Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:52:32 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4z_14511/11_2022/7z4z_14511.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4z_14511/11_2022/7z4z_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_14511/11_2022/7z4z_14511.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4z_14511/11_2022/7z4z_14511.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4z_14511/11_2022/7z4z_14511.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4z_14511/11_2022/7z4z_14511.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/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: 3.35, per 1000 atoms: 0.70 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: 2.04 Conformation dependent library (CDL) restraints added in 778.4 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: 0.19 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: 1.02 Time building geometry restraints manager: 2.20 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 2.440 nonbonded pdb=" OD1 ASN A 189 " pdb=" N GLU A 190 " model vdw 2.309 2.520 nonbonded pdb=" O GLU B 641 " pdb=" ND1 HIS B 645 " model vdw 2.329 2.520 nonbonded pdb=" OD2 ASP A 181 " pdb=" NH1 ARG B 743 " model vdw 2.391 2.520 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 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 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. 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: 0.400 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: 2.160 Check model and map are aligned: 0.080 Convert atoms to be neutral: 0.050 Process input model: 17.460 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.010 Internal consistency checks: 0.000 Total: 23.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 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 % 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 *********************** 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 : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.1665 time to fit residues: 46.0703 Evaluate side-chains 178 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 0.472 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7366 ------------------------------------------------------------------------------- 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: 0.0170 chunk 27 optimal weight: 0.0980 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 overall best weight: 0.8220 ------------------------------------------------------------------------------- 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 676 ASN ** 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: 0.7362 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 4906 Z= 0.212 Angle : 0.683 9.415 6696 Z= 0.337 Chirality : 0.046 0.180 799 Planarity : 0.005 0.061 881 Dihedral : 4.646 20.944 697 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.30 % Allowed : 12.25 % Favored : 87.44 % Rotamer Outliers : 4.41 % 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: -3.52 (0.29), residues: 661 helix: -0.36 (0.36), residues: 194 sheet: -2.81 (1.10), residues: 15 loop : -3.52 (0.25), residues: 452 *********************** 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: 20 poor density : 208 time to evaluate : 0.587 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 9 residues processed: 213 average time/residue: 0.1597 time to fit residues: 42.8323 Evaluate side-chains 203 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 194 time to evaluate : 0.629 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0449 time to fit residues: 1.5404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 0.0370 chunk 18 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 0.0370 chunk 16 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 47 optimal weight: 7.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 ASN D 676 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.3179 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= 0.185 Angle : 0.661 10.438 6696 Z= 0.325 Chirality : 0.045 0.172 799 Planarity : 0.005 0.060 881 Dihedral : 4.456 20.330 697 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.80 % Favored : 87.90 % Rotamer Outliers : 3.74 % 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: -2.93 (0.30), residues: 661 helix: 0.41 (0.38), residues: 191 sheet: -0.88 (1.08), residues: 23 loop : -3.36 (0.25), residues: 447 *********************** 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 210 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 193 time to evaluate : 0.605 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 200 average time/residue: 0.1612 time to fit residues: 40.5759 Evaluate side-chains 190 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 183 time to evaluate : 0.543 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0482 time to fit residues: 1.3907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 C 118 ASN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 4906 Z= 0.311 Angle : 0.732 9.838 6696 Z= 0.370 Chirality : 0.048 0.180 799 Planarity : 0.005 0.061 881 Dihedral : 5.091 24.864 697 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.15 % Allowed : 15.58 % Favored : 84.27 % Rotamer Outliers : 6.17 % 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: -2.71 (0.31), residues: 661 helix: 0.83 (0.39), residues: 192 sheet: -0.62 (1.09), residues: 23 loop : -3.36 (0.26), residues: 446 *********************** 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 223 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 195 time to evaluate : 0.619 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 19 residues processed: 203 average time/residue: 0.1672 time to fit residues: 42.9463 Evaluate side-chains 204 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 185 time to evaluate : 0.558 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.0616 time to fit residues: 2.6923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 46 optimal weight: 0.6980 chunk 25 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 32 optimal weight: 0.0170 chunk 56 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 overall best weight: 1.3020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 655 GLN C 118 ASN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 4906 Z= 0.226 Angle : 0.670 10.917 6696 Z= 0.335 Chirality : 0.046 0.175 799 Planarity : 0.005 0.059 881 Dihedral : 4.880 22.371 697 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.30 % Allowed : 13.77 % Favored : 85.93 % Rotamer Outliers : 3.30 % 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: -2.34 (0.32), residues: 661 helix: 1.21 (0.39), residues: 192 sheet: 1.12 (1.55), residues: 11 loop : -3.15 (0.26), residues: 458 *********************** 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 201 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 186 time to evaluate : 0.631 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 191 average time/residue: 0.1710 time to fit residues: 40.6554 Evaluate side-chains 191 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 182 time to evaluate : 0.583 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0511 time to fit residues: 1.5785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 8.9990 chunk 12 optimal weight: 0.0570 chunk 36 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 chunk 5 optimal weight: 0.8980 chunk 20 optimal weight: 0.0060 chunk 33 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.6716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 4906 Z= 0.181 Angle : 0.663 11.434 6696 Z= 0.324 Chirality : 0.046 0.170 799 Planarity : 0.005 0.057 881 Dihedral : 4.570 20.391 697 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.30 % Allowed : 14.22 % Favored : 85.48 % Rotamer Outliers : 1.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.33), residues: 661 helix: 1.27 (0.39), residues: 198 sheet: 1.67 (1.50), residues: 11 loop : -3.03 (0.27), residues: 452 *********************** 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 194 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 187 time to evaluate : 0.514 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 189 average time/residue: 0.1787 time to fit residues: 41.9815 Evaluate side-chains 188 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 184 time to evaluate : 0.546 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1194 time to fit residues: 1.4026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 45 optimal weight: 0.0060 chunk 52 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 28 optimal weight: 0.2980 chunk 25 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN B 757 GLN ** D 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.4829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 4906 Z= 0.219 Angle : 0.681 11.490 6696 Z= 0.337 Chirality : 0.046 0.173 799 Planarity : 0.005 0.056 881 Dihedral : 4.682 21.902 697 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.30 % Allowed : 14.83 % Favored : 84.87 % Rotamer Outliers : 1.98 % 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: -2.01 (0.33), residues: 661 helix: 1.46 (0.39), residues: 198 sheet: 1.72 (1.50), residues: 11 loop : -2.99 (0.27), residues: 452 *********************** 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 201 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 192 time to evaluate : 0.600 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 196 average time/residue: 0.1708 time to fit residues: 41.9992 Evaluate side-chains 193 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 187 time to evaluate : 0.590 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0574 time to fit residues: 1.3304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 12 optimal weight: 0.3980 chunk 39 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 118 ASN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.4983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 4906 Z= 0.199 Angle : 0.697 11.734 6696 Z= 0.341 Chirality : 0.046 0.166 799 Planarity : 0.005 0.058 881 Dihedral : 4.536 21.313 697 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.30 % Allowed : 13.77 % Favored : 85.93 % Rotamer Outliers : 1.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.33), residues: 661 helix: 1.52 (0.39), residues: 198 sheet: 1.88 (1.51), residues: 11 loop : -2.95 (0.27), residues: 452 *********************** 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 201 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 192 time to evaluate : 0.601 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 193 average time/residue: 0.1647 time to fit residues: 40.0411 Evaluate side-chains 197 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 190 time to evaluate : 0.661 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0933 time to fit residues: 1.7929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 25 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 55 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.5105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 4906 Z= 0.219 Angle : 0.726 12.028 6696 Z= 0.357 Chirality : 0.047 0.181 799 Planarity : 0.005 0.056 881 Dihedral : 4.673 21.425 697 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.30 % Allowed : 14.37 % Favored : 85.33 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.33), residues: 661 helix: 1.62 (0.40), residues: 197 sheet: -0.24 (1.26), residues: 17 loop : -2.92 (0.28), residues: 447 *********************** REFINEMENT MACRO_CYCLE 9 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 195 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 192 time to evaluate : 0.602 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 194 average time/residue: 0.1592 time to fit residues: 39.2693 Evaluate side-chains 188 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 187 time to evaluate : 0.615 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0454 time to fit residues: 0.9152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 40 optimal weight: 0.0570 chunk 54 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 118 ASN ** D 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.5331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 4906 Z= 0.244 Angle : 0.772 11.958 6696 Z= 0.380 Chirality : 0.047 0.174 799 Planarity : 0.005 0.057 881 Dihedral : 4.757 21.125 697 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.30 % Allowed : 14.37 % Favored : 85.33 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.33), residues: 661 helix: 1.60 (0.40), residues: 198 sheet: -0.28 (1.25), residues: 17 loop : -2.83 (0.28), residues: 446 ********************** REFINEMENT MACRO_CYCLE 10 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 190 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 186 time to evaluate : 0.598 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 186 average time/residue: 0.1593 time to fit residues: 37.5174 Evaluate side-chains 187 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 184 time to evaluate : 0.587 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0447 time to fit residues: 1.0669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 14 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 21 optimal weight: 0.0070 chunk 53 optimal weight: 30.0000 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 59 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.7000 ------------------------------------------------------------------------------- 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** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.146589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.117400 restraints weight = 8286.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.120783 restraints weight = 4897.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.123090 restraints weight = 3422.903| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.5392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 4906 Z= 0.200 Angle : 0.746 12.358 6696 Z= 0.363 Chirality : 0.047 0.175 799 Planarity : 0.005 0.056 881 Dihedral : 4.563 24.072 697 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.30 % Allowed : 13.77 % Favored : 85.93 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.34), residues: 661 helix: 1.75 (0.40), residues: 198 sheet: -0.32 (1.18), residues: 21 loop : -2.73 (0.28), residues: 442 =============================================================================== Job complete usr+sys time: 1428.72 seconds wall clock time: 26 minutes 28.35 seconds (1588.35 seconds total)