Starting phenix.real_space_refine on Thu Sep 18 09:05:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r2q_53537/09_2025/9r2q_53537.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r2q_53537/09_2025/9r2q_53537.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9r2q_53537/09_2025/9r2q_53537.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r2q_53537/09_2025/9r2q_53537.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9r2q_53537/09_2025/9r2q_53537.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r2q_53537/09_2025/9r2q_53537.map" } resolution = 3.2 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 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= 0.002 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 283 5.49 5 S 14 5.16 5 C 8991 2.51 5 N 3012 2.21 5 O 3555 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15855 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" 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: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 789 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} 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: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2891 Classifications: {'DNA': 142} Link IDs: {'rna3p': 141} Chain: "J" Number of atoms: 2928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2928 Classifications: {'DNA': 142} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 141} Chain: "K" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1017 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PTRANS': 14, 'TRANS': 185} Unresolved non-hydrogen bonds: 575 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 8, 'PHE:plan': 5, 'ARG:plan': 18, 'HIS:plan': 7, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 8, 'GLU:plan': 11} Unresolved non-hydrogen planarities: 343 Chain: "L" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1017 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PTRANS': 14, 'TRANS': 185} Unresolved non-hydrogen bonds: 575 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 8, 'PHE:plan': 5, 'ARG:plan': 18, 'HIS:plan': 7, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 8, 'GLU:plan': 11} Unresolved non-hydrogen planarities: 343 Chain: "M" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1017 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PTRANS': 14, 'TRANS': 185} Unresolved non-hydrogen bonds: 575 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 8, 'PHE:plan': 5, 'ARG:plan': 18, 'HIS:plan': 7, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 8, 'GLU:plan': 11} Unresolved non-hydrogen planarities: 343 Chain: "N" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1017 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PTRANS': 14, 'TRANS': 185} Unresolved non-hydrogen bonds: 575 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 8, 'PHE:plan': 5, 'ARG:plan': 18, 'HIS:plan': 7, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 8, 'GLU:plan': 11} Unresolved non-hydrogen planarities: 343 Time building chain proxies: 3.65, per 1000 atoms: 0.23 Number of scatterers: 15855 At special positions: 0 Unit cell: (107.315, 116.61, 185.055, 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 14 16.00 P 283 15.00 O 3555 8.00 N 3012 7.00 C 8991 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 465.8 milliseconds Enol-peptide restraints added in 1.2 microseconds 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2896 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 18 sheets defined 41.6% alpha, 15.1% beta 142 base pairs and 278 stacking pairs defined. Time for finding SS restraints: 2.38 Creating SS restraints... Processing helix chain 'A' and resid 46 through 58 removed outlier: 4.514A pdb=" N ARG A 50 " --> pdb=" O THR A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 77 Processing helix chain 'A' and resid 86 through 115 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 49 through 77 removed outlier: 4.493A pdb=" N GLU B 53 " --> pdb=" O GLY B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'C' and resid 19 through 23 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 46 through 74 removed outlier: 4.112A pdb=" N VAL C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'D' and resid 38 through 50 Processing helix chain 'D' and resid 56 through 86 Processing helix chain 'D' and resid 91 through 103 Processing helix chain 'D' and resid 104 through 125 Processing helix chain 'E' and resid 45 through 58 Processing helix chain 'E' and resid 66 through 80 removed outlier: 4.238A pdb=" N ASP E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE E 79 " --> pdb=" O ILE E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 115 Processing helix chain 'E' and resid 121 through 132 Processing helix chain 'F' and resid 26 through 30 Processing helix chain 'F' and resid 31 through 42 Processing helix chain 'F' and resid 50 through 77 removed outlier: 3.554A pdb=" N GLU F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 94 removed outlier: 3.881A pdb=" N GLN F 94 " --> pdb=" O ALA F 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 23 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 74 removed outlier: 4.080A pdb=" N VAL G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 91 Processing helix chain 'G' and resid 93 through 98 Processing helix chain 'G' and resid 113 through 117 Processing helix chain 'H' and resid 38 through 50 removed outlier: 4.842A pdb=" N LYS H 47 " --> pdb=" O TYR H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 85 Processing helix chain 'H' and resid 91 through 103 removed outlier: 3.600A pdb=" N ARG H 100 " --> pdb=" O GLN H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 125 removed outlier: 3.540A pdb=" N HIS H 110 " --> pdb=" O GLU H 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 165 through 169 Processing helix chain 'K' and resid 176 through 182 Processing helix chain 'K' and resid 277 through 289 Processing helix chain 'L' and resid 176 through 182 Processing helix chain 'L' and resid 277 through 289 Processing helix chain 'M' and resid 104 through 108 removed outlier: 4.005A pdb=" N TYR M 107 " --> pdb=" O GLN M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 165 through 169 Processing helix chain 'M' and resid 176 through 182 Processing helix chain 'M' and resid 277 through 288 Processing helix chain 'N' and resid 176 through 182 Processing helix chain 'N' and resid 277 through 289 Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.961A pdb=" N ARG A 84 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA3, first strand: chain 'B' and resid 98 through 99 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.099A pdb=" N ARG C 43 " --> pdb=" O ILE D 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 103 removed outlier: 6.611A pdb=" N THR C 102 " --> pdb=" O TYR F 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.853A pdb=" N ARG E 84 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 119 through 120 Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44 removed outlier: 6.792A pdb=" N ARG G 43 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79 Processing sheet with id=AB2, first strand: chain 'K' and resid 110 through 112 Processing sheet with id=AB3, first strand: chain 'K' and resid 124 through 127 removed outlier: 6.215A pdb=" N MET K 133 " --> pdb=" O ARG K 273 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU K 257 " --> pdb=" O LEU K 265 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ARG K 267 " --> pdb=" O ILE K 255 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE K 255 " --> pdb=" O ARG K 267 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N SER K 269 " --> pdb=" O THR K 253 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR K 253 " --> pdb=" O SER K 269 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLU K 271 " --> pdb=" O ILE K 251 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ILE K 251 " --> pdb=" O GLU K 271 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ALA K 161 " --> pdb=" O HIS K 214 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N HIS K 214 " --> pdb=" O ALA K 161 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 110 through 113 Processing sheet with id=AB5, first strand: chain 'L' and resid 124 through 127 removed outlier: 3.903A pdb=" N ILE L 251 " --> pdb=" O VAL L 272 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ALA L 161 " --> pdb=" O HIS L 214 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS L 214 " --> pdb=" O ALA L 161 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 110 through 112 Processing sheet with id=AB7, first strand: chain 'M' and resid 124 through 127 removed outlier: 3.980A pdb=" N ILE M 251 " --> pdb=" O VAL M 272 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ALA M 161 " --> pdb=" O HIS M 214 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N HIS M 214 " --> pdb=" O ALA M 161 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 110 through 112 Processing sheet with id=AB9, first strand: chain 'N' and resid 124 through 127 removed outlier: 3.984A pdb=" N ILE N 251 " --> pdb=" O VAL N 272 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ALA N 161 " --> pdb=" O HIS N 214 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N HIS N 214 " --> pdb=" O ALA N 161 " (cutoff:3.500A) 616 hydrogen bonds defined for protein. 1734 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 361 hydrogen bonds 722 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 278 stacking parallelities Total time for adding SS restraints: 3.25 Time building geometry restraints manager: 1.58 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: 2714 1.33 - 1.45: 5265 1.45 - 1.57: 8172 1.57 - 1.69: 524 1.69 - 1.82: 24 Bond restraints: 16699 Sorted by residual: bond pdb=" P DA J 59 " pdb=" O5' DA J 59 " ideal model delta sigma weight residual 1.600 1.554 0.046 2.00e-02 2.50e+03 5.38e+00 bond pdb=" C5' DC I 80 " pdb=" C4' DC I 80 " ideal model delta sigma weight residual 1.518 1.473 0.045 2.00e-02 2.50e+03 5.07e+00 bond pdb=" P DA J 60 " pdb=" O5' DA J 60 " ideal model delta sigma weight residual 1.600 1.557 0.043 2.00e-02 2.50e+03 4.71e+00 bond pdb=" P DC I 80 " pdb=" O5' DC I 80 " ideal model delta sigma weight residual 1.600 1.558 0.042 2.00e-02 2.50e+03 4.35e+00 bond pdb=" P DT I 31 " pdb=" O5' DT I 31 " ideal model delta sigma weight residual 1.600 1.559 0.041 2.00e-02 2.50e+03 4.21e+00 ... (remaining 16694 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 21683 1.69 - 3.38: 1952 3.38 - 5.07: 297 5.07 - 6.77: 43 6.77 - 8.46: 3 Bond angle restraints: 23978 Sorted by residual: angle pdb=" C4' DA I 90 " pdb=" C3' DA I 90 " pdb=" O3' DA I 90 " ideal model delta sigma weight residual 110.00 102.65 7.35 1.50e+00 4.44e-01 2.40e+01 angle pdb=" O3' DT J 58 " pdb=" P DA J 59 " pdb=" O5' DA J 59 " ideal model delta sigma weight residual 104.00 96.69 7.31 1.50e+00 4.44e-01 2.37e+01 angle pdb=" CA TYR H 43 " pdb=" CB TYR H 43 " pdb=" CG TYR H 43 " ideal model delta sigma weight residual 113.90 122.36 -8.46 1.80e+00 3.09e-01 2.21e+01 angle pdb=" C4' DA I 120 " pdb=" C3' DA I 120 " pdb=" O3' DA I 120 " ideal model delta sigma weight residual 110.00 103.39 6.61 1.50e+00 4.44e-01 1.94e+01 angle pdb=" O3' DA I 90 " pdb=" P DA I 91 " pdb=" O5' DA I 91 " ideal model delta sigma weight residual 104.00 97.46 6.54 1.50e+00 4.44e-01 1.90e+01 ... (remaining 23973 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 6961 17.28 - 34.56: 923 34.56 - 51.84: 1121 51.84 - 69.12: 307 69.12 - 86.40: 3 Dihedral angle restraints: 9315 sinusoidal: 4849 harmonic: 4466 Sorted by residual: dihedral pdb=" CA ARG E 43 " pdb=" C ARG E 43 " pdb=" N PRO E 44 " pdb=" CA PRO E 44 " ideal model delta harmonic sigma weight residual -180.00 -154.66 -25.34 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA ARG A 84 " pdb=" C ARG A 84 " pdb=" N PHE A 85 " pdb=" CA PHE A 85 " ideal model delta harmonic sigma weight residual -180.00 -154.84 -25.16 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA TYR E 42 " pdb=" C TYR E 42 " pdb=" N ARG E 43 " pdb=" CA ARG E 43 " ideal model delta harmonic sigma weight residual 180.00 157.11 22.89 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 9312 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 2165 0.072 - 0.144: 510 0.144 - 0.215: 109 0.215 - 0.287: 30 0.287 - 0.359: 2 Chirality restraints: 2816 Sorted by residual: chirality pdb=" CA TYR H 43 " pdb=" N TYR H 43 " pdb=" C TYR H 43 " pdb=" CB TYR H 43 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" CA ARG L 248 " pdb=" N ARG L 248 " pdb=" C ARG L 248 " pdb=" CB ARG L 248 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CA ARG K 248 " pdb=" N ARG K 248 " pdb=" C ARG K 248 " pdb=" CB ARG K 248 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 2813 not shown) Planarity restraints: 2173 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT J 28 " -0.050 2.00e-02 2.50e+03 2.25e-02 1.27e+01 pdb=" N1 DT J 28 " 0.040 2.00e-02 2.50e+03 pdb=" C2 DT J 28 " 0.001 2.00e-02 2.50e+03 pdb=" O2 DT J 28 " 0.017 2.00e-02 2.50e+03 pdb=" N3 DT J 28 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DT J 28 " -0.008 2.00e-02 2.50e+03 pdb=" O4 DT J 28 " -0.019 2.00e-02 2.50e+03 pdb=" C5 DT J 28 " 0.005 2.00e-02 2.50e+03 pdb=" C7 DT J 28 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DT J 28 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 120 " 0.045 2.00e-02 2.50e+03 1.92e-02 1.01e+01 pdb=" N9 DA I 120 " -0.038 2.00e-02 2.50e+03 pdb=" C8 DA I 120 " -0.007 2.00e-02 2.50e+03 pdb=" N7 DA I 120 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DA I 120 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DA I 120 " 0.007 2.00e-02 2.50e+03 pdb=" N6 DA I 120 " 0.015 2.00e-02 2.50e+03 pdb=" N1 DA I 120 " 0.006 2.00e-02 2.50e+03 pdb=" C2 DA I 120 " -0.009 2.00e-02 2.50e+03 pdb=" N3 DA I 120 " -0.010 2.00e-02 2.50e+03 pdb=" C4 DA I 120 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J 18 " -0.045 2.00e-02 2.50e+03 1.82e-02 9.97e+00 pdb=" N9 DG J 18 " 0.036 2.00e-02 2.50e+03 pdb=" C8 DG J 18 " 0.011 2.00e-02 2.50e+03 pdb=" N7 DG J 18 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DG J 18 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG J 18 " -0.006 2.00e-02 2.50e+03 pdb=" O6 DG J 18 " -0.018 2.00e-02 2.50e+03 pdb=" N1 DG J 18 " -0.005 2.00e-02 2.50e+03 pdb=" C2 DG J 18 " -0.000 2.00e-02 2.50e+03 pdb=" N2 DG J 18 " 0.012 2.00e-02 2.50e+03 pdb=" N3 DG J 18 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DG J 18 " 0.003 2.00e-02 2.50e+03 ... (remaining 2170 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3623 2.80 - 3.33: 13670 3.33 - 3.85: 28072 3.85 - 4.38: 33714 4.38 - 4.90: 47627 Nonbonded interactions: 126706 Sorted by model distance: nonbonded pdb=" OG SER C 19 " pdb=" O LEU C 24 " model vdw 2.281 3.040 nonbonded pdb=" N ARG C 18 " pdb=" OP1 DT I 31 " model vdw 2.311 3.120 nonbonded pdb=" N GLU F 53 " pdb=" OE1 GLU F 53 " model vdw 2.313 3.120 nonbonded pdb=" OG1 THR D 91 " pdb=" OE1 GLU D 94 " model vdw 2.355 3.040 nonbonded pdb=" O6 DG I 126 " pdb=" N6 DA J 21 " model vdw 2.373 3.120 ... (remaining 126701 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 18 through 119) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'L' selection = 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: 3.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.680 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 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 : 0.007 0.056 16699 Z= 0.350 Angle : 1.015 8.457 23978 Z= 0.609 Chirality : 0.068 0.359 2816 Planarity : 0.007 0.068 2173 Dihedral : 25.241 86.404 6419 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.44 % Allowed : 2.48 % Favored : 97.08 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.20), residues: 1528 helix: -0.37 (0.18), residues: 607 sheet: 1.19 (0.29), residues: 272 loop : 0.39 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 33 TYR 0.041 0.003 TYR H 43 PHE 0.026 0.003 PHE H 71 TRP 0.000 0.000 TRP K 146 HIS 0.010 0.002 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00722 (16699) covalent geometry : angle 1.01539 (23978) hydrogen bonds : bond 0.14570 ( 977) hydrogen bonds : angle 6.02213 ( 2456) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 284 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.7970 (tt0) cc_final: 0.7658 (tt0) REVERT: G 69 ASN cc_start: 0.8146 (m-40) cc_final: 0.7784 (m-40) outliers start: 3 outliers final: 0 residues processed: 286 average time/residue: 0.1778 time to fit residues: 67.8109 Evaluate side-chains 214 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 40.0000 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 50.0000 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS A 69 GLN B 26 ASN D 64 ASN D 68 ASN E 94 GLN F 26 ASN G 113 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.139457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.092624 restraints weight = 37075.954| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.41 r_work: 0.3127 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 16699 Z= 0.242 Angle : 0.626 7.215 23978 Z= 0.365 Chirality : 0.041 0.131 2816 Planarity : 0.006 0.052 2173 Dihedral : 28.646 75.171 4750 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 3.06 % Allowed : 9.18 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.21), residues: 1528 helix: 1.86 (0.20), residues: 613 sheet: 1.01 (0.28), residues: 324 loop : 0.77 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 80 TYR 0.015 0.001 TYR F 89 PHE 0.016 0.001 PHE A 68 TRP 0.000 0.000 TRP K 146 HIS 0.008 0.001 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00545 (16699) covalent geometry : angle 0.62603 (23978) hydrogen bonds : bond 0.04947 ( 977) hydrogen bonds : angle 3.81440 ( 2456) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 237 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8773 (tt0) cc_final: 0.8451 (tt0) REVERT: D 36 GLU cc_start: 0.5726 (tp30) cc_final: 0.5525 (tp30) REVERT: E 40 HIS cc_start: 0.8078 (t70) cc_final: 0.7662 (t-90) REVERT: E 121 MET cc_start: 0.7965 (mtp) cc_final: 0.7669 (mtt) REVERT: H 58 LYS cc_start: 0.9155 (mttt) cc_final: 0.8935 (mtpp) outliers start: 21 outliers final: 14 residues processed: 247 average time/residue: 0.1587 time to fit residues: 53.7272 Evaluate side-chains 230 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 216 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 36 ARG Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 48 GLN Chi-restraints excluded: chain H residue 124 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 89 optimal weight: 4.9990 chunk 177 optimal weight: 50.0000 chunk 158 optimal weight: 10.0000 chunk 168 optimal weight: 30.0000 chunk 125 optimal weight: 0.3980 chunk 106 optimal weight: 7.9990 chunk 47 optimal weight: 0.4980 chunk 143 optimal weight: 0.5980 chunk 140 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 175 optimal weight: 0.0470 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN C 85 GLN D 64 ASN D 96 GLN F 26 ASN H 85 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.142989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.096238 restraints weight = 37604.686| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.43 r_work: 0.3206 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16699 Z= 0.146 Angle : 0.533 11.025 23978 Z= 0.313 Chirality : 0.036 0.181 2816 Planarity : 0.004 0.041 2173 Dihedral : 27.375 71.835 4750 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.48 % Allowed : 11.52 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.54 (0.21), residues: 1528 helix: 2.62 (0.20), residues: 615 sheet: 1.30 (0.29), residues: 304 loop : 1.03 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 70 TYR 0.011 0.001 TYR F 89 PHE 0.009 0.001 PHE E 68 TRP 0.000 0.000 TRP K 146 HIS 0.004 0.001 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00310 (16699) covalent geometry : angle 0.53314 (23978) hydrogen bonds : bond 0.04125 ( 977) hydrogen bonds : angle 3.25788 ( 2456) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 243 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: A 106 GLU cc_start: 0.8073 (tp30) cc_final: 0.7823 (tp30) REVERT: B 92 LYS cc_start: 0.8831 (tttt) cc_final: 0.8527 (ttpt) REVERT: C 100 ARG cc_start: 0.8919 (mmm160) cc_final: 0.8536 (mmt-90) REVERT: D 87 ARG cc_start: 0.8489 (mmt-90) cc_final: 0.7829 (mmm160) REVERT: E 40 HIS cc_start: 0.8235 (t70) cc_final: 0.7812 (t-90) REVERT: G 36 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.8054 (tmm-80) REVERT: G 51 TYR cc_start: 0.9384 (t80) cc_final: 0.9146 (t80) REVERT: H 58 LYS cc_start: 0.9243 (mttt) cc_final: 0.8968 (mmmt) outliers start: 17 outliers final: 8 residues processed: 250 average time/residue: 0.1637 time to fit residues: 56.0476 Evaluate side-chains 225 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 216 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 26 ASN Chi-restraints excluded: chain G residue 36 ARG Chi-restraints excluded: chain H residue 124 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 20 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 110 optimal weight: 50.0000 chunk 41 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 GLN D 64 ASN D 68 ASN D 96 GLN E 69 GLN F 26 ASN F 76 HIS H 85 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.134070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.086742 restraints weight = 36752.177| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.23 r_work: 0.3051 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 16699 Z= 0.313 Angle : 0.662 11.588 23978 Z= 0.379 Chirality : 0.045 0.195 2816 Planarity : 0.005 0.063 2173 Dihedral : 28.381 78.704 4750 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.06 % Allowed : 12.97 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.35 (0.21), residues: 1528 helix: 2.32 (0.20), residues: 619 sheet: 1.16 (0.29), residues: 312 loop : 1.13 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 30 TYR 0.017 0.002 TYR F 89 PHE 0.024 0.002 PHE A 68 TRP 0.000 0.000 TRP K 146 HIS 0.004 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00716 (16699) covalent geometry : angle 0.66155 (23978) hydrogen bonds : bond 0.05258 ( 977) hydrogen bonds : angle 3.55645 ( 2456) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 232 time to evaluate : 0.472 Fit side-chains REVERT: B 92 LYS cc_start: 0.9193 (tttt) cc_final: 0.8880 (ttpt) REVERT: C 77 THR cc_start: 0.8834 (p) cc_final: 0.8541 (t) REVERT: C 78 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.8241 (ttm170) REVERT: C 100 ARG cc_start: 0.8914 (mmm160) cc_final: 0.8583 (mmt-90) REVERT: D 36 GLU cc_start: 0.5941 (tm-30) cc_final: 0.5589 (tm-30) REVERT: D 88 SER cc_start: 0.9157 (OUTLIER) cc_final: 0.8953 (p) REVERT: D 114 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8770 (mm-30) REVERT: E 40 HIS cc_start: 0.8334 (t70) cc_final: 0.8026 (t-90) REVERT: E 60 GLU cc_start: 0.8527 (pp20) cc_final: 0.7952 (pp20) REVERT: E 82 ASP cc_start: 0.8937 (t0) cc_final: 0.8477 (t70) REVERT: E 121 MET cc_start: 0.8431 (mtp) cc_final: 0.8197 (mtt) REVERT: F 94 GLN cc_start: 0.8880 (mm-40) cc_final: 0.8664 (mm-40) REVERT: H 89 THR cc_start: 0.9371 (m) cc_final: 0.9137 (t) outliers start: 21 outliers final: 12 residues processed: 242 average time/residue: 0.1556 time to fit residues: 52.0893 Evaluate side-chains 233 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 219 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 26 ASN Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 48 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 74 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 106 optimal weight: 8.9990 chunk 151 optimal weight: 3.9990 chunk 139 optimal weight: 50.0000 chunk 173 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 68 optimal weight: 0.0370 chunk 114 optimal weight: 50.0000 chunk 100 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 overall best weight: 2.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 50 HIS D 64 ASN E 94 GLN F 26 ASN F 76 HIS H 85 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.134461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.087589 restraints weight = 36599.488| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.18 r_work: 0.3072 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16699 Z= 0.226 Angle : 0.577 11.850 23978 Z= 0.336 Chirality : 0.040 0.153 2816 Planarity : 0.004 0.039 2173 Dihedral : 28.034 71.268 4750 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.62 % Allowed : 14.72 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.62 (0.21), residues: 1528 helix: 2.61 (0.20), residues: 625 sheet: 1.19 (0.30), residues: 312 loop : 1.23 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 30 TYR 0.016 0.001 TYR B 89 PHE 0.017 0.001 PHE H 71 TRP 0.000 0.000 TRP K 146 HIS 0.006 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00515 (16699) covalent geometry : angle 0.57702 (23978) hydrogen bonds : bond 0.04146 ( 977) hydrogen bonds : angle 3.27533 ( 2456) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 228 time to evaluate : 0.474 Fit side-chains REVERT: A 106 GLU cc_start: 0.8138 (tp30) cc_final: 0.7857 (tp30) REVERT: B 92 LYS cc_start: 0.9159 (tttt) cc_final: 0.8837 (ttpt) REVERT: C 21 ARG cc_start: 0.9102 (tpp80) cc_final: 0.8824 (ttm-80) REVERT: C 77 THR cc_start: 0.8823 (p) cc_final: 0.8597 (t) REVERT: C 100 ARG cc_start: 0.8911 (mmm160) cc_final: 0.8593 (mmt-90) REVERT: D 36 GLU cc_start: 0.5877 (tm-30) cc_final: 0.5530 (tm-30) REVERT: D 68 ASN cc_start: 0.9079 (m-40) cc_final: 0.8793 (m-40) REVERT: E 40 HIS cc_start: 0.8362 (t70) cc_final: 0.8054 (t-90) REVERT: E 60 GLU cc_start: 0.8571 (pp20) cc_final: 0.8061 (pp20) REVERT: E 82 ASP cc_start: 0.8943 (t0) cc_final: 0.8489 (t70) REVERT: F 94 GLN cc_start: 0.8830 (mm-40) cc_final: 0.8509 (mm-40) REVERT: H 89 THR cc_start: 0.9405 (m) cc_final: 0.9133 (t) REVERT: H 94 GLU cc_start: 0.9161 (mp0) cc_final: 0.8957 (mp0) outliers start: 18 outliers final: 11 residues processed: 239 average time/residue: 0.1512 time to fit residues: 49.7202 Evaluate side-chains 231 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 220 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain F residue 26 ASN Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain H residue 124 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 43 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 126 optimal weight: 9.9990 chunk 100 optimal weight: 0.3980 chunk 71 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 175 optimal weight: 10.0000 chunk 116 optimal weight: 40.0000 chunk 48 optimal weight: 0.8980 chunk 170 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN D 50 HIS D 64 ASN D 96 GLN F 26 ASN H 85 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.137214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.090272 restraints weight = 36901.852| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.25 r_work: 0.3136 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.4974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 16699 Z= 0.147 Angle : 0.529 11.675 23978 Z= 0.311 Chirality : 0.036 0.150 2816 Planarity : 0.004 0.039 2173 Dihedral : 27.458 74.114 4750 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.60 % Allowed : 16.47 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.86 (0.21), residues: 1528 helix: 2.86 (0.20), residues: 625 sheet: 1.31 (0.30), residues: 312 loop : 1.32 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 80 TYR 0.015 0.001 TYR B 89 PHE 0.018 0.001 PHE H 71 TRP 0.000 0.000 TRP K 146 HIS 0.003 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00324 (16699) covalent geometry : angle 0.52884 (23978) hydrogen bonds : bond 0.03563 ( 977) hydrogen bonds : angle 3.04597 ( 2456) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 239 time to evaluate : 0.441 Fit side-chains REVERT: A 106 GLU cc_start: 0.8103 (tp30) cc_final: 0.7877 (tp30) REVERT: B 92 LYS cc_start: 0.9124 (tttt) cc_final: 0.8801 (ttpt) REVERT: C 21 ARG cc_start: 0.9072 (tpp80) cc_final: 0.8797 (ttm-80) REVERT: C 77 THR cc_start: 0.8798 (p) cc_final: 0.8541 (t) REVERT: C 100 ARG cc_start: 0.8830 (mmm160) cc_final: 0.8536 (mmt-90) REVERT: D 36 GLU cc_start: 0.5740 (tm-30) cc_final: 0.5421 (tm-30) REVERT: D 68 ASN cc_start: 0.9034 (m-40) cc_final: 0.8756 (m110) REVERT: D 114 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8818 (mm-30) REVERT: E 40 HIS cc_start: 0.8357 (t70) cc_final: 0.8058 (t-90) REVERT: E 82 ASP cc_start: 0.8922 (t0) cc_final: 0.8557 (t70) REVERT: F 94 GLN cc_start: 0.8754 (mm-40) cc_final: 0.8406 (mm-40) REVERT: G 36 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.8023 (ttp-110) REVERT: H 69 ASP cc_start: 0.8971 (t0) cc_final: 0.8713 (t0) REVERT: H 89 THR cc_start: 0.9354 (m) cc_final: 0.9108 (t) outliers start: 11 outliers final: 6 residues processed: 244 average time/residue: 0.1594 time to fit residues: 53.0195 Evaluate side-chains 231 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 224 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain F residue 26 ASN Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 36 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 67 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 122 optimal weight: 7.9990 chunk 156 optimal weight: 30.0000 chunk 43 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 123 optimal weight: 9.9990 chunk 118 optimal weight: 50.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS D 64 ASN D 96 GLN F 26 ASN ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.135231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.088354 restraints weight = 36491.908| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.20 r_work: 0.3097 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 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 : 0.004 0.070 16699 Z= 0.193 Angle : 0.554 12.999 23978 Z= 0.321 Chirality : 0.038 0.177 2816 Planarity : 0.004 0.038 2173 Dihedral : 27.577 72.432 4750 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.19 % Allowed : 16.18 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.87 (0.22), residues: 1528 helix: 2.89 (0.20), residues: 625 sheet: 1.16 (0.30), residues: 320 loop : 1.39 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 100 TYR 0.012 0.001 TYR D 41 PHE 0.014 0.001 PHE A 68 TRP 0.000 0.000 TRP K 146 HIS 0.004 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00438 (16699) covalent geometry : angle 0.55437 (23978) hydrogen bonds : bond 0.03768 ( 977) hydrogen bonds : angle 3.09113 ( 2456) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 220 time to evaluate : 0.402 Fit side-chains REVERT: B 26 ASN cc_start: 0.8728 (m110) cc_final: 0.8321 (m-40) REVERT: B 92 LYS cc_start: 0.9159 (tttt) cc_final: 0.8828 (ttpt) REVERT: C 21 ARG cc_start: 0.9070 (tpp80) cc_final: 0.8785 (ttm-80) REVERT: C 77 THR cc_start: 0.8874 (p) cc_final: 0.8602 (t) REVERT: C 100 ARG cc_start: 0.8911 (mmm160) cc_final: 0.8618 (mmt-90) REVERT: D 36 GLU cc_start: 0.5807 (tm-30) cc_final: 0.5512 (tm-30) REVERT: D 68 ASN cc_start: 0.9063 (m-40) cc_final: 0.8751 (m110) REVERT: E 40 HIS cc_start: 0.8338 (t70) cc_final: 0.8071 (t-90) REVERT: E 82 ASP cc_start: 0.8900 (t0) cc_final: 0.8552 (t70) REVERT: F 94 GLN cc_start: 0.8819 (mm-40) cc_final: 0.8444 (mm-40) REVERT: G 36 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.8058 (ttp-110) REVERT: H 89 THR cc_start: 0.9382 (m) cc_final: 0.9111 (t) outliers start: 15 outliers final: 10 residues processed: 228 average time/residue: 0.1521 time to fit residues: 47.6251 Evaluate side-chains 227 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 216 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 36 ARG Chi-restraints excluded: chain H residue 124 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 15 optimal weight: 0.9980 chunk 135 optimal weight: 8.9990 chunk 142 optimal weight: 50.0000 chunk 123 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 105 optimal weight: 20.0000 chunk 166 optimal weight: 0.0870 chunk 102 optimal weight: 50.0000 overall best weight: 1.1360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN B 76 HIS D 50 HIS D 64 ASN D 96 GLN H 85 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.135846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.089150 restraints weight = 36767.567| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.20 r_work: 0.3113 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.5141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 16699 Z= 0.155 Angle : 0.541 12.293 23978 Z= 0.314 Chirality : 0.037 0.149 2816 Planarity : 0.004 0.043 2173 Dihedral : 27.566 72.704 4750 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.19 % Allowed : 16.62 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.91 (0.22), residues: 1528 helix: 2.91 (0.20), residues: 625 sheet: 1.20 (0.30), residues: 320 loop : 1.42 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 30 TYR 0.011 0.001 TYR D 41 PHE 0.013 0.001 PHE A 68 TRP 0.000 0.000 TRP K 146 HIS 0.003 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00344 (16699) covalent geometry : angle 0.54116 (23978) hydrogen bonds : bond 0.03582 ( 977) hydrogen bonds : angle 3.04812 ( 2456) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 225 time to evaluate : 0.470 Fit side-chains REVERT: B 26 ASN cc_start: 0.8748 (m110) cc_final: 0.8326 (m-40) REVERT: B 92 LYS cc_start: 0.9136 (tttt) cc_final: 0.8805 (ttpt) REVERT: C 21 ARG cc_start: 0.9054 (tpp80) cc_final: 0.8776 (ttm-80) REVERT: C 36 ARG cc_start: 0.8625 (ttm170) cc_final: 0.8237 (mtm180) REVERT: C 77 THR cc_start: 0.8867 (p) cc_final: 0.8603 (t) REVERT: C 100 ARG cc_start: 0.8911 (mmm160) cc_final: 0.8627 (mmt-90) REVERT: D 36 GLU cc_start: 0.5730 (tm-30) cc_final: 0.5424 (tm-30) REVERT: D 68 ASN cc_start: 0.9047 (m-40) cc_final: 0.8735 (m110) REVERT: E 40 HIS cc_start: 0.8312 (t70) cc_final: 0.8073 (t-90) REVERT: E 82 ASP cc_start: 0.8889 (t0) cc_final: 0.8539 (t70) REVERT: F 94 GLN cc_start: 0.8787 (mm-40) cc_final: 0.8391 (mm-40) REVERT: G 36 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.8026 (ttp-110) REVERT: H 89 THR cc_start: 0.9374 (m) cc_final: 0.9107 (t) outliers start: 15 outliers final: 11 residues processed: 232 average time/residue: 0.1532 time to fit residues: 48.8921 Evaluate side-chains 231 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 219 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 36 ARG Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain H residue 124 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 45 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 104 optimal weight: 50.0000 chunk 95 optimal weight: 4.9990 chunk 166 optimal weight: 20.0000 chunk 175 optimal weight: 0.5980 chunk 102 optimal weight: 50.0000 chunk 157 optimal weight: 30.0000 chunk 30 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 150 optimal weight: 50.0000 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 64 ASN H 85 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.130611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.082899 restraints weight = 36499.965| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.18 r_work: 0.2986 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.5588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 16699 Z= 0.328 Angle : 0.665 15.343 23978 Z= 0.378 Chirality : 0.044 0.180 2816 Planarity : 0.005 0.047 2173 Dihedral : 28.523 78.774 4750 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.62 % Allowed : 16.76 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.57 (0.21), residues: 1528 helix: 2.49 (0.20), residues: 627 sheet: 1.05 (0.30), residues: 312 loop : 1.39 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 100 TYR 0.013 0.002 TYR F 52 PHE 0.023 0.002 PHE A 68 TRP 0.000 0.000 TRP K 146 HIS 0.003 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00749 (16699) covalent geometry : angle 0.66499 (23978) hydrogen bonds : bond 0.04934 ( 977) hydrogen bonds : angle 3.45392 ( 2456) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 221 time to evaluate : 0.352 Fit side-chains REVERT: B 26 ASN cc_start: 0.8756 (m110) cc_final: 0.8314 (m-40) REVERT: B 92 LYS cc_start: 0.9244 (tttt) cc_final: 0.8915 (ttpt) REVERT: B 93 ARG cc_start: 0.8946 (ptm160) cc_final: 0.8678 (ptm160) REVERT: C 21 ARG cc_start: 0.9102 (tpp80) cc_final: 0.8858 (ttm-80) REVERT: C 77 THR cc_start: 0.8952 (p) cc_final: 0.8719 (t) REVERT: C 100 ARG cc_start: 0.8945 (mmm160) cc_final: 0.8616 (mmt-90) REVERT: D 36 GLU cc_start: 0.6290 (tm-30) cc_final: 0.5985 (tm-30) REVERT: D 52 ASP cc_start: 0.8712 (p0) cc_final: 0.8496 (p0) REVERT: D 68 ASN cc_start: 0.9191 (m-40) cc_final: 0.8840 (m-40) REVERT: D 109 LYS cc_start: 0.8779 (ttpt) cc_final: 0.8554 (ttpt) REVERT: E 40 HIS cc_start: 0.8341 (t70) cc_final: 0.8117 (t-90) REVERT: E 82 ASP cc_start: 0.8914 (t0) cc_final: 0.8463 (t70) REVERT: G 95 ASN cc_start: 0.9164 (t0) cc_final: 0.8921 (t0) REVERT: H 89 THR cc_start: 0.9405 (m) cc_final: 0.9103 (t) outliers start: 18 outliers final: 14 residues processed: 231 average time/residue: 0.1462 time to fit residues: 46.7552 Evaluate side-chains 231 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 217 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 48 GLN Chi-restraints excluded: chain H residue 124 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 131 optimal weight: 5.9990 chunk 139 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 179 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 126 optimal weight: 0.0980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN D 96 GLN H 85 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.132066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.084316 restraints weight = 36772.916| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.17 r_work: 0.3032 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.5756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 16699 Z= 0.216 Angle : 0.591 13.627 23978 Z= 0.338 Chirality : 0.039 0.154 2816 Planarity : 0.005 0.062 2173 Dihedral : 28.088 76.026 4750 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.90 % Allowed : 17.06 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.62 (0.22), residues: 1528 helix: 2.66 (0.20), residues: 627 sheet: 1.00 (0.30), residues: 320 loop : 1.32 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 100 TYR 0.014 0.002 TYR D 41 PHE 0.013 0.001 PHE A 68 TRP 0.000 0.000 TRP K 146 HIS 0.013 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00492 (16699) covalent geometry : angle 0.59055 (23978) hydrogen bonds : bond 0.03956 ( 977) hydrogen bonds : angle 3.24850 ( 2456) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 220 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: B 85 MET cc_start: 0.8532 (mmm) cc_final: 0.8188 (tmm) REVERT: B 92 LYS cc_start: 0.9176 (tttt) cc_final: 0.8853 (ttpt) REVERT: B 93 ARG cc_start: 0.8892 (ptm160) cc_final: 0.8581 (ptm160) REVERT: C 21 ARG cc_start: 0.9076 (tpp80) cc_final: 0.8812 (ttm-80) REVERT: C 36 ARG cc_start: 0.8715 (ttm110) cc_final: 0.8175 (mtm180) REVERT: C 77 THR cc_start: 0.8941 (p) cc_final: 0.8718 (t) REVERT: C 100 ARG cc_start: 0.8927 (mmm160) cc_final: 0.8595 (mmt-90) REVERT: D 36 GLU cc_start: 0.6184 (tm-30) cc_final: 0.5979 (tm-30) REVERT: D 68 ASN cc_start: 0.9099 (m-40) cc_final: 0.8768 (m110) REVERT: E 82 ASP cc_start: 0.8895 (t0) cc_final: 0.8555 (t70) REVERT: H 89 THR cc_start: 0.9395 (m) cc_final: 0.9109 (t) outliers start: 13 outliers final: 11 residues processed: 226 average time/residue: 0.1540 time to fit residues: 47.7896 Evaluate side-chains 228 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 217 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 36 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 164 optimal weight: 20.0000 chunk 62 optimal weight: 0.0040 chunk 84 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 159 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 146 optimal weight: 20.0000 chunk 52 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 64 ASN D 96 GLN H 85 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.134501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.087359 restraints weight = 36922.555| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.21 r_work: 0.3094 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.5835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16699 Z= 0.145 Angle : 0.548 13.645 23978 Z= 0.317 Chirality : 0.037 0.173 2816 Planarity : 0.004 0.038 2173 Dihedral : 27.708 77.656 4750 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.90 % Allowed : 17.20 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.76 (0.22), residues: 1528 helix: 2.79 (0.21), residues: 627 sheet: 1.09 (0.30), residues: 320 loop : 1.36 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 100 TYR 0.015 0.001 TYR B 89 PHE 0.019 0.001 PHE A 68 TRP 0.000 0.000 TRP K 146 HIS 0.003 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00317 (16699) covalent geometry : angle 0.54809 (23978) hydrogen bonds : bond 0.03428 ( 977) hydrogen bonds : angle 3.08133 ( 2456) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5739.16 seconds wall clock time: 98 minutes 6.15 seconds (5886.15 seconds total)