891' Processing helix chain 'A' and resid 927 through 939 Processing helix chain 'A' and resid 959 through 967 Processing helix chain 'A' and resid 970 through 980 Processing helix chain 'B' and resid 103 through 116 removed outlier: 3.589A pdb=" N LEU B 107 " --> pdb=" O THR B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 141 removed outlier: 3.605A pdb=" N GLY B 141 " --> pdb=" O GLY B 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 17 removed outlier: 3.616A pdb=" N LYS C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS C 17 " --> pdb=" O ASP C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 49 removed outlier: 3.610A pdb=" N LEU C 48 " --> pdb=" O PRO C 45 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS C 49 " --> pdb=" O TYR C 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 49' Processing helix chain 'C' and resid 100 through 114 removed outlier: 3.642A pdb=" N VAL C 104 " --> pdb=" O LYS C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 132 Processing helix chain 'C' and resid 132 through 148 Processing helix chain 'D' and resid 103 through 116 removed outlier: 4.677A pdb=" N GLN D 109 " --> pdb=" O ALA D 105 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLN D 110 " --> pdb=" O HIS D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 141 removed outlier: 3.991A pdb=" N GLU D 139 " --> pdb=" O PRO D 136 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLY D 141 " --> pdb=" O GLY D 138 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 removed outlier: 7.869A pdb=" N HIS A 62 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL A 37 " --> pdb=" O HIS A 62 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU A 36 " --> pdb=" O VAL A 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 150 through 152 removed outlier: 3.630A pdb=" N VAL A 155 " --> pdb=" O ARG A 152 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 168 Processing sheet with id=AA4, first strand: chain 'A' and resid 226 through 227 removed outlier: 4.404A pdb=" N LEU A 208 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A 254 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS A 183 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 509 through 512 removed outlier: 6.853A pdb=" N LEU A 464 " --> pdb=" O ILE A 510 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU A 512 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N VAL A 466 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU A 437 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 559 " --> pdb=" O PHE A 574 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 904 through 906 Processing sheet with id=AA7, first strand: chain 'A' and resid 917 through 920 removed outlier: 6.354A pdb=" N LEU A 917 " --> pdb=" O HIS A1009 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLU A1011 " --> pdb=" O LEU A 917 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL A 919 " --> pdb=" O GLU A1011 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE A 945 " --> pdb=" O SER A 995 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ARG A 944 " --> pdb=" O ALA A 955 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA A 955 " --> pdb=" O ARG A 944 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU A 946 " --> pdb=" O LEU A 953 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 93 through 95 removed outlier: 6.689A pdb=" N LEU B 85 " --> pdb=" O VAL B 148 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N MET B 150 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ARG B 87 " --> pdb=" O MET B 150 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N LEU B 152 " --> pdb=" O ARG B 87 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 22 through 26 removed outlier: 6.025A pdb=" N ASN C 24 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LEU C 38 " --> pdb=" O ASN C 24 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 85 through 86 removed outlier: 7.757A pdb=" N LEU D 85 " --> pdb=" O VAL D 148 " (cutoff:3.500A) removed outlier: 9.398A pdb=" N MET D 150 " --> pdb=" O LEU D 85 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASN D 151 " --> pdb=" O TRP D 123 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N TRP D 123 " --> pdb=" O ASN D 151 " (cutoff:3.500A) 411 hydrogen bonds defined for protein. 1146 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: 3.72 Time building geometry restraints manager: 4.45 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: 3379 1.34 - 1.46: 1342 1.46 - 1.57: 5665 1.57 - 1.69: 4 1.69 - 1.81: 57 Bond restraints: 10447 Sorted by residual: bond pdb=" C1' AMP B1101 " pdb=" O4' AMP B1101 " ideal model delta sigma weight residual 1.415 1.624 -0.209 1.50e-02 4.44e+03 1.94e+02 bond pdb=" C1' AMP B1101 " pdb=" C2' AMP B1101 " ideal model delta sigma weight residual 1.526 1.363 0.163 1.50e-02 4.44e+03 1.17e+02 bond pdb=" C4' AMP B1101 " pdb=" O4' AMP B1101 " ideal model delta sigma weight residual 1.454 1.294 0.160 1.50e-02 4.44e+03 1.13e+02 bond pdb=" C6 AMP B1101 " pdb=" N6 AMP B1101 " ideal model delta sigma weight residual 1.355 1.499 -0.144 2.00e-02 2.50e+03 5.15e+01 bond pdb=" C4 AMP B1101 " pdb=" C5 AMP B1101 " ideal model delta sigma weight residual 1.490 1.375 0.115 2.00e-02 2.50e+03 3.30e+01 ... (remaining 10442 not shown) Histogram of bond angle deviations from ideal: 94.58 - 102.59: 36 102.59 - 110.60: 3292 110.60 - 118.61: 5178 118.61 - 126.62: 5507 126.62 - 134.63: 211 Bond angle restraints: 14224 Sorted by residual: angle pdb=" N9 AMP B1101 " pdb=" C1' AMP B1101 " pdb=" O4' AMP B1101 " ideal model delta sigma weight residual 108.20 94.58 13.62 1.50e+00 4.44e-01 8.24e+01 angle pdb=" C2' AMP B1101 " pdb=" C1' AMP B1101 " pdb=" N9 AMP B1101 " ideal model delta sigma weight residual 114.00 126.43 -12.43 1.50e+00 4.44e-01 6.87e+01 angle pdb=" C1' AMP B1101 " pdb=" C2' AMP B1101 " pdb=" C3' AMP B1101 " ideal model delta sigma weight residual 101.50 106.56 -5.06 1.00e+00 1.00e+00 2.56e+01 angle pdb=" O2P AMP B1101 " pdb=" P AMP B1101 " pdb=" O3P AMP B1101 " ideal model delta sigma weight residual 119.90 106.91 12.99 3.00e+00 1.11e-01 1.87e+01 angle pdb=" C GLY A 187 " pdb=" N SER A 188 " pdb=" CA SER A 188 " ideal model delta sigma weight residual 121.80 132.20 -10.40 2.44e+00 1.68e-01 1.82e+01 ... (remaining 14219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 5885 17.67 - 35.35: 323 35.35 - 53.02: 65 53.02 - 70.70: 14 70.70 - 88.37: 8 Dihedral angle restraints: 6295 sinusoidal: 2548 harmonic: 3747 Sorted by residual: dihedral pdb=" CA SER A 188 " pdb=" C SER A 188 " pdb=" N PRO A 189 " pdb=" CA PRO A 189 " ideal model delta harmonic sigma weight residual 180.00 162.10 17.90 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA GLN A 923 " pdb=" C GLN A 923 " pdb=" N PRO A 924 " pdb=" CA PRO A 924 " ideal model delta harmonic sigma weight residual 180.00 162.54 17.46 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" C1' AMP B1101 " pdb=" C4' AMP B1101 " pdb=" O4' AMP B1101 " pdb=" C5' AMP B1101 " ideal model delta sinusoidal sigma weight residual -123.00 -145.10 22.10 1 8.00e+00 1.56e-02 1.10e+01 ... (remaining 6292 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 987 0.029 - 0.058: 416 0.058 - 0.087: 106 0.087 - 0.116: 69 0.116 - 0.145: 10 Chirality restraints: 1588 Sorted by residual: chirality pdb=" C2' AMP B1101 " pdb=" C1' AMP B1101 " pdb=" C3' AMP B1101 " pdb=" O2' AMP B1101 " both_signs ideal model delta sigma weight residual False -2.52 -2.37 -0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA ILE A 945 " pdb=" N ILE A 945 " pdb=" C ILE A 945 " pdb=" CB ILE A 945 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CB ILE A 184 " pdb=" CA ILE A 184 " pdb=" CG1 ILE A 184 " pdb=" CG2 ILE A 184 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.13 2.00e-01 2.50e+01 4.15e-01 ... (remaining 1585 not shown) Planarity restraints: 1865 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 517 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO A 518 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 518 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 518 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 188 " 0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO A 189 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 189 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 189 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 923 " -0.018 5.00e-02 4.00e+02 2.76e-02 1.22e+00 pdb=" N PRO A 924 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 924 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 924 " -0.015 5.00e-02 4.00e+02 ... (remaining 1862 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 1 2.04 - 2.76: 1481 2.76 - 3.47: 14129 3.47 - 4.19: 22738 4.19 - 4.90: 41480 Nonbonded interactions: 79829 Sorted by model distance: nonbonded pdb=" NZ LYS C 121 " pdb=" C GLY D 157 " model vdw 1.330 3.350 nonbonded pdb=" OE1 GLU A 925 " pdb=" OG1 THR A 972 " model vdw 2.204 3.040 nonbonded pdb=" O TYR A 514 " pdb=" OH TYR A 524 " model vdw 2.219 3.040 nonbonded pdb=" NZ LYS C 121 " pdb=" O GLY D 157 " model vdw 2.230 3.120 nonbonded pdb=" OH TYR C 46 " pdb=" O TYR C 75 " model vdw 2.235 3.040 ... (remaining 79824 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 'B' and resid 82 through 157) selection = chain 'D' } 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: 3.300 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: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 32.100 Find NCS groups from input model: 0.150 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: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.209 10447 Z= 0.313 Angle : 0.583 13.618 14224 Z= 0.292 Chirality : 0.038 0.145 1588 Planarity : 0.004 0.048 1865 Dihedral : 11.987 88.369 3868 Min Nonbonded Distance : 1.330 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.41 % Favored : 96.43 % Rotamer: Outliers : 2.00 % Allowed : 7.45 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.48 (0.24), residues: 1289 helix: 1.53 (0.24), residues: 457 sheet: -0.62 (0.40), residues: 171 loop : -0.21 (0.25), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 95 HIS 0.002 0.001 HIS A 275 PHE 0.008 0.001 PHE A 146 TYR 0.008 0.001 TYR C 61 ARG 0.002 0.000 ARG C 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 133 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8696 (mp) REVERT: A 225 PRO cc_start: 0.8058 (Cg_exo) cc_final: 0.7802 (Cg_endo) REVERT: A 273 GLN cc_start: 0.7357 (tm-30) cc_final: 0.6964 (tm-30) REVERT: A 373 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8519 (mm) REVERT: A 508 GLN cc_start: 0.7662 (mm-40) cc_final: 0.7171 (mt0) REVERT: A 531 ARG cc_start: 0.7921 (mtm110) cc_final: 0.7513 (ptp-110) REVERT: A 638 THR cc_start: 0.3737 (OUTLIER) cc_final: 0.3268 (m) REVERT: A 738 MET cc_start: 0.3515 (ppp) cc_final: 0.0513 (mmm) REVERT: C 5 MET cc_start: 0.8894 (tpt) cc_final: 0.8506 (tpt) REVERT: C 43 GLN cc_start: 0.7700 (tm-30) cc_final: 0.7496 (tm-30) REVERT: C 70 PHE cc_start: 0.8614 (OUTLIER) cc_final: 0.8004 (m-80) REVERT: D 99 ARG cc_start: 0.8030 (mmp-170) cc_final: 0.7529 (mmm160) outliers start: 22 outliers final: 10 residues processed: 152 average time/residue: 0.2481 time to fit residues: 51.9159 Evaluate side-chains 119 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 105 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain D residue 110 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 8.9990 chunk 74 optimal weight: 9.9990 chunk 116 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 HIS A 199 ASN A 634 GLN A 637 HIS A 786 GLN A 817 HIS A1009 HIS B 106 HIS B 110 GLN C 103 GLN D 106 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10447 Z= 0.264 Angle : 0.590 10.389 14224 Z= 0.288 Chirality : 0.040 0.247 1588 Planarity : 0.004 0.056 1865 Dihedral : 6.095 59.006 1432 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.03 % Favored : 96.90 % Rotamer: Outliers : 2.36 % Allowed : 10.45 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.36 (0.24), residues: 1289 helix: 1.48 (0.24), residues: 469 sheet: -0.65 (0.40), residues: 170 loop : -0.37 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 677 HIS 0.008 0.001 HIS A 682 PHE 0.014 0.001 PHE A 481 TYR 0.013 0.001 TYR B 140 ARG 0.005 0.000 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 111 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8837 (mp) REVERT: A 225 PRO cc_start: 0.8163 (Cg_exo) cc_final: 0.7942 (Cg_endo) REVERT: A 231 ARG cc_start: 0.6732 (ttm170) cc_final: 0.6501 (ttm170) REVERT: A 273 GLN cc_start: 0.7383 (tm-30) cc_final: 0.6975 (tm-30) REVERT: A 508 GLN cc_start: 0.7667 (mm-40) cc_final: 0.7161 (mt0) REVERT: A 531 ARG cc_start: 0.7918 (mtm110) cc_final: 0.7520 (ptp-110) REVERT: A 568 TRP cc_start: 0.8864 (m100) cc_final: 0.8580 (m100) REVERT: A 638 THR cc_start: 0.3711 (OUTLIER) cc_final: 0.3415 (m) REVERT: A 738 MET cc_start: 0.3577 (ppp) cc_final: 0.0627 (mmm) REVERT: C 5 MET cc_start: 0.8910 (tpt) cc_final: 0.8495 (tpt) REVERT: C 43 GLN cc_start: 0.7677 (tm-30) cc_final: 0.7467 (tm-30) REVERT: C 70 PHE cc_start: 0.8596 (OUTLIER) cc_final: 0.7921 (m-80) REVERT: D 99 ARG cc_start: 0.8142 (mmp-170) cc_final: 0.7590 (mmm160) REVERT: D 110 GLN cc_start: 0.1744 (OUTLIER) cc_final: 0.1250 (mp10) outliers start: 26 outliers final: 13 residues processed: 129 average time/residue: 0.2464 time to fit residues: 44.5248 Evaluate side-chains 124 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 107 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain D residue 110 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 0.0770 chunk 36 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 32 optimal weight: 0.5980 chunk 116 optimal weight: 0.8980 chunk 125 optimal weight: 9.9990 chunk 103 optimal weight: 0.2980 chunk 115 optimal weight: 9.9990 chunk 39 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 610 HIS A 908 HIS A 939 HIS C 103 GLN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10447 Z= 0.160 Angle : 0.538 10.360 14224 Z= 0.257 Chirality : 0.038 0.127 1588 Planarity : 0.004 0.054 1865 Dihedral : 5.937 58.722 1428 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.10 % Favored : 96.82 % Rotamer: Outliers : 2.09 % Allowed : 11.91 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.47 (0.24), residues: 1289 helix: 1.62 (0.24), residues: 468 sheet: -0.68 (0.40), residues: 164 loop : -0.33 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 677 HIS 0.004 0.001 HIS A 682 PHE 0.013 0.001 PHE A 481 TYR 0.007 0.001 TYR A 547 ARG 0.004 0.000 ARG C 23 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 115 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8798 (mp) REVERT: A 225 PRO cc_start: 0.8281 (Cg_exo) cc_final: 0.8044 (Cg_endo) REVERT: A 231 ARG cc_start: 0.6658 (ttm170) cc_final: 0.6354 (ttm170) REVERT: A 273 GLN cc_start: 0.7336 (tm-30) cc_final: 0.7055 (tm-30) REVERT: A 373 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8482 (mm) REVERT: A 508 GLN cc_start: 0.7653 (mm-40) cc_final: 0.7386 (pt0) REVERT: A 531 ARG cc_start: 0.7914 (mtm110) cc_final: 0.7521 (ptp-110) REVERT: A 568 TRP cc_start: 0.8867 (m100) cc_final: 0.8599 (m100) REVERT: A 638 THR cc_start: 0.3769 (OUTLIER) cc_final: 0.3497 (m) REVERT: A 738 MET cc_start: 0.3706 (ppp) cc_final: 0.0844 (mmm) REVERT: B 140 TYR cc_start: 0.8108 (m-80) cc_final: 0.7461 (m-10) REVERT: C 5 MET cc_start: 0.8863 (tpt) cc_final: 0.8480 (tpt) REVERT: C 43 GLN cc_start: 0.7679 (tm-30) cc_final: 0.7445 (tm-30) REVERT: C 128 LEU cc_start: 0.8313 (mp) cc_final: 0.7987 (tt) REVERT: D 99 ARG cc_start: 0.8153 (mmp-170) cc_final: 0.7663 (mmm160) REVERT: D 110 GLN cc_start: 0.1804 (OUTLIER) cc_final: 0.1379 (mp10) outliers start: 23 outliers final: 12 residues processed: 132 average time/residue: 0.2364 time to fit residues: 44.2483 Evaluate side-chains 127 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 111 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain D residue 110 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 60 optimal weight: 20.0000 chunk 12 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10447 Z= 0.314 Angle : 0.577 10.335 14224 Z= 0.276 Chirality : 0.040 0.131 1588 Planarity : 0.004 0.056 1865 Dihedral : 6.123 59.741 1426 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.95 % Favored : 96.97 % Rotamer: Outliers : 2.73 % Allowed : 11.91 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.31 (0.24), residues: 1289 helix: 1.46 (0.24), residues: 471 sheet: -0.71 (0.40), residues: 170 loop : -0.42 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 677 HIS 0.003 0.001 HIS A 291 PHE 0.011 0.001 PHE A 481 TYR 0.009 0.001 TYR C 61 ARG 0.005 0.000 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 108 time to evaluate : 1.168 Fit side-chains revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8918 (mp) REVERT: A 225 PRO cc_start: 0.8243 (Cg_exo) cc_final: 0.7995 (Cg_endo) REVERT: A 231 ARG cc_start: 0.6691 (ttm170) cc_final: 0.6421 (ttm170) REVERT: A 273 GLN cc_start: 0.7332 (tm-30) cc_final: 0.7053 (tm-30) REVERT: A 373 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8610 (mm) REVERT: A 508 GLN cc_start: 0.7664 (mm-40) cc_final: 0.7240 (pt0) REVERT: A 531 ARG cc_start: 0.7910 (mtm110) cc_final: 0.7489 (ptp-110) REVERT: A 568 TRP cc_start: 0.8896 (m100) cc_final: 0.8610 (m100) REVERT: A 638 THR cc_start: 0.3855 (OUTLIER) cc_final: 0.3558 (m) REVERT: A 713 GLN cc_start: 0.9047 (tt0) cc_final: 0.8726 (pp30) REVERT: A 738 MET cc_start: 0.3780 (ppp) cc_final: 0.0964 (mmm) REVERT: A 864 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8702 (mt) REVERT: B 140 TYR cc_start: 0.8214 (m-80) cc_final: 0.7896 (m-10) REVERT: C 5 MET cc_start: 0.8894 (tpt) cc_final: 0.8507 (tpt) REVERT: C 43 GLN cc_start: 0.7694 (tm-30) cc_final: 0.7455 (tm-30) REVERT: C 70 PHE cc_start: 0.8634 (OUTLIER) cc_final: 0.7914 (m-80) REVERT: C 128 LEU cc_start: 0.8243 (mp) cc_final: 0.7858 (tt) REVERT: D 99 ARG cc_start: 0.8174 (mmp-170) cc_final: 0.7675 (mmm160) REVERT: D 110 GLN cc_start: 0.2112 (OUTLIER) cc_final: 0.1779 (mp10) outliers start: 30 outliers final: 16 residues processed: 132 average time/residue: 0.2299 time to fit residues: 42.9961 Evaluate side-chains 126 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 104 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain D residue 110 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- 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: 56.4137 > 50: distance: 68 - 95: 5.582 distance: 70 - 79: 6.590 distance: 71 - 92: 17.243 distance: 79 - 80: 9.956 distance: 80 - 81: 11.521 distance: 81 - 82: 11.419 distance: 81 - 88: 10.967 distance: 83 - 84: 4.403 distance: 84 - 85: 3.741 distance: 88 - 89: 16.719 distance: 89 - 90: 23.408 distance: 90 - 91: 21.640 distance: 90 - 92: 34.416 distance: 92 - 93: 15.516 distance: 93 - 94: 41.676 distance: 93 - 96: 25.177 distance: 94 - 95: 29.887 distance: 94 - 101: 56.414 distance: 96 - 97: 14.104 distance: 97 - 98: 5.391 distance: 98 - 99: 3.299 distance: 101 - 102: 55.064 distance: 101 - 107: 39.324 distance: 102 - 103: 33.405 distance: 102 - 105: 35.202 distance: 103 - 104: 15.180 distance: 103 - 108: 24.604 distance: 105 - 106: 12.831 distance: 106 - 107: 17.991 distance: 108 - 109: 8.154 distance: 109 - 110: 5.875 distance: 109 - 112: 5.821 distance: 110 - 111: 9.288 distance: 110 - 116: 4.599 distance: 112 - 113: 5.759 distance: 113 - 115: 3.036 distance: 116 - 117: 6.137 distance: 117 - 118: 12.387 distance: 117 - 120: 8.735 distance: 118 - 119: 10.964 distance: 118 - 125: 12.913 distance: 120 - 121: 6.722 distance: 121 - 122: 3.306 distance: 125 - 126: 9.724 distance: 126 - 127: 24.540 distance: 126 - 129: 4.886 distance: 127 - 128: 17.219 distance: 127 - 133: 26.035 distance: 129 - 130: 6.139 distance: 130 - 131: 3.938 distance: 130 - 132: 5.007 distance: 133 - 134: 31.335 distance: 134 - 135: 30.804 distance: 134 - 137: 39.374 distance: 135 - 136: 16.598 distance: 135 - 142: 6.593 distance: 137 - 138: 7.615 distance: 138 - 139: 12.033 distance: 139 - 140: 3.525 distance: 139 - 141: 8.476 distance: 142 - 143: 8.597 distance: 143 - 144: 12.556 distance: 143 - 146: 24.002 distance: 144 - 145: 22.175 distance: 144 - 150: 22.482 distance: 146 - 147: 29.410 distance: 147 - 148: 20.106 distance: 147 - 149: 26.591 distance: 150 - 151: 23.737 distance: 150 - 156: 8.941 distance: 151 - 152: 32.948 distance: 151 - 154: 31.577 distance: 152 - 153: 18.662 distance: 152 - 157: 18.658 distance: 153 - 167: 8.916 distance: 154 - 155: 16.423 distance: 155 - 156: 8.841