Starting phenix.real_space_refine on Fri Aug 2 19:48:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4z_14511/08_2024/7z4z_14511.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4z_14511/08_2024/7z4z_14511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4z_14511/08_2024/7z4z_14511.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4z_14511/08_2024/7z4z_14511.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4z_14511/08_2024/7z4z_14511.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4z_14511/08_2024/7z4z_14511.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 11 5.16 5 C 3082 2.51 5 N 838 2.21 5 O 886 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 113": "OE1" <-> "OE2" Residue "B PHE 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B ASP 754": "OD1" <-> "OD2" Residue "C GLU 113": "OE1" <-> "OE2" Residue "C PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 668": "OD1" <-> "OD2" Residue "D ASP 781": "OD1" <-> "OD2" Residue "D ASP 787": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 4817 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1096 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 7, 'TRANS': 141} Chain breaks: 1 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 72 Chain: "B" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1317 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 13, 'TRANS': 174} Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 162 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 4, 'GLU:plan': 10, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 114 Chain: "C" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1111 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 7, 'TRANS': 144} Chain breaks: 1 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 89 Chain: "D" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1293 Classifications: {'peptide': 184} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 13, 'TRANS': 170} Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 229 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 101 Time building chain proxies: 3.52, per 1000 atoms: 0.73 Number of scatterers: 4817 At special positions: 0 Unit cell: (67.828, 74.392, 110.494, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 11 16.00 O 886 8.00 N 838 7.00 C 3082 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 967.5 milliseconds 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1282 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 3 sheets defined 29.1% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 63 through 74 removed outlier: 4.007A pdb=" N ASN A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ARG A 72 " --> pdb=" O GLN A 68 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYS A 73 " --> pdb=" O GLU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 124 removed outlier: 3.664A pdb=" N GLU A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 645 removed outlier: 3.799A pdb=" N TYR B 643 " --> pdb=" O GLU B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 654 Processing helix chain 'B' and resid 703 through 710 removed outlier: 3.698A pdb=" N ASN B 709 " --> pdb=" O GLU B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 767 removed outlier: 3.517A pdb=" N GLN B 767 " --> pdb=" O ILE B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 807 Processing helix chain 'C' and resid 62 through 74 removed outlier: 3.853A pdb=" N GLN C 68 " --> pdb=" O ARG C 64 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS C 71 " --> pdb=" O ASN C 67 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG C 72 " --> pdb=" O GLN C 68 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS C 73 " --> pdb=" O GLU C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 107 removed outlier: 3.716A pdb=" N GLN C 107 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 126 removed outlier: 4.070A pdb=" N VAL C 120 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS C 121 " --> pdb=" O SER C 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 641 removed outlier: 3.915A pdb=" N GLU D 641 " --> pdb=" O GLY D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 703 through 709 removed outlier: 4.299A pdb=" N ASN D 709 " --> pdb=" O GLU D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 734 through 736 No H-bonds generated for 'chain 'D' and resid 734 through 736' Processing helix chain 'D' and resid 754 through 770 removed outlier: 3.641A pdb=" N SER D 758 " --> pdb=" O ASP D 754 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL D 759 " --> pdb=" O ASN D 755 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU D 760 " --> pdb=" O ARG D 756 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS D 768 " --> pdb=" O GLN D 764 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 805 removed outlier: 3.617A pdb=" N TYR D 805 " --> pdb=" O GLU D 801 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 179 through 182 removed outlier: 3.800A pdb=" N SER A 171 " --> pdb=" O LYS A 182 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE C 97 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TYR A 174 " --> pdb=" O LEU C 95 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU C 95 " --> pdb=" O TYR A 174 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY C 170 " --> pdb=" O PHE A 99 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 725 through 732 removed outlier: 6.856A pdb=" N VAL B 695 " --> pdb=" O PHE B 677 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE B 677 " --> pdb=" O VAL B 695 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLU B 697 " --> pdb=" O VAL B 675 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL B 673 " --> pdb=" O LEU B 699 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ARG B 701 " --> pdb=" O TRP B 671 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N TRP B 671 " --> pdb=" O ARG B 701 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY B 672 " --> pdb=" O VAL B 660 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LYS B 661 " --> pdb=" O SER B 737 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 727 through 732 removed outlier: 3.701A pdb=" N VAL D 673 " --> pdb=" O LEU D 699 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ASP D 668 " --> pdb=" O ASN D 664 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ASN D 664 " --> pdb=" O ASP D 668 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLY D 670 " --> pdb=" O VAL D 662 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL D 662 " --> pdb=" O GLY D 670 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ARG D 658 " --> pdb=" O VAL D 674 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N VAL D 742 " --> pdb=" O LEU D 659 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N LYS D 661 " --> pdb=" O SER D 740 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N SER D 740 " --> pdb=" O LYS D 661 " (cutoff:3.500A) 146 hydrogen bonds defined for protein. 420 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: 1.11 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 827 1.29 - 1.42: 1136 1.42 - 1.55: 2927 1.55 - 1.68: 0 1.68 - 1.81: 16 Bond restraints: 4906 Sorted by residual: bond pdb=" C PHE C 207 " pdb=" O PHE C 207 " ideal model delta sigma weight residual 1.230 1.164 0.066 1.74e-02 3.30e+03 1.44e+01 bond pdb=" CG ASP B 754 " pdb=" OD1 ASP B 754 " ideal model delta sigma weight residual 1.249 1.185 0.064 1.90e-02 2.77e+03 1.15e+01 bond pdb=" N ARG B 751 " pdb=" CA ARG B 751 " ideal model delta sigma weight residual 1.457 1.504 -0.047 1.41e-02 5.03e+03 1.11e+01 bond pdb=" CA PHE C 207 " pdb=" C PHE C 207 " ideal model delta sigma weight residual 1.532 1.490 0.042 1.41e-02 5.03e+03 9.05e+00 bond pdb=" N VAL B 753 " pdb=" CA VAL B 753 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.90e+00 ... (remaining 4901 not shown) Histogram of bond angle deviations from ideal: 99.26 - 106.20: 161 106.20 - 113.14: 2683 113.14 - 120.09: 1639 120.09 - 127.03: 2166 127.03 - 133.98: 47 Bond angle restraints: 6696 Sorted by residual: angle pdb=" N ASN B 755 " pdb=" CA ASN B 755 " pdb=" C ASN B 755 " ideal model delta sigma weight residual 112.23 99.26 12.97 1.26e+00 6.30e-01 1.06e+02 angle pdb=" CA ASP B 754 " pdb=" CB ASP B 754 " pdb=" CG ASP B 754 " ideal model delta sigma weight residual 112.60 105.68 6.92 1.00e+00 1.00e+00 4.78e+01 angle pdb=" N ASP B 754 " pdb=" CA ASP B 754 " pdb=" C ASP B 754 " ideal model delta sigma weight residual 114.75 107.82 6.93 1.26e+00 6.30e-01 3.03e+01 angle pdb=" C VAL C 206 " pdb=" N PHE C 207 " pdb=" CA PHE C 207 " ideal model delta sigma weight residual 123.04 115.84 7.20 1.59e+00 3.96e-01 2.05e+01 angle pdb=" CA ASP B 754 " pdb=" C ASP B 754 " pdb=" N ASN B 755 " ideal model delta sigma weight residual 119.80 114.03 5.77 1.34e+00 5.57e-01 1.85e+01 ... (remaining 6691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 2712 17.69 - 35.37: 220 35.37 - 53.06: 42 53.06 - 70.74: 8 70.74 - 88.43: 4 Dihedral angle restraints: 2986 sinusoidal: 1024 harmonic: 1962 Sorted by residual: dihedral pdb=" C ARG B 751 " pdb=" N ARG B 751 " pdb=" CA ARG B 751 " pdb=" CB ARG B 751 " ideal model delta harmonic sigma weight residual -122.60 -137.03 14.43 0 2.50e+00 1.60e-01 3.33e+01 dihedral pdb=" N ARG B 751 " pdb=" C ARG B 751 " pdb=" CA ARG B 751 " pdb=" CB ARG B 751 " ideal model delta harmonic sigma weight residual 122.80 136.97 -14.17 0 2.50e+00 1.60e-01 3.21e+01 dihedral pdb=" CA ALA A 165 " pdb=" C ALA A 165 " pdb=" N PHE A 166 " pdb=" CA PHE A 166 " ideal model delta harmonic sigma weight residual -180.00 -152.43 -27.57 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 2983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 756 0.100 - 0.200: 41 0.200 - 0.299: 1 0.299 - 0.399: 0 0.399 - 0.499: 1 Chirality restraints: 799 Sorted by residual: chirality pdb=" CA ARG B 751 " pdb=" N ARG B 751 " pdb=" C ARG B 751 " pdb=" CB ARG B 751 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.22e+00 chirality pdb=" CA HIS C 209 " pdb=" N HIS C 209 " pdb=" C HIS C 209 " pdb=" CB HIS C 209 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA ASN B 755 " pdb=" N ASN B 755 " pdb=" C ASN B 755 " pdb=" CB ASN B 755 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.47e-01 ... (remaining 796 not shown) Planarity restraints: 881 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 754 " 0.019 2.00e-02 2.50e+03 3.93e-02 1.54e+01 pdb=" C ASP B 754 " -0.068 2.00e-02 2.50e+03 pdb=" O ASP B 754 " 0.027 2.00e-02 2.50e+03 pdb=" N ASN B 755 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 207 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.19e+00 pdb=" C PHE C 207 " 0.046 2.00e-02 2.50e+03 pdb=" O PHE C 207 " -0.018 2.00e-02 2.50e+03 pdb=" N SER C 208 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS D 719 " 0.043 5.00e-02 4.00e+02 6.50e-02 6.77e+00 pdb=" N PRO D 720 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO D 720 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 720 " 0.036 5.00e-02 4.00e+02 ... (remaining 878 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 1476 2.82 - 3.34: 4438 3.34 - 3.86: 7059 3.86 - 4.38: 7728 4.38 - 4.90: 13370 Nonbonded interactions: 34071 Sorted by model distance: nonbonded pdb=" O LEU A 77 " pdb=" OG1 THR A 78 " model vdw 2.305 3.040 nonbonded pdb=" OD1 ASN A 189 " pdb=" N GLU A 190 " model vdw 2.309 3.120 nonbonded pdb=" O GLU B 641 " pdb=" ND1 HIS B 645 " model vdw 2.329 3.120 nonbonded pdb=" OD2 ASP A 181 " pdb=" NH1 ARG B 743 " model vdw 2.391 3.120 nonbonded pdb=" N ASN B 755 " pdb=" N ARG B 756 " model vdw 2.402 2.560 ... (remaining 34066 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' and (resid 61 through 78 or (resid 79 and (name N or name CA or name \ C or name O or name CB )) or resid 80 through 89 or (resid 90 through 91 and (na \ me N or name CA or name C or name O or name CB )) or resid 92 through 100 or (re \ sid 101 through 103 and (name N or name CA or name C or name O or name CB )) or \ resid 104 through 120 or (resid 121 and (name N or name CA or name C or name O o \ r name CB )) or resid 122 through 123 or (resid 124 through 125 and (name N or n \ ame CA or name C or name O or name CB )) or resid 126 through 131 or (resid 132 \ through 136 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 7 through 148 or (resid 149 through 165 and (name N or name CA or name C or name \ O or name CB )) or resid 166 through 195 or (resid 196 and (name N or name CA o \ r name C or name O or name CB )) or resid 197 through 198 or (resid 199 and (nam \ e N or name CA or name C or name O or name CB )) or resid 200 through 208 or (re \ sid 209 and (name N or name CA or name C or name O or name CB )) or resid 210 th \ rough 218)) selection = (chain 'C' and ((resid 61 through 66 and (name N or name CA or name C or name O \ or name CB )) or resid 67 through 68 or (resid 69 and (name N or name CA or name \ C or name O or name CB )) or resid 70 through 84 or (resid 85 through 91 and (n \ ame N or name CA or name C or name O or name CB )) or resid 92 through 130 or (r \ esid 131 through 136 and (name N or name CA or name C or name O or name CB )) or \ resid 137 through 147 or (resid 148 through 165 and (name N or name CA or name \ C or name O or name CB )) or resid 166 through 168 or (resid 169 and (name N or \ name CA or name C or name O or name CB )) or resid 170 through 211 or (resid 212 \ through 214 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 15 through 218)) } ncs_group { reference = (chain 'B' and (resid 624 through 637 or (resid 638 through 639 and (name N or n \ ame CA or name C or name O or name CB )) or resid 640 through 703 or (resid 704 \ and (name N or name CA or name C or name O or name CB )) or resid 705 through 72 \ 4 or (resid 725 through 726 and (name N or name CA or name C or name O or name C \ B )) or resid 727 through 744 or (resid 745 and (name N or name CA or name C or \ name O or name CB )) or resid 746 through 773 or (resid 774 and (name N or name \ CA or name C or name O or name CB )) or resid 775 through 792 or (resid 793 thro \ ugh 794 and (name N or name CA or name C or name O or name CB )) or resid 795 or \ (resid 796 through 807 and (name N or name CA or name C or name O or name CB )) \ )) selection = (chain 'D' and (resid 624 through 641 or (resid 642 and (name N or name CA or na \ me C or name O or name CB )) or resid 643 through 663 or (resid 664 through 665 \ and (name N or name CA or name C or name O or name CB )) or resid 666 or (resid \ 667 and (name N or name CA or name C or name O or name CB )) or resid 668 throug \ h 677 or (resid 678 through 684 and (name N or name CA or name C or name O or na \ me CB )) or resid 685 through 718 or (resid 719 and (name N or name CA or name C \ or name O or name CB )) or resid 720 or (resid 721 through 723 and (name N or n \ ame CA or name C or name O or name CB )) or resid 724 through 730 or (resid 731 \ and (name N or name CA or name C or name O or name CB )) or resid 732 through 76 \ 3 or (resid 764 and (name N or name CA or name C or name O or name CB )) or resi \ d 765 through 779 or (resid 780 and (name N or name CA or name C or name O or na \ me CB )) or resid 781 through 801 or (resid 802 through 807 and (name N or name \ CA or name C or name O or name CB )))) } 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=0.00 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.360 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.770 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 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 : 0.003 0.066 4906 Z= 0.232 Angle : 0.751 12.974 6696 Z= 0.431 Chirality : 0.050 0.499 799 Planarity : 0.006 0.065 881 Dihedral : 14.175 88.428 1704 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.61 % Allowed : 2.12 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.16 % 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: -4.82 (0.25), residues: 661 helix: -2.09 (0.32), residues: 184 sheet: -1.39 (1.44), residues: 16 loop : -4.10 (0.22), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 198 HIS 0.002 0.000 HIS B 645 PHE 0.039 0.001 PHE C 207 TYR 0.008 0.001 TYR D 649 ARG 0.002 0.000 ARG D 701 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 658 ARG cc_start: 0.8583 (mmm160) cc_final: 0.8160 (mmm160) REVERT: B 708 LYS cc_start: 0.9000 (tppt) cc_final: 0.8467 (mtmm) REVERT: B 761 LYS cc_start: 0.8256 (mtpp) cc_final: 0.7627 (mptt) REVERT: C 173 LEU cc_start: 0.9141 (tp) cc_final: 0.8753 (tp) REVERT: C 191 ASN cc_start: 0.9025 (t0) cc_final: 0.8719 (t0) REVERT: D 642 GLU cc_start: 0.7054 (mm-30) cc_final: 0.6767 (mp0) REVERT: D 655 GLN cc_start: 0.8109 (mt0) cc_final: 0.7851 (mt0) REVERT: D 768 LYS cc_start: 0.8696 (pttm) cc_final: 0.7556 (tppt) REVERT: D 788 GLN cc_start: 0.7973 (mp10) cc_final: 0.7748 (mp10) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.1780 time to fit residues: 49.1659 Evaluate side-chains 181 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 27 optimal weight: 0.0470 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 757 GLN C 67 ASN C 118 ASN ** D 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 764 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 4906 Z= 0.258 Angle : 0.719 9.259 6696 Z= 0.361 Chirality : 0.047 0.190 799 Planarity : 0.005 0.062 881 Dihedral : 4.843 20.550 697 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.45 % Allowed : 12.41 % Favored : 87.14 % Rotamer: Outliers : 4.63 % Allowed : 16.30 % Favored : 79.07 % 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: -3.58 (0.29), residues: 661 helix: -0.36 (0.36), residues: 194 sheet: -1.34 (1.13), residues: 21 loop : -3.68 (0.24), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 198 HIS 0.005 0.001 HIS C 109 PHE 0.010 0.001 PHE C 115 TYR 0.007 0.001 TYR A 203 ARG 0.005 0.001 ARG D 751 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 207 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ARG cc_start: 0.6844 (tpt170) cc_final: 0.6185 (tpt170) REVERT: A 111 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7206 (mt-10) REVERT: B 708 LYS cc_start: 0.9089 (tppt) cc_final: 0.8434 (mtmm) REVERT: B 725 GLU cc_start: 0.7316 (tm-30) cc_final: 0.6941 (tm-30) REVERT: B 761 LYS cc_start: 0.8286 (mtpp) cc_final: 0.7593 (mptt) REVERT: C 115 PHE cc_start: 0.8307 (t80) cc_final: 0.8082 (t80) REVERT: C 173 LEU cc_start: 0.9156 (tp) cc_final: 0.8741 (tp) REVERT: C 189 ASN cc_start: 0.8534 (m110) cc_final: 0.8147 (m110) REVERT: C 203 TYR cc_start: 0.8419 (p90) cc_final: 0.7934 (p90) REVERT: D 646 LYS cc_start: 0.7782 (mmmt) cc_final: 0.7432 (mmmt) REVERT: D 764 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7975 (mt0) REVERT: D 768 LYS cc_start: 0.8702 (pttm) cc_final: 0.7922 (tppt) outliers start: 21 outliers final: 13 residues processed: 212 average time/residue: 0.1690 time to fit residues: 44.7791 Evaluate side-chains 214 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 200 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain B residue 645 HIS Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 785 ILE Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain D residue 650 CYS Chi-restraints excluded: chain D residue 710 SER Chi-restraints excluded: chain D residue 733 VAL Chi-restraints excluded: chain D residue 764 GLN Chi-restraints excluded: chain D residue 781 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 0.0030 chunk 18 optimal weight: 7.9990 chunk 49 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 20 optimal weight: 0.3980 chunk 47 optimal weight: 1.9990 overall best weight: 0.8194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 767 GLN C 67 ASN ** D 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 4906 Z= 0.204 Angle : 0.675 10.364 6696 Z= 0.336 Chirality : 0.046 0.178 799 Planarity : 0.005 0.064 881 Dihedral : 4.797 22.186 697 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.89 % Favored : 88.80 % Rotamer: Outliers : 4.19 % Allowed : 23.57 % Favored : 72.25 % 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: -2.89 (0.31), residues: 661 helix: 0.46 (0.38), residues: 193 sheet: -0.11 (1.72), residues: 11 loop : -3.34 (0.25), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 671 HIS 0.002 0.001 HIS A 109 PHE 0.008 0.001 PHE C 115 TYR 0.009 0.001 TYR D 649 ARG 0.009 0.000 ARG D 751 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 198 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: A 108 TYR cc_start: 0.8334 (m-80) cc_final: 0.7916 (m-80) REVERT: B 661 LYS cc_start: 0.6311 (OUTLIER) cc_final: 0.5600 (tttp) REVERT: B 708 LYS cc_start: 0.9074 (tppt) cc_final: 0.8437 (mttp) REVERT: B 725 GLU cc_start: 0.7382 (tm-30) cc_final: 0.6935 (tm-30) REVERT: B 761 LYS cc_start: 0.8264 (mtpp) cc_final: 0.7467 (mmtm) REVERT: C 173 LEU cc_start: 0.9134 (tp) cc_final: 0.8714 (tp) REVERT: C 189 ASN cc_start: 0.8287 (m110) cc_final: 0.8086 (m110) REVERT: C 191 ASN cc_start: 0.8973 (t0) cc_final: 0.8764 (t0) REVERT: C 193 GLN cc_start: 0.8340 (tp40) cc_final: 0.8114 (tp40) REVERT: D 768 LYS cc_start: 0.8651 (pttm) cc_final: 0.7895 (tppp) outliers start: 19 outliers final: 10 residues processed: 207 average time/residue: 0.1606 time to fit residues: 42.0115 Evaluate side-chains 203 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 192 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain B residue 643 TYR Chi-restraints excluded: chain B residue 661 LYS Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 767 GLN Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain D residue 650 CYS Chi-restraints excluded: chain D residue 709 ASN Chi-restraints excluded: chain D residue 781 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 30 optimal weight: 10.0000 chunk 6 optimal weight: 0.2980 chunk 28 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 709 ASN C 67 ASN ** D 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4906 Z= 0.201 Angle : 0.664 10.787 6696 Z= 0.333 Chirality : 0.046 0.172 799 Planarity : 0.005 0.067 881 Dihedral : 4.728 20.450 697 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.15 % Allowed : 13.31 % Favored : 86.54 % Rotamer: Outliers : 5.73 % Allowed : 25.99 % Favored : 68.28 % 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: -2.59 (0.31), residues: 661 helix: 0.86 (0.38), residues: 192 sheet: 0.27 (1.60), residues: 11 loop : -3.21 (0.26), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 671 HIS 0.003 0.001 HIS A 109 PHE 0.011 0.001 PHE C 115 TYR 0.008 0.001 TYR A 108 ARG 0.004 0.000 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 196 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7423 (mt-10) REVERT: B 661 LYS cc_start: 0.6221 (OUTLIER) cc_final: 0.5637 (tttp) REVERT: B 708 LYS cc_start: 0.9061 (tppt) cc_final: 0.8388 (mttp) REVERT: B 725 GLU cc_start: 0.7438 (tm-30) cc_final: 0.6925 (tm-30) REVERT: B 761 LYS cc_start: 0.8290 (mtpp) cc_final: 0.7506 (mmtm) REVERT: C 173 LEU cc_start: 0.9138 (tp) cc_final: 0.8715 (tp) REVERT: C 189 ASN cc_start: 0.8342 (m110) cc_final: 0.8037 (m110) REVERT: C 193 GLN cc_start: 0.8305 (tp40) cc_final: 0.8088 (tp40) REVERT: C 203 TYR cc_start: 0.7962 (p90) cc_final: 0.7664 (p90) REVERT: C 207 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.7387 (m-80) REVERT: D 768 LYS cc_start: 0.8669 (pttm) cc_final: 0.7891 (tppp) REVERT: D 782 ASP cc_start: 0.8208 (m-30) cc_final: 0.7869 (m-30) REVERT: D 788 GLN cc_start: 0.7985 (mp10) cc_final: 0.7745 (mp10) outliers start: 26 outliers final: 18 residues processed: 204 average time/residue: 0.1643 time to fit residues: 42.0288 Evaluate side-chains 208 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 188 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain B residue 643 TYR Chi-restraints excluded: chain B residue 645 HIS Chi-restraints excluded: chain B residue 661 LYS Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain D residue 650 CYS Chi-restraints excluded: chain D residue 709 ASN Chi-restraints excluded: chain D residue 710 SER Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 733 VAL Chi-restraints excluded: chain D residue 781 ASP Chi-restraints excluded: chain D residue 790 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 0.0970 chunk 25 optimal weight: 5.9990 chunk 53 optimal weight: 40.0000 chunk 43 optimal weight: 0.1980 chunk 32 optimal weight: 0.2980 chunk 56 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 overall best weight: 1.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN C 118 ASN ** D 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4906 Z= 0.226 Angle : 0.688 10.925 6696 Z= 0.338 Chirality : 0.046 0.174 799 Planarity : 0.005 0.066 881 Dihedral : 4.843 21.854 697 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.30 % Allowed : 13.31 % Favored : 86.38 % Rotamer: Outliers : 6.61 % Allowed : 26.43 % Favored : 66.96 % 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: -2.31 (0.32), residues: 661 helix: 1.33 (0.39), residues: 192 sheet: 0.46 (1.52), residues: 11 loop : -3.16 (0.26), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 671 HIS 0.003 0.001 HIS A 109 PHE 0.009 0.001 PHE C 115 TYR 0.008 0.001 TYR D 649 ARG 0.007 0.001 ARG D 751 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 192 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7545 (mt-10) REVERT: B 661 LYS cc_start: 0.6440 (OUTLIER) cc_final: 0.6230 (mttp) REVERT: B 663 LYS cc_start: 0.7773 (mmtm) cc_final: 0.7519 (ptmt) REVERT: B 705 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8339 (tm-30) REVERT: B 708 LYS cc_start: 0.9010 (tppt) cc_final: 0.8342 (mttp) REVERT: B 725 GLU cc_start: 0.7517 (tm-30) cc_final: 0.7049 (tm-30) REVERT: B 761 LYS cc_start: 0.8318 (mtpp) cc_final: 0.7556 (mmtm) REVERT: C 189 ASN cc_start: 0.8363 (m110) cc_final: 0.8145 (m110) REVERT: C 193 GLN cc_start: 0.8354 (tp40) cc_final: 0.8020 (tp40) REVERT: C 203 TYR cc_start: 0.7926 (p90) cc_final: 0.7708 (p90) REVERT: D 768 LYS cc_start: 0.8422 (pttm) cc_final: 0.7818 (tppp) REVERT: D 782 ASP cc_start: 0.8246 (m-30) cc_final: 0.7976 (m-30) REVERT: D 787 ASP cc_start: 0.7241 (OUTLIER) cc_final: 0.7039 (m-30) outliers start: 30 outliers final: 23 residues processed: 201 average time/residue: 0.1795 time to fit residues: 45.0445 Evaluate side-chains 209 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 184 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain B residue 643 TYR Chi-restraints excluded: chain B residue 645 HIS Chi-restraints excluded: chain B residue 661 LYS Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 726 MET Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain D residue 650 CYS Chi-restraints excluded: chain D residue 659 LEU Chi-restraints excluded: chain D residue 696 VAL Chi-restraints excluded: chain D residue 709 ASN Chi-restraints excluded: chain D residue 710 SER Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 733 VAL Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 777 LEU Chi-restraints excluded: chain D residue 781 ASP Chi-restraints excluded: chain D residue 787 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 20.0000 chunk 12 optimal weight: 0.0470 chunk 36 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 20 optimal weight: 20.0000 chunk 33 optimal weight: 0.3980 chunk 60 optimal weight: 4.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 757 GLN C 118 ASN ** D 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4906 Z= 0.178 Angle : 0.663 11.540 6696 Z= 0.325 Chirality : 0.045 0.169 799 Planarity : 0.005 0.064 881 Dihedral : 4.565 21.687 697 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.30 % Allowed : 12.71 % Favored : 86.99 % Rotamer: Outliers : 6.83 % Allowed : 25.55 % Favored : 67.62 % 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: -2.10 (0.32), residues: 661 helix: 1.42 (0.39), residues: 198 sheet: 0.88 (1.48), residues: 11 loop : -3.05 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 671 HIS 0.002 0.001 HIS A 109 PHE 0.008 0.001 PHE B 669 TYR 0.006 0.001 TYR A 203 ARG 0.010 0.001 ARG D 751 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 190 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7695 (mt-10) REVERT: B 661 LYS cc_start: 0.6373 (OUTLIER) cc_final: 0.5656 (tttp) REVERT: B 663 LYS cc_start: 0.7882 (mmtm) cc_final: 0.7627 (ptmt) REVERT: B 725 GLU cc_start: 0.7541 (tm-30) cc_final: 0.7042 (tm-30) REVERT: B 761 LYS cc_start: 0.8286 (mtpp) cc_final: 0.7526 (mmtm) REVERT: C 189 ASN cc_start: 0.8382 (m110) cc_final: 0.8143 (m-40) REVERT: C 193 GLN cc_start: 0.8424 (tp40) cc_final: 0.8212 (tp40) REVERT: C 207 PHE cc_start: 0.8085 (OUTLIER) cc_final: 0.7355 (m-80) REVERT: D 664 ASN cc_start: 0.7822 (t0) cc_final: 0.7420 (t0) REVERT: D 667 ASP cc_start: 0.7859 (m-30) cc_final: 0.7639 (m-30) REVERT: D 768 LYS cc_start: 0.8450 (pttm) cc_final: 0.7849 (tppp) REVERT: D 782 ASP cc_start: 0.8208 (m-30) cc_final: 0.7841 (m-30) REVERT: D 787 ASP cc_start: 0.7267 (m-30) cc_final: 0.6964 (m-30) outliers start: 31 outliers final: 19 residues processed: 201 average time/residue: 0.1719 time to fit residues: 43.2396 Evaluate side-chains 205 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 184 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain B residue 643 TYR Chi-restraints excluded: chain B residue 645 HIS Chi-restraints excluded: chain B residue 661 LYS Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 726 MET Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain D residue 650 CYS Chi-restraints excluded: chain D residue 696 VAL Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 709 ASN Chi-restraints excluded: chain D residue 710 SER Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 733 VAL Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 781 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4906 Z= 0.189 Angle : 0.697 11.859 6696 Z= 0.339 Chirality : 0.046 0.168 799 Planarity : 0.005 0.062 881 Dihedral : 4.535 21.307 697 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.30 % Allowed : 13.01 % Favored : 86.69 % Rotamer: Outliers : 6.17 % Allowed : 28.19 % Favored : 65.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.33), residues: 661 helix: 1.56 (0.39), residues: 197 sheet: 1.00 (1.47), residues: 11 loop : -3.03 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 198 HIS 0.002 0.001 HIS B 645 PHE 0.007 0.001 PHE B 669 TYR 0.008 0.001 TYR D 649 ARG 0.008 0.000 ARG D 751 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 183 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7750 (mt-10) REVERT: B 661 LYS cc_start: 0.6393 (OUTLIER) cc_final: 0.5813 (tttp) REVERT: B 663 LYS cc_start: 0.7790 (mmtm) cc_final: 0.7529 (ptmt) REVERT: B 725 GLU cc_start: 0.7544 (tm-30) cc_final: 0.7017 (tm-30) REVERT: B 761 LYS cc_start: 0.8278 (mtpp) cc_final: 0.7540 (mmtm) REVERT: C 189 ASN cc_start: 0.8436 (m110) cc_final: 0.8198 (m-40) REVERT: D 664 ASN cc_start: 0.7881 (t0) cc_final: 0.7446 (t0) REVERT: D 667 ASP cc_start: 0.7869 (m-30) cc_final: 0.7585 (m-30) REVERT: D 768 LYS cc_start: 0.8347 (pttm) cc_final: 0.7754 (tppp) REVERT: D 782 ASP cc_start: 0.8092 (m-30) cc_final: 0.7879 (m-30) REVERT: D 787 ASP cc_start: 0.7192 (OUTLIER) cc_final: 0.6896 (m-30) outliers start: 28 outliers final: 18 residues processed: 192 average time/residue: 0.1796 time to fit residues: 43.0436 Evaluate side-chains 197 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 177 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain B residue 643 TYR Chi-restraints excluded: chain B residue 645 HIS Chi-restraints excluded: chain B residue 661 LYS Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 726 MET Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain D residue 663 LYS Chi-restraints excluded: chain D residue 696 VAL Chi-restraints excluded: chain D residue 709 ASN Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 781 ASP Chi-restraints excluded: chain D residue 787 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 12 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 786 GLN ** D 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.4867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4906 Z= 0.284 Angle : 0.772 11.764 6696 Z= 0.382 Chirality : 0.047 0.174 799 Planarity : 0.005 0.064 881 Dihedral : 5.050 24.611 697 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.30 % Allowed : 15.58 % Favored : 84.11 % Rotamer: Outliers : 7.49 % Allowed : 26.65 % Favored : 65.86 % 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: -2.10 (0.32), residues: 661 helix: 1.41 (0.39), residues: 195 sheet: 0.71 (1.46), residues: 11 loop : -3.00 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 671 HIS 0.003 0.001 HIS B 645 PHE 0.014 0.002 PHE A 166 TYR 0.017 0.002 TYR D 649 ARG 0.007 0.001 ARG D 751 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 194 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 661 LYS cc_start: 0.6606 (OUTLIER) cc_final: 0.6398 (mttp) REVERT: B 663 LYS cc_start: 0.7823 (mmtm) cc_final: 0.7564 (ptmt) REVERT: B 725 GLU cc_start: 0.7449 (tm-30) cc_final: 0.6862 (tm-30) REVERT: B 761 LYS cc_start: 0.8346 (mtpp) cc_final: 0.7637 (mmtm) REVERT: B 790 LEU cc_start: 0.9052 (mm) cc_final: 0.8773 (mm) REVERT: C 113 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7656 (mt-10) REVERT: C 189 ASN cc_start: 0.8559 (m110) cc_final: 0.8352 (m110) REVERT: D 667 ASP cc_start: 0.8164 (m-30) cc_final: 0.7890 (m-30) REVERT: D 768 LYS cc_start: 0.8551 (pttm) cc_final: 0.7833 (tppp) outliers start: 34 outliers final: 22 residues processed: 202 average time/residue: 0.1780 time to fit residues: 44.8797 Evaluate side-chains 210 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 187 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain B residue 643 TYR Chi-restraints excluded: chain B residue 645 HIS Chi-restraints excluded: chain B residue 661 LYS Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 726 MET Chi-restraints excluded: chain B residue 786 GLN Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain D residue 650 CYS Chi-restraints excluded: chain D residue 659 LEU Chi-restraints excluded: chain D residue 663 LYS Chi-restraints excluded: chain D residue 696 VAL Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 781 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- 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: 56.2153 > 50: distance: 48 - 181: 5.806 distance: 86 - 138: 20.330 distance: 89 - 135: 29.509 distance: 98 - 124: 30.269 distance: 101 - 121: 9.293 distance: 116 - 121: 6.869 distance: 121 - 122: 15.585 distance: 122 - 123: 8.781 distance: 122 - 125: 20.811 distance: 123 - 128: 9.123 distance: 125 - 126: 25.530 distance: 125 - 127: 7.056 distance: 128 - 129: 3.117 distance: 128 - 134: 24.284 distance: 129 - 130: 14.011 distance: 129 - 132: 17.054 distance: 130 - 131: 27.292 distance: 130 - 135: 25.580 distance: 132 - 133: 16.312 distance: 133 - 134: 8.447 distance: 135 - 136: 13.940 distance: 136 - 137: 22.398 distance: 136 - 139: 5.914 distance: 137 - 138: 18.262 distance: 137 - 140: 11.684 distance: 140 - 141: 19.297 distance: 141 - 142: 23.811 distance: 141 - 144: 17.700 distance: 142 - 143: 18.961 distance: 142 - 148: 14.500 distance: 144 - 145: 25.984 distance: 145 - 146: 19.530 distance: 145 - 147: 33.537 distance: 148 - 149: 5.792 distance: 149 - 150: 15.878 distance: 149 - 152: 29.230 distance: 150 - 151: 14.374 distance: 150 - 155: 3.872 distance: 152 - 153: 23.130 distance: 152 - 154: 5.774 distance: 156 - 157: 9.096 distance: 156 - 159: 11.747 distance: 157 - 165: 11.012 distance: 159 - 160: 5.297 distance: 160 - 161: 23.613 distance: 160 - 162: 27.246 distance: 161 - 163: 21.229 distance: 162 - 164: 19.437 distance: 163 - 164: 20.618 distance: 165 - 166: 11.485 distance: 166 - 167: 6.787 distance: 166 - 169: 19.464 distance: 167 - 168: 4.333 distance: 167 - 173: 4.949 distance: 169 - 170: 14.212 distance: 170 - 171: 13.535 distance: 170 - 172: 19.201 distance: 173 - 174: 8.004 distance: 174 - 175: 7.925 distance: 174 - 177: 3.989 distance: 175 - 176: 8.093 distance: 175 - 181: 9.464 distance: 177 - 178: 12.781 distance: 178 - 179: 11.478 distance: 178 - 180: 16.924 distance: 181 - 182: 5.834 distance: 182 - 183: 9.138 distance: 182 - 185: 10.093 distance: 183 - 184: 11.662 distance: 183 - 187: 8.090 distance: 185 - 186: 8.942 distance: 188 - 189: 17.400 distance: 188 - 191: 18.319 distance: 189 - 190: 22.345 distance: 189 - 192: 4.861