Starting phenix.real_space_refine on Sat Mar 16 19:06:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syp_40889/03_2024/8syp_40889.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syp_40889/03_2024/8syp_40889.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syp_40889/03_2024/8syp_40889.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syp_40889/03_2024/8syp_40889.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syp_40889/03_2024/8syp_40889.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syp_40889/03_2024/8syp_40889.pdb" } resolution = 2.6 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= 0.068 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 294 5.49 5 S 32 5.16 5 C 8814 2.51 5 N 2809 2.21 5 O 3523 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "E GLU 73": "OE1" <-> "OE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "H GLU 90": "OE1" <-> "OE2" Residue "M GLU 23": "OE1" <-> "OE2" Residue "M GLU 32": "OE1" <-> "OE2" Residue "M GLU 35": "OE1" <-> "OE2" Residue "M TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 251": "OE1" <-> "OE2" Residue "M GLU 263": "OE1" <-> "OE2" Residue "N GLU 35": "OE1" <-> "OE2" Residue "N TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 84": "OE1" <-> "OE2" Residue "N GLU 237": "OE1" <-> "OE2" Residue "N GLU 251": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15472 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 3015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3015 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3012 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "M" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1769 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "N" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1769 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Time building chain proxies: 7.84, per 1000 atoms: 0.51 Number of scatterers: 15472 At special positions: 0 Unit cell: (141.504, 125.664, 126.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 294 15.00 O 3523 8.00 N 2809 7.00 C 8814 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS M 44 " - pdb=" SG CYS M 118 " distance=2.03 Simple disulfide: pdb=" SG CYS M 181 " - pdb=" SG CYS M 246 " distance=2.03 Simple disulfide: pdb=" SG CYS N 44 " - pdb=" SG CYS N 118 " distance=2.03 Simple disulfide: pdb=" SG CYS N 181 " - pdb=" SG CYS N 246 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.89 Conformation dependent library (CDL) restraints added in 2.0 seconds 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2230 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 22 sheets defined 47.2% alpha, 19.3% beta 134 base pairs and 277 stacking pairs defined. Time for finding SS restraints: 6.83 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.918A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.780A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.405A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.793A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.751A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.689A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.859A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.348A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.729A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 50 through 52 No H-bonds generated for 'chain 'M' and resid 50 through 52' Processing helix chain 'M' and resid 84 through 87 removed outlier: 4.004A pdb=" N LYS M 87 " --> pdb=" O GLU M 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 84 through 87' Processing helix chain 'M' and resid 109 through 113 removed outlier: 3.877A pdb=" N SER M 113 " --> pdb=" O SER M 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 237 through 241 removed outlier: 3.577A pdb=" N ASP M 240 " --> pdb=" O GLU M 237 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR M 241 " --> pdb=" O SER M 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 237 through 241' Processing helix chain 'N' and resid 50 through 52 No H-bonds generated for 'chain 'N' and resid 50 through 52' Processing helix chain 'N' and resid 84 through 87 removed outlier: 3.966A pdb=" N LYS N 87 " --> pdb=" O GLU N 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 84 through 87' Processing helix chain 'N' and resid 109 through 113 removed outlier: 3.927A pdb=" N SER N 113 " --> pdb=" O SER N 110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.666A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.524A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.216A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.903A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.212A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'M' and resid 25 through 26 Processing sheet with id=AB3, first strand: chain 'M' and resid 32 through 34 removed outlier: 3.513A pdb=" N GLY M 71 " --> pdb=" O TRP M 58 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LYS M 60 " --> pdb=" O TRP M 69 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP M 69 " --> pdb=" O LYS M 60 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR M 62 " --> pdb=" O LEU M 67 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LEU M 67 " --> pdb=" O THR M 62 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 32 through 34 removed outlier: 4.077A pdb=" N TYR M 131 " --> pdb=" O ARG M 120 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N SER M 122 " --> pdb=" O LEU M 129 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU M 129 " --> pdb=" O SER M 122 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 40 through 43 removed outlier: 3.519A pdb=" N VAL M 40 " --> pdb=" O LEU M 105 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 163 through 164 removed outlier: 3.637A pdb=" N VAL M 177 " --> pdb=" O ILE M 233 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE M 229 " --> pdb=" O CYS M 181 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP M 228 " --> pdb=" O SER M 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 168 through 171 removed outlier: 6.665A pdb=" N LEU M 191 " --> pdb=" O TYR M 207 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N TYR M 207 " --> pdb=" O LEU M 191 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TRP M 193 " --> pdb=" O LEU M 205 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 25 through 27 Processing sheet with id=AB9, first strand: chain 'N' and resid 32 through 34 removed outlier: 6.766A pdb=" N GLU N 32 " --> pdb=" O THR N 139 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY N 71 " --> pdb=" O TRP N 58 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LYS N 60 " --> pdb=" O TRP N 69 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N TRP N 69 " --> pdb=" O LYS N 60 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR N 62 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N LEU N 67 " --> pdb=" O THR N 62 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 32 through 34 removed outlier: 6.766A pdb=" N GLU N 32 " --> pdb=" O THR N 139 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TYR N 131 " --> pdb=" O ARG N 120 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N SER N 122 " --> pdb=" O LEU N 129 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU N 129 " --> pdb=" O SER N 122 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 40 through 43 removed outlier: 3.513A pdb=" N MET N 42 " --> pdb=" O MET N 103 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 163 through 164 Processing sheet with id=AC4, first strand: chain 'N' and resid 168 through 171 removed outlier: 6.757A pdb=" N LEU N 191 " --> pdb=" O TYR N 207 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N TYR N 207 " --> pdb=" O LEU N 191 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TRP N 193 " --> pdb=" O LEU N 205 " (cutoff:3.500A) 532 hydrogen bonds defined for protein. 1494 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 335 hydrogen bonds 662 hydrogen bond angles 0 basepair planarities 134 basepair parallelities 277 stacking parallelities Total time for adding SS restraints: 6.12 Time building geometry restraints manager: 7.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3177 1.33 - 1.46: 5535 1.46 - 1.58: 7031 1.58 - 1.70: 572 1.70 - 1.83: 52 Bond restraints: 16367 Sorted by residual: bond pdb=" O3' DT J 91 " pdb=" P DT J 92 " ideal model delta sigma weight residual 1.607 1.386 0.221 1.50e-02 4.44e+03 2.18e+02 bond pdb=" O3' DT J 92 " pdb=" P DG J 93 " ideal model delta sigma weight residual 1.607 1.392 0.215 1.50e-02 4.44e+03 2.05e+02 bond pdb=" O3' DG I 75 " pdb=" P DA I 76 " ideal model delta sigma weight residual 1.607 1.491 0.116 1.50e-02 4.44e+03 5.95e+01 bond pdb=" O3' DA I 72 " pdb=" P DT I 73 " ideal model delta sigma weight residual 1.607 1.517 0.090 1.50e-02 4.44e+03 3.61e+01 bond pdb=" O3' DT I 66 " pdb=" P DT I 67 " ideal model delta sigma weight residual 1.607 1.535 0.072 1.50e-02 4.44e+03 2.28e+01 ... (remaining 16362 not shown) Histogram of bond angle deviations from ideal: 77.82 - 91.67: 2 91.67 - 105.52: 1489 105.52 - 119.37: 13731 119.37 - 133.22: 8141 133.22 - 147.08: 13 Bond angle restraints: 23376 Sorted by residual: angle pdb=" C3' DT J 92 " pdb=" O3' DT J 92 " pdb=" P DG J 93 " ideal model delta sigma weight residual 120.20 91.39 28.81 1.50e+00 4.44e-01 3.69e+02 angle pdb=" C3' DT J 91 " pdb=" O3' DT J 91 " pdb=" P DT J 92 " ideal model delta sigma weight residual 120.20 147.08 -26.88 1.50e+00 4.44e-01 3.21e+02 angle pdb=" O3' DT J 92 " pdb=" P DG J 93 " pdb=" O5' DG J 93 " ideal model delta sigma weight residual 104.00 77.82 26.18 1.50e+00 4.44e-01 3.05e+02 angle pdb=" O3' DT J 91 " pdb=" P DT J 92 " pdb=" O5' DT J 92 " ideal model delta sigma weight residual 104.00 125.36 -21.36 1.50e+00 4.44e-01 2.03e+02 angle pdb=" O3' DT J 92 " pdb=" P DG J 93 " pdb=" OP2 DG J 93 " ideal model delta sigma weight residual 108.00 130.70 -22.70 3.00e+00 1.11e-01 5.72e+01 ... (remaining 23371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 7439 35.46 - 70.92: 1625 70.92 - 106.37: 23 106.37 - 141.83: 1 141.83 - 177.29: 4 Dihedral angle restraints: 9092 sinusoidal: 5611 harmonic: 3481 Sorted by residual: dihedral pdb=" C4' DC I 20 " pdb=" C3' DC I 20 " pdb=" O3' DC I 20 " pdb=" P DT I 21 " ideal model delta sinusoidal sigma weight residual -140.00 37.29 -177.29 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC I 92 " pdb=" C3' DC I 92 " pdb=" O3' DC I 92 " pdb=" P DT I 93 " ideal model delta sinusoidal sigma weight residual -140.00 36.59 -176.59 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG I 53 " pdb=" C3' DG I 53 " pdb=" O3' DG I 53 " pdb=" P DC I 54 " ideal model delta sinusoidal sigma weight residual -140.00 34.03 -174.03 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 9089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2300 0.069 - 0.138: 290 0.138 - 0.207: 34 0.207 - 0.277: 8 0.277 - 0.346: 1 Chirality restraints: 2633 Sorted by residual: chirality pdb=" P DA I 76 " pdb=" OP1 DA I 76 " pdb=" OP2 DA I 76 " pdb=" O5' DA I 76 " both_signs ideal model delta sigma weight residual True 2.35 -2.00 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CA ASP E 81 " pdb=" N ASP E 81 " pdb=" C ASP E 81 " pdb=" CB ASP E 81 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" P DA I 72 " pdb=" OP1 DA I 72 " pdb=" OP2 DA I 72 " pdb=" O5' DA I 72 " both_signs ideal model delta sigma weight residual True 2.35 -2.10 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 2630 not shown) Planarity restraints: 1931 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR N 62 " 0.082 5.00e-02 4.00e+02 1.24e-01 2.46e+01 pdb=" N PRO N 63 " -0.215 5.00e-02 4.00e+02 pdb=" CA PRO N 63 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO N 63 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU N 111 " 0.018 2.00e-02 2.50e+03 3.57e-02 1.27e+01 pdb=" C GLU N 111 " -0.062 2.00e-02 2.50e+03 pdb=" O GLU N 111 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP N 112 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 24 " 0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C ASP F 24 " -0.059 2.00e-02 2.50e+03 pdb=" O ASP F 24 " 0.023 2.00e-02 2.50e+03 pdb=" N ASN F 25 " 0.019 2.00e-02 2.50e+03 ... (remaining 1928 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3382 2.80 - 3.32: 12276 3.32 - 3.85: 29836 3.85 - 4.37: 35468 4.37 - 4.90: 52364 Nonbonded interactions: 133326 Sorted by model distance: nonbonded pdb=" OG1 THR A 118 " pdb=" CD ARG B 45 " model vdw 2.273 3.440 nonbonded pdb=" O2 DC I 134 " pdb=" N2 DG J 29 " model vdw 2.288 2.496 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.289 2.440 nonbonded pdb=" N2 DG I 25 " pdb=" O2 DC J 138 " model vdw 2.301 2.496 nonbonded pdb=" CG LYS B 77 " pdb=" NH2 ARG D 89 " model vdw 2.325 3.520 ... (remaining 133321 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 38 through 133) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 101) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 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: 3.790 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 47.190 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.221 16367 Z= 0.340 Angle : 0.982 28.811 23376 Z= 0.560 Chirality : 0.049 0.346 2633 Planarity : 0.008 0.124 1931 Dihedral : 27.373 177.288 6850 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.59 % Allowed : 24.80 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.22), residues: 1175 helix: 0.09 (0.20), residues: 538 sheet: -0.13 (0.35), residues: 238 loop : -1.08 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP N 199 HIS 0.007 0.001 HIS M 249 PHE 0.009 0.002 PHE A 67 TYR 0.018 0.002 TYR N 72 ARG 0.020 0.001 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 241 time to evaluate : 1.452 Fit side-chains revert: symmetry clash REVERT: D 39 TYR cc_start: 0.8305 (t80) cc_final: 0.7890 (t80) REVERT: M 34 VAL cc_start: 0.9151 (t) cc_final: 0.8902 (p) REVERT: M 64 ARG cc_start: 0.8341 (ttm110) cc_final: 0.8005 (ttp80) REVERT: M 65 GLN cc_start: 0.8614 (mt0) cc_final: 0.8248 (mt0) REVERT: N 172 SER cc_start: 0.8915 (m) cc_final: 0.8570 (p) outliers start: 6 outliers final: 5 residues processed: 245 average time/residue: 1.7160 time to fit residues: 452.3923 Evaluate side-chains 223 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 218 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 163 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 43 optimal weight: 0.0000 chunk 68 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 overall best weight: 2.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16367 Z= 0.320 Angle : 0.605 8.863 23376 Z= 0.354 Chirality : 0.038 0.164 2633 Planarity : 0.005 0.077 1931 Dihedral : 29.795 179.207 4567 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.43 % Allowed : 22.83 % Favored : 72.74 % 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: 0.79 (0.24), residues: 1175 helix: 1.79 (0.21), residues: 540 sheet: 0.20 (0.35), residues: 222 loop : -0.98 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 58 HIS 0.003 0.001 HIS N 249 PHE 0.009 0.001 PHE H 67 TYR 0.014 0.001 TYR N 72 ARG 0.007 0.000 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 211 time to evaluate : 1.233 Fit side-chains revert: symmetry clash REVERT: E 76 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8420 (pt0) REVERT: F 24 ASP cc_start: 0.7456 (t70) cc_final: 0.7113 (t70) REVERT: G 13 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8240 (ttmm) REVERT: G 92 GLU cc_start: 0.8446 (mt-10) cc_final: 0.7934 (mt-10) REVERT: H 65 ASP cc_start: 0.9032 (t70) cc_final: 0.8700 (t0) REVERT: M 34 VAL cc_start: 0.9249 (t) cc_final: 0.8937 (p) REVERT: M 84 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7883 (tp30) REVERT: N 172 SER cc_start: 0.8814 (m) cc_final: 0.8450 (p) REVERT: N 206 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.9108 (mp) outliers start: 45 outliers final: 17 residues processed: 231 average time/residue: 1.6354 time to fit residues: 406.6653 Evaluate side-chains 224 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 203 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 84 GLU Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 159 ASP Chi-restraints excluded: chain M residue 223 SER Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain N residue 206 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 20.0000 chunk 40 optimal weight: 0.1980 chunk 108 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 131 optimal weight: 10.0000 chunk 141 optimal weight: 7.9990 chunk 116 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS C 104 GLN ** N 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 249 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 16367 Z= 0.296 Angle : 0.583 7.758 23376 Z= 0.341 Chirality : 0.037 0.164 2633 Planarity : 0.004 0.062 1931 Dihedral : 29.771 179.222 4562 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.84 % Allowed : 22.15 % Favored : 74.02 % 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: 1.30 (0.25), residues: 1175 helix: 2.33 (0.22), residues: 544 sheet: 0.32 (0.35), residues: 222 loop : -0.87 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 58 HIS 0.004 0.001 HIS N 249 PHE 0.008 0.001 PHE A 67 TYR 0.016 0.001 TYR N 72 ARG 0.006 0.000 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 204 time to evaluate : 1.358 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9144 (ttmm) cc_final: 0.8913 (ttpp) REVERT: A 120 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8392 (mtt) REVERT: C 71 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8325 (ttm-80) REVERT: D 65 ASP cc_start: 0.8913 (t0) cc_final: 0.8624 (t0) REVERT: E 76 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8393 (tt0) REVERT: E 122 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8693 (ptpt) REVERT: G 13 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8248 (ttmm) REVERT: G 92 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8079 (mt-10) REVERT: H 65 ASP cc_start: 0.9022 (t70) cc_final: 0.8689 (t0) REVERT: M 34 VAL cc_start: 0.9221 (t) cc_final: 0.8895 (p) REVERT: N 112 ASP cc_start: 0.8721 (m-30) cc_final: 0.8477 (m-30) REVERT: N 172 SER cc_start: 0.8742 (m) cc_final: 0.8268 (p) REVERT: N 206 ILE cc_start: 0.9338 (OUTLIER) cc_final: 0.9110 (mp) outliers start: 39 outliers final: 21 residues processed: 225 average time/residue: 1.6288 time to fit residues: 395.3783 Evaluate side-chains 228 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 201 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain M residue 159 ASP Chi-restraints excluded: chain M residue 223 SER Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 206 ILE Chi-restraints excluded: chain N residue 218 SER Chi-restraints excluded: chain N residue 239 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 131 optimal weight: 0.6980 chunk 139 optimal weight: 0.0170 chunk 68 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16367 Z= 0.176 Angle : 0.552 6.955 23376 Z= 0.327 Chirality : 0.035 0.161 2633 Planarity : 0.004 0.054 1931 Dihedral : 29.665 179.708 4562 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.15 % Allowed : 23.62 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.25), residues: 1175 helix: 2.68 (0.22), residues: 542 sheet: 0.40 (0.36), residues: 222 loop : -0.81 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 199 HIS 0.003 0.001 HIS M 249 PHE 0.008 0.001 PHE E 67 TYR 0.012 0.001 TYR N 72 ARG 0.008 0.000 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 207 time to evaluate : 1.351 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9127 (ttmm) cc_final: 0.8899 (ttpp) REVERT: C 71 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8322 (ttm-80) REVERT: D 39 TYR cc_start: 0.8308 (t80) cc_final: 0.7554 (t80) REVERT: D 65 ASP cc_start: 0.8950 (t0) cc_final: 0.8579 (t0) REVERT: E 76 GLN cc_start: 0.8622 (tt0) cc_final: 0.8351 (tt0) REVERT: E 120 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.7843 (mtt) REVERT: E 122 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8576 (ptpt) REVERT: G 13 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8248 (ttmm) REVERT: G 92 GLU cc_start: 0.8391 (mt-10) cc_final: 0.7870 (mt-10) REVERT: H 65 ASP cc_start: 0.8971 (t70) cc_final: 0.8658 (t0) REVERT: M 34 VAL cc_start: 0.9278 (t) cc_final: 0.8972 (p) REVERT: N 103 MET cc_start: 0.8266 (ttt) cc_final: 0.7997 (ttt) REVERT: N 172 SER cc_start: 0.8614 (m) cc_final: 0.8260 (p) REVERT: N 206 ILE cc_start: 0.9301 (OUTLIER) cc_final: 0.9096 (mp) outliers start: 32 outliers final: 9 residues processed: 225 average time/residue: 1.6346 time to fit residues: 396.7055 Evaluate side-chains 217 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 203 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 206 ILE Chi-restraints excluded: chain N residue 218 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 0.5980 chunk 79 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 0.8980 chunk 124 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16367 Z= 0.307 Angle : 0.582 7.058 23376 Z= 0.341 Chirality : 0.038 0.163 2633 Planarity : 0.004 0.048 1931 Dihedral : 29.697 178.821 4560 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.44 % Allowed : 22.54 % Favored : 74.02 % 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 (0.25), residues: 1175 helix: 2.67 (0.22), residues: 544 sheet: 0.49 (0.36), residues: 222 loop : -0.80 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 58 HIS 0.003 0.001 HIS B 75 PHE 0.008 0.001 PHE E 104 TYR 0.016 0.001 TYR N 72 ARG 0.011 0.000 ARG M 176 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 201 time to evaluate : 1.398 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9158 (ttmm) cc_final: 0.8928 (ttpp) REVERT: C 71 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8314 (ttm-80) REVERT: D 39 TYR cc_start: 0.8397 (t80) cc_final: 0.7664 (t80) REVERT: D 65 ASP cc_start: 0.8997 (t0) cc_final: 0.8634 (t0) REVERT: E 76 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8388 (tt0) REVERT: E 122 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8677 (ptpt) REVERT: G 13 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8239 (ttmm) REVERT: G 92 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8032 (mt-10) REVERT: H 65 ASP cc_start: 0.9032 (t70) cc_final: 0.8703 (t0) REVERT: M 34 VAL cc_start: 0.9328 (t) cc_final: 0.8982 (p) REVERT: M 169 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8579 (ptp) REVERT: N 64 ARG cc_start: 0.8126 (ttp-170) cc_final: 0.7893 (ttp-170) REVERT: N 172 SER cc_start: 0.8608 (m) cc_final: 0.8268 (p) REVERT: N 206 ILE cc_start: 0.9333 (OUTLIER) cc_final: 0.9100 (mp) outliers start: 35 outliers final: 16 residues processed: 218 average time/residue: 1.6648 time to fit residues: 391.4549 Evaluate side-chains 221 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 199 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 159 ASP Chi-restraints excluded: chain M residue 169 MET Chi-restraints excluded: chain M residue 223 SER Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain N residue 206 ILE Chi-restraints excluded: chain N residue 218 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 139 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 73 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 25 GLN ** N 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16367 Z= 0.226 Angle : 0.574 7.807 23376 Z= 0.337 Chirality : 0.036 0.171 2633 Planarity : 0.004 0.048 1931 Dihedral : 29.712 178.907 4560 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.15 % Allowed : 23.52 % Favored : 73.33 % 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: 1.71 (0.25), residues: 1175 helix: 2.73 (0.22), residues: 544 sheet: 0.51 (0.36), residues: 222 loop : -0.77 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 58 HIS 0.004 0.001 HIS B 75 PHE 0.008 0.001 PHE E 67 TYR 0.016 0.001 TYR N 72 ARG 0.014 0.000 ARG N 176 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 200 time to evaluate : 1.320 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9141 (ttmm) cc_final: 0.8908 (ttpp) REVERT: C 71 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8326 (ttm-80) REVERT: D 39 TYR cc_start: 0.8364 (t80) cc_final: 0.7614 (t80) REVERT: D 65 ASP cc_start: 0.8992 (t0) cc_final: 0.8611 (t0) REVERT: E 76 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8374 (tt0) REVERT: E 122 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8663 (ptpt) REVERT: G 13 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8233 (ttmm) REVERT: G 92 GLU cc_start: 0.8416 (mt-10) cc_final: 0.7974 (mt-10) REVERT: H 65 ASP cc_start: 0.9021 (t70) cc_final: 0.8692 (t0) REVERT: M 34 VAL cc_start: 0.9304 (t) cc_final: 0.8967 (p) REVERT: M 57 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.8304 (mm-40) REVERT: M 84 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7794 (tp30) REVERT: M 169 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8587 (ptp) REVERT: N 172 SER cc_start: 0.8596 (m) cc_final: 0.8257 (p) REVERT: N 175 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7940 (pm20) REVERT: N 206 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.9093 (mp) outliers start: 32 outliers final: 18 residues processed: 218 average time/residue: 1.6209 time to fit residues: 381.1612 Evaluate side-chains 226 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 199 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 57 GLN Chi-restraints excluded: chain M residue 84 GLU Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 159 ASP Chi-restraints excluded: chain M residue 169 MET Chi-restraints excluded: chain M residue 223 SER Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 175 GLU Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain N residue 206 ILE Chi-restraints excluded: chain N residue 218 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 138 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 16367 Z= 0.382 Angle : 0.609 7.996 23376 Z= 0.353 Chirality : 0.039 0.162 2633 Planarity : 0.004 0.037 1931 Dihedral : 29.876 179.970 4560 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.64 % Allowed : 22.64 % Favored : 73.72 % 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: 1.58 (0.25), residues: 1175 helix: 2.59 (0.22), residues: 544 sheet: 0.53 (0.36), residues: 222 loop : -0.82 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 58 HIS 0.003 0.001 HIS M 249 PHE 0.009 0.002 PHE E 104 TYR 0.016 0.002 TYR N 72 ARG 0.011 0.000 ARG M 176 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 204 time to evaluate : 1.517 Fit side-chains revert: symmetry clash REVERT: C 71 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8326 (ttm-80) REVERT: D 39 TYR cc_start: 0.8449 (t80) cc_final: 0.7702 (t80) REVERT: D 65 ASP cc_start: 0.9036 (t0) cc_final: 0.8626 (t0) REVERT: E 76 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8427 (tt0) REVERT: E 122 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8741 (ptpt) REVERT: G 13 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8250 (ttmm) REVERT: G 92 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8196 (mt-10) REVERT: H 65 ASP cc_start: 0.9040 (t70) cc_final: 0.8707 (t0) REVERT: M 34 VAL cc_start: 0.9253 (t) cc_final: 0.8942 (p) REVERT: M 84 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7719 (tm-30) REVERT: N 64 ARG cc_start: 0.8118 (ttp-170) cc_final: 0.7882 (ttp-170) REVERT: N 172 SER cc_start: 0.8673 (m) cc_final: 0.8315 (p) REVERT: N 206 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.9100 (mp) REVERT: N 235 ASN cc_start: 0.8630 (OUTLIER) cc_final: 0.8386 (p0) REVERT: N 261 LYS cc_start: 0.9216 (OUTLIER) cc_final: 0.8981 (ttmm) outliers start: 37 outliers final: 17 residues processed: 225 average time/residue: 1.6109 time to fit residues: 390.4805 Evaluate side-chains 226 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 201 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 84 GLU Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain M residue 159 ASP Chi-restraints excluded: chain M residue 168 SER Chi-restraints excluded: chain M residue 223 SER Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain N residue 206 ILE Chi-restraints excluded: chain N residue 218 SER Chi-restraints excluded: chain N residue 235 ASN Chi-restraints excluded: chain N residue 261 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 126 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16367 Z= 0.248 Angle : 0.587 9.453 23376 Z= 0.342 Chirality : 0.037 0.157 2633 Planarity : 0.004 0.045 1931 Dihedral : 29.856 179.942 4560 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.05 % Allowed : 23.33 % Favored : 73.62 % 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: 1.64 (0.25), residues: 1175 helix: 2.66 (0.22), residues: 544 sheet: 0.54 (0.36), residues: 222 loop : -0.80 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 58 HIS 0.003 0.001 HIS M 249 PHE 0.008 0.001 PHE E 67 TYR 0.013 0.001 TYR N 72 ARG 0.013 0.000 ARG N 176 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 206 time to evaluate : 1.340 Fit side-chains revert: symmetry clash REVERT: C 71 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8318 (ttm-80) REVERT: D 39 TYR cc_start: 0.8385 (t80) cc_final: 0.7632 (t80) REVERT: D 65 ASP cc_start: 0.9023 (t0) cc_final: 0.8616 (t0) REVERT: E 76 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8401 (tt0) REVERT: E 122 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8689 (ptpt) REVERT: G 13 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8248 (ttmm) REVERT: G 51 MET cc_start: 0.8331 (tpt) cc_final: 0.8065 (tpt) REVERT: G 92 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8148 (mt-10) REVERT: H 65 ASP cc_start: 0.9027 (t70) cc_final: 0.8704 (t0) REVERT: M 34 VAL cc_start: 0.9240 (t) cc_final: 0.8935 (p) REVERT: M 57 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.8320 (mm-40) REVERT: M 84 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7682 (tm-30) REVERT: N 64 ARG cc_start: 0.8125 (ttp-170) cc_final: 0.7901 (ttp-170) REVERT: N 112 ASP cc_start: 0.8753 (m-30) cc_final: 0.8478 (m-30) REVERT: N 172 SER cc_start: 0.8669 (m) cc_final: 0.8313 (p) REVERT: N 175 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7976 (pm20) REVERT: N 206 ILE cc_start: 0.9332 (OUTLIER) cc_final: 0.9098 (mp) REVERT: N 261 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.9008 (ttmm) outliers start: 31 outliers final: 15 residues processed: 225 average time/residue: 1.6597 time to fit residues: 402.2571 Evaluate side-chains 227 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 203 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 57 GLN Chi-restraints excluded: chain M residue 84 GLU Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain M residue 159 ASP Chi-restraints excluded: chain M residue 168 SER Chi-restraints excluded: chain M residue 223 SER Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 175 GLU Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain N residue 206 ILE Chi-restraints excluded: chain N residue 218 SER Chi-restraints excluded: chain N residue 261 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 3.9990 chunk 121 optimal weight: 0.0000 chunk 129 optimal weight: 0.0570 chunk 77 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 overall best weight: 0.4902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16367 Z= 0.172 Angle : 0.581 10.484 23376 Z= 0.338 Chirality : 0.036 0.152 2633 Planarity : 0.004 0.064 1931 Dihedral : 29.831 179.980 4560 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.66 % Allowed : 24.21 % Favored : 73.13 % 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: 1.71 (0.25), residues: 1175 helix: 2.72 (0.22), residues: 544 sheet: 0.55 (0.36), residues: 222 loop : -0.76 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 58 HIS 0.003 0.001 HIS B 75 PHE 0.009 0.001 PHE E 67 TYR 0.016 0.001 TYR N 76 ARG 0.015 0.001 ARG N 176 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 205 time to evaluate : 1.399 Fit side-chains revert: symmetry clash REVERT: C 71 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8330 (ttm-80) REVERT: D 39 TYR cc_start: 0.8322 (t80) cc_final: 0.7584 (t80) REVERT: D 65 ASP cc_start: 0.9010 (t0) cc_final: 0.8575 (t0) REVERT: E 76 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8359 (tt0) REVERT: G 13 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8243 (ttmm) REVERT: G 92 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8102 (mt-10) REVERT: H 65 ASP cc_start: 0.9011 (t70) cc_final: 0.8694 (t0) REVERT: M 34 VAL cc_start: 0.9233 (t) cc_final: 0.8927 (p) REVERT: N 64 ARG cc_start: 0.8128 (ttp-170) cc_final: 0.7901 (ttp-170) REVERT: N 112 ASP cc_start: 0.8729 (m-30) cc_final: 0.8475 (m-30) REVERT: N 172 SER cc_start: 0.8573 (m) cc_final: 0.8266 (p) REVERT: N 175 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7905 (pm20) REVERT: N 206 ILE cc_start: 0.9298 (OUTLIER) cc_final: 0.9077 (mp) REVERT: N 235 ASN cc_start: 0.8499 (OUTLIER) cc_final: 0.7547 (p0) REVERT: N 261 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.9004 (ttmm) outliers start: 27 outliers final: 12 residues processed: 220 average time/residue: 1.6740 time to fit residues: 396.5001 Evaluate side-chains 226 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 207 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 159 ASP Chi-restraints excluded: chain M residue 168 SER Chi-restraints excluded: chain M residue 223 SER Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 175 GLU Chi-restraints excluded: chain N residue 206 ILE Chi-restraints excluded: chain N residue 235 ASN Chi-restraints excluded: chain N residue 261 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 132 optimal weight: 0.6980 chunk 114 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 85 GLN ** N 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 16367 Z= 0.332 Angle : 0.607 11.090 23376 Z= 0.349 Chirality : 0.038 0.158 2633 Planarity : 0.004 0.043 1931 Dihedral : 29.776 179.608 4560 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.87 % Allowed : 25.10 % Favored : 73.03 % 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: 1.62 (0.25), residues: 1175 helix: 2.66 (0.22), residues: 544 sheet: 0.48 (0.36), residues: 222 loop : -0.81 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 58 HIS 0.003 0.001 HIS M 249 PHE 0.008 0.001 PHE F 61 TYR 0.016 0.001 TYR N 72 ARG 0.017 0.001 ARG N 176 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 202 time to evaluate : 1.161 Fit side-chains revert: symmetry clash REVERT: C 71 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.8323 (ttm-80) REVERT: D 39 TYR cc_start: 0.8415 (t80) cc_final: 0.7693 (t80) REVERT: D 65 ASP cc_start: 0.9012 (t0) cc_final: 0.8588 (t0) REVERT: E 76 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8406 (tt0) REVERT: G 13 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8255 (ttmm) REVERT: G 92 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8096 (mt-10) REVERT: H 65 ASP cc_start: 0.9027 (t70) cc_final: 0.8697 (t0) REVERT: M 34 VAL cc_start: 0.9247 (t) cc_final: 0.8942 (p) REVERT: N 64 ARG cc_start: 0.8104 (ttp-170) cc_final: 0.7877 (ttp-170) REVERT: N 112 ASP cc_start: 0.8748 (m-30) cc_final: 0.8461 (m-30) REVERT: N 172 SER cc_start: 0.8592 (m) cc_final: 0.8300 (p) REVERT: N 175 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7997 (pm20) REVERT: N 206 ILE cc_start: 0.9342 (OUTLIER) cc_final: 0.9106 (mp) REVERT: N 235 ASN cc_start: 0.8680 (OUTLIER) cc_final: 0.8428 (p0) outliers start: 19 outliers final: 12 residues processed: 214 average time/residue: 1.6869 time to fit residues: 390.2555 Evaluate side-chains 219 residues out of total 1021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 201 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain M residue 159 ASP Chi-restraints excluded: chain M residue 168 SER Chi-restraints excluded: chain M residue 223 SER Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 175 GLU Chi-restraints excluded: chain N residue 206 ILE Chi-restraints excluded: chain N residue 235 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 GLN ** 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 = 0.3647 r_free = 0.3647 target = 0.111177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.069302 restraints weight = 25485.424| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 1.85 r_work: 0.2656 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2514 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16367 Z= 0.195 Angle : 0.581 9.435 23376 Z= 0.338 Chirality : 0.036 0.152 2633 Planarity : 0.004 0.042 1931 Dihedral : 29.761 179.946 4560 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.77 % Allowed : 25.20 % Favored : 73.03 % 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: 1.70 (0.25), residues: 1175 helix: 2.73 (0.22), residues: 544 sheet: 0.48 (0.36), residues: 222 loop : -0.76 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 58 HIS 0.003 0.001 HIS M 249 PHE 0.009 0.001 PHE E 67 TYR 0.011 0.001 TYR N 72 ARG 0.011 0.000 ARG M 176 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6370.87 seconds wall clock time: 112 minutes 37.91 seconds (6757.91 seconds total)