Starting phenix.real_space_refine on Fri Jul 3 18:53:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r04_53478/07_2026/9r04_53478.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r04_53478/07_2026/9r04_53478.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9r04_53478/07_2026/9r04_53478.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r04_53478/07_2026/9r04_53478.map" model { file = "/net/cci-nas-00/data/ceres_data/9r04_53478/07_2026/9r04_53478.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r04_53478/07_2026/9r04_53478.cif" } resolution = 4.2 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= 0.003 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 Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 3.71, per 1000 atoms: 0.23 Number of scatterers: 15855 At special positions: 0 Unit cell: (157.08, 121.44, 166.32, 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: 1.43 Conformation dependent library (CDL) restraints added in 641.4 milliseconds 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: 45 helices and 16 sheets defined 40.9% alpha, 14.9% beta 142 base pairs and 268 stacking pairs defined. Time for finding SS restraints: 2.24 Creating SS restraints... Processing helix chain 'A' and resid 47 through 58 Processing helix chain 'A' and resid 64 through 78 removed outlier: 4.207A pdb=" N ASP A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) 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: 4.248A pdb=" N GLU B 53 " --> pdb=" O GLY B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 94 removed outlier: 4.170A pdb=" N GLN B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) 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: 3.975A 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 85 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: 4.182A pdb=" N ASP E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) removed outlier: 3.917A 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 Processing helix chain 'F' and resid 83 through 94 removed outlier: 3.847A 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: 3.946A 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 48 Processing helix chain 'H' and resid 56 through 85 Processing helix chain 'H' and resid 91 through 103 removed outlier: 3.516A pdb=" N ARG H 100 " --> pdb=" O GLN H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 125 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 165 through 169 Processing helix chain 'M' and resid 176 through 182 Processing helix chain 'M' and resid 277 through 289 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 119 through 120 Processing sheet with id=AA2, first strand: chain 'B' and resid 98 through 99 Processing sheet with id=AA3, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA4, first strand: chain 'C' and resid 101 through 103 removed outlier: 6.706A pdb=" N THR C 102 " --> pdb=" O TYR F 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.843A pdb=" N ARG E 84 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 119 through 120 Processing sheet with id=AA7, first strand: chain 'G' and resid 43 through 44 removed outlier: 6.800A pdb=" N ARG G 43 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 78 through 79 Processing sheet with id=AA9, first strand: chain 'K' and resid 110 through 112 Processing sheet with id=AB1, first strand: chain 'K' and resid 124 through 127 removed outlier: 3.896A pdb=" N ILE K 251 " --> pdb=" O VAL K 272 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ALA K 161 " --> pdb=" O HIS K 214 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N HIS K 214 " --> pdb=" O ALA K 161 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 110 through 113 Processing sheet with id=AB3, first strand: chain 'L' and resid 124 through 127 removed outlier: 3.802A pdb=" N ILE L 251 " --> pdb=" O VAL L 272 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ALA L 161 " --> pdb=" O HIS L 214 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N HIS L 214 " --> pdb=" O ALA L 161 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 110 through 112 Processing sheet with id=AB5, first strand: chain 'M' and resid 124 through 127 removed outlier: 3.917A pdb=" N ILE M 251 " --> pdb=" O VAL M 272 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ALA M 161 " --> pdb=" O HIS M 214 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N HIS M 214 " --> pdb=" O ALA M 161 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 110 through 113 Processing sheet with id=AB7, first strand: chain 'N' and resid 124 through 127 removed outlier: 6.431A pdb=" N LEU N 257 " --> pdb=" O LEU N 265 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ARG N 267 " --> pdb=" O ILE N 255 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE N 255 " --> pdb=" O ARG N 267 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER N 269 " --> pdb=" O THR N 253 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR N 253 " --> pdb=" O SER N 269 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLU N 271 " --> pdb=" O ILE N 251 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ILE N 251 " --> pdb=" O GLU N 271 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ALA N 161 " --> pdb=" O HIS N 214 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N HIS N 214 " --> pdb=" O ALA N 161 " (cutoff:3.500A) 617 hydrogen bonds defined for protein. 1746 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 360 hydrogen bonds 720 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 268 stacking parallelities Total time for adding SS restraints: 3.30 Time building geometry restraints manager: 1.98 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: 2493 1.33 - 1.45: 5221 1.45 - 1.57: 8399 1.57 - 1.69: 562 1.69 - 1.81: 24 Bond restraints: 16699 Sorted by residual: bond pdb=" C3' DT I 48 " pdb=" C2' DT I 48 " ideal model delta sigma weight residual 1.516 1.561 -0.045 8.00e-03 1.56e+04 3.20e+01 bond pdb=" C3' DT I 58 " pdb=" C2' DT I 58 " ideal model delta sigma weight residual 1.516 1.561 -0.045 8.00e-03 1.56e+04 3.11e+01 bond pdb=" C3' DT J 89 " pdb=" C2' DT J 89 " ideal model delta sigma weight residual 1.516 1.560 -0.044 8.00e-03 1.56e+04 3.03e+01 bond pdb=" C3' DT J 99 " pdb=" C2' DT J 99 " ideal model delta sigma weight residual 1.516 1.559 -0.043 8.00e-03 1.56e+04 2.89e+01 bond pdb=" C3' DC J 48 " pdb=" C2' DC J 48 " ideal model delta sigma weight residual 1.516 1.559 -0.043 8.00e-03 1.56e+04 2.89e+01 ... (remaining 16694 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 21469 1.85 - 3.70: 2012 3.70 - 5.56: 374 5.56 - 7.41: 88 7.41 - 9.26: 35 Bond angle restraints: 23978 Sorted by residual: angle pdb=" O4' DC I 119 " pdb=" C1' DC I 119 " pdb=" N1 DC I 119 " ideal model delta sigma weight residual 108.00 103.64 4.36 7.00e-01 2.04e+00 3.88e+01 angle pdb=" O4' DG J 134 " pdb=" C1' DG J 134 " pdb=" N9 DG J 134 " ideal model delta sigma weight residual 108.00 112.06 -4.06 7.00e-01 2.04e+00 3.36e+01 angle pdb=" O4' DC I 47 " pdb=" C1' DC I 47 " pdb=" N1 DC I 47 " ideal model delta sigma weight residual 108.00 104.16 3.84 7.00e-01 2.04e+00 3.00e+01 angle pdb=" O4' DT J 99 " pdb=" C1' DT J 99 " pdb=" N1 DT J 99 " ideal model delta sigma weight residual 108.00 104.26 3.74 7.00e-01 2.04e+00 2.85e+01 angle pdb=" O4' DT J 28 " pdb=" C1' DT J 28 " pdb=" N1 DT J 28 " ideal model delta sigma weight residual 108.00 104.31 3.69 7.00e-01 2.04e+00 2.78e+01 ... (remaining 23973 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.64: 7017 16.64 - 33.27: 812 33.27 - 49.91: 962 49.91 - 66.54: 512 66.54 - 83.18: 12 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 -153.24 -26.76 0 5.00e+00 4.00e-02 2.86e+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 -156.52 -23.48 0 5.00e+00 4.00e-02 2.20e+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 180.00 157.27 22.73 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 9312 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1821 0.060 - 0.119: 630 0.119 - 0.179: 306 0.179 - 0.239: 56 0.239 - 0.299: 3 Chirality restraints: 2816 Sorted by residual: chirality pdb=" C3' DG J 95 " pdb=" C4' DG J 95 " pdb=" O3' DG J 95 " pdb=" C2' DG J 95 " both_signs ideal model delta sigma weight residual False -2.73 -2.43 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C3' DG J 94 " pdb=" C4' DG J 94 " pdb=" O3' DG J 94 " pdb=" C2' DG J 94 " both_signs ideal model delta sigma weight residual False -2.73 -2.46 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C3' DA J 113 " pdb=" C4' DA J 113 " pdb=" O3' DA J 113 " pdb=" C2' DA J 113 " both_signs ideal model delta sigma weight residual False -2.73 -2.49 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 2813 not shown) Planarity restraints: 2173 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT J 28 " 0.062 2.00e-02 2.50e+03 2.90e-02 2.10e+01 pdb=" N1 DT J 28 " -0.059 2.00e-02 2.50e+03 pdb=" C2 DT J 28 " -0.007 2.00e-02 2.50e+03 pdb=" O2 DT J 28 " -0.012 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 " 0.023 2.00e-02 2.50e+03 pdb=" C5 DT J 28 " -0.005 2.00e-02 2.50e+03 pdb=" C7 DT J 28 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DT J 28 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 119 " -0.056 2.00e-02 2.50e+03 2.74e-02 1.69e+01 pdb=" N1 DC I 119 " 0.051 2.00e-02 2.50e+03 pdb=" C2 DC I 119 " 0.008 2.00e-02 2.50e+03 pdb=" O2 DC I 119 " 0.008 2.00e-02 2.50e+03 pdb=" N3 DC I 119 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DC I 119 " 0.004 2.00e-02 2.50e+03 pdb=" N4 DC I 119 " -0.029 2.00e-02 2.50e+03 pdb=" C5 DC I 119 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DC I 119 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 48 " 0.049 2.00e-02 2.50e+03 2.49e-02 1.40e+01 pdb=" N1 DC J 48 " -0.050 2.00e-02 2.50e+03 pdb=" C2 DC J 48 " -0.006 2.00e-02 2.50e+03 pdb=" O2 DC J 48 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DC J 48 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DC J 48 " -0.004 2.00e-02 2.50e+03 pdb=" N4 DC J 48 " 0.025 2.00e-02 2.50e+03 pdb=" C5 DC J 48 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DC J 48 " -0.006 2.00e-02 2.50e+03 ... (remaining 2170 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 272 2.66 - 3.22: 14167 3.22 - 3.78: 26892 3.78 - 4.34: 35243 4.34 - 4.90: 49930 Nonbonded interactions: 126504 Sorted by model distance: nonbonded pdb=" N GLU F 53 " pdb=" OE1 GLU F 53 " model vdw 2.101 3.120 nonbonded pdb=" OG SER C 19 " pdb=" O LEU C 24 " model vdw 2.366 3.040 nonbonded pdb=" N4 DC I 119 " pdb=" O4 DT J 28 " model vdw 2.402 3.120 nonbonded pdb=" OG SER D 88 " pdb=" O3' DA I 39 " model vdw 2.450 3.040 nonbonded pdb=" OG1 THR D 91 " pdb=" OE1 GLU D 94 " model vdw 2.488 3.040 ... (remaining 126499 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 Set stop_for_unknowns flag: 0.010 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.130 Find NCS groups from input model: 0.180 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: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 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 : 0.009 0.065 16699 Z= 0.821 Angle : 1.223 9.261 23978 Z= 0.829 Chirality : 0.074 0.299 2816 Planarity : 0.010 0.098 2173 Dihedral : 25.010 83.176 6419 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 0.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.09 % Favored : 97.84 % Rotamer: Outliers : 0.58 % Allowed : 3.35 % Favored : 96.06 % 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 are not related in a simple way. whole: -0.06 (0.20), residues: 1528 helix: -0.84 (0.17), residues: 600 sheet: 1.15 (0.30), residues: 276 loop : 0.48 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 18 TYR 0.037 0.003 TYR D 41 PHE 0.029 0.005 PHE A 79 TRP 0.000 0.000 TRP K 146 HIS 0.019 0.003 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00903 / 0.82 (16699) covalent geometry : angle 1.22316 / 0.83 (23978) hydrogen bonds : bond 0.13808 / 9.53 ( 977) hydrogen bonds : angle 6.41728 / 4.72 ( 2466) *********************** 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 306 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 302 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.5262 (OUTLIER) cc_final: 0.4854 (tpt90) REVERT: A 61 LEU cc_start: 0.8893 (mt) cc_final: 0.7604 (mp) REVERT: A 106 GLU cc_start: 0.9034 (tt0) cc_final: 0.8679 (tp30) REVERT: B 45 LYS cc_start: 0.8398 (tttt) cc_final: 0.7952 (ttmm) REVERT: B 50 LEU cc_start: 0.9251 (mt) cc_final: 0.8777 (mp) REVERT: B 64 GLU cc_start: 0.8933 (tt0) cc_final: 0.8547 (pt0) REVERT: C 75 LYS cc_start: 0.8754 (mttt) cc_final: 0.8446 (mmtt) REVERT: C 79 ILE cc_start: 0.9260 (mt) cc_final: 0.9046 (mm) REVERT: C 96 LYS cc_start: 0.9154 (tttp) cc_final: 0.8820 (ttpt) REVERT: C 100 ARG cc_start: 0.8032 (mmt-90) cc_final: 0.7778 (mmm-85) REVERT: C 102 THR cc_start: 0.8865 (m) cc_final: 0.8332 (p) REVERT: D 41 TYR cc_start: 0.9090 (m-80) cc_final: 0.8713 (m-80) REVERT: D 60 MET cc_start: 0.8863 (tpp) cc_final: 0.8574 (tpp) REVERT: D 63 MET cc_start: 0.9039 (mmm) cc_final: 0.8768 (mmp) REVERT: D 94 GLU cc_start: 0.9186 (mp0) cc_final: 0.8927 (mp0) REVERT: E 68 PHE cc_start: 0.8118 (t80) cc_final: 0.7670 (t80) REVERT: E 81 THR cc_start: 0.8252 (p) cc_final: 0.7250 (p) REVERT: E 121 MET cc_start: 0.8069 (mmm) cc_final: 0.7734 (mmm) REVERT: F 45 LYS cc_start: 0.9200 (tttt) cc_final: 0.8572 (pttm) REVERT: F 64 GLU cc_start: 0.9198 (mt-10) cc_final: 0.8931 (mt-10) REVERT: F 86 ASP cc_start: 0.7662 (m-30) cc_final: 0.7444 (m-30) REVERT: F 94 GLN cc_start: 0.9067 (mm-40) cc_final: 0.8755 (mm110) REVERT: F 101 PHE cc_start: 0.8363 (m-80) cc_final: 0.8126 (m-80) REVERT: G 18 ARG cc_start: 0.8396 (mtm-85) cc_final: 0.7905 (mtm110) REVERT: G 26 PHE cc_start: 0.8826 (m-80) cc_final: 0.8168 (m-80) REVERT: G 51 TYR cc_start: 0.9132 (t80) cc_final: 0.8906 (t80) REVERT: G 105 GLN cc_start: 0.7875 (mp10) cc_final: 0.7512 (mp10) REVERT: H 48 GLN cc_start: 0.8448 (mt0) cc_final: 0.8170 (mt0) REVERT: H 52 ASP cc_start: 0.9297 (p0) cc_final: 0.8977 (p0) REVERT: H 83 HIS cc_start: 0.8374 (t70) cc_final: 0.7959 (t70) REVERT: H 94 GLU cc_start: 0.8939 (mp0) cc_final: 0.8686 (mp0) REVERT: H 96 GLN cc_start: 0.8472 (tm130) cc_final: 0.7994 (tm-30) REVERT: H 100 ARG cc_start: 0.8844 (mtt-85) cc_final: 0.8474 (mpp80) REVERT: H 103 LEU cc_start: 0.9459 (mt) cc_final: 0.9259 (mp) REVERT: H 107 LEU cc_start: 0.9072 (mt) cc_final: 0.8518 (mt) outliers start: 4 outliers final: 1 residues processed: 305 average time/residue: 0.1328 time to fit residues: 57.9330 Evaluate side-chains 214 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 212 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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: 20.0000 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 30.0000 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 50.0000 overall best weight: 5.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 HIS D 85 ASN E 69 GLN E 86 GLN ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 25 GLN G 32 HIS H 96 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.114196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.076762 restraints weight = 66991.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.078640 restraints weight = 30348.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.079833 restraints weight = 19296.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.080531 restraints weight = 15013.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.080901 restraints weight = 13201.789| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.166 16699 Z= 0.315 Angle : 0.881 8.928 23978 Z= 0.471 Chirality : 0.049 0.219 2816 Planarity : 0.006 0.081 2173 Dihedral : 29.401 84.310 4750 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % 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 are not related in a simple way. whole: 1.18 (0.21), residues: 1528 helix: 0.97 (0.20), residues: 615 sheet: 0.86 (0.29), residues: 320 loop : 0.78 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 70 TYR 0.031 0.003 TYR H 43 PHE 0.015 0.003 PHE C 26 TRP 0.000 0.000 TRP K 146 HIS 0.010 0.002 HIS E 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00631 / 0.32 (16699) covalent geometry : angle 0.88062 / 0.47 (23978) hydrogen bonds : bond 0.07565 / 5.23 ( 977) hydrogen bonds : angle 4.61791 / 3.44 ( 2466) *********************** 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 222 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8616 (mt) cc_final: 0.8315 (mt) REVERT: A 94 GLN cc_start: 0.8365 (tm-30) cc_final: 0.7546 (tm-30) REVERT: A 107 ASP cc_start: 0.8235 (m-30) cc_final: 0.8015 (m-30) REVERT: A 121 MET cc_start: 0.7720 (mtm) cc_final: 0.7514 (mtm) REVERT: B 45 LYS cc_start: 0.9283 (tttt) cc_final: 0.8967 (ttmt) REVERT: B 67 ILE cc_start: 0.9607 (mt) cc_final: 0.9396 (mt) REVERT: C 28 VAL cc_start: 0.9047 (m) cc_final: 0.8842 (p) REVERT: C 39 ASN cc_start: 0.6993 (m-40) cc_final: 0.6322 (t0) REVERT: C 57 GLU cc_start: 0.8732 (pp20) cc_final: 0.8424 (pp20) REVERT: C 100 ARG cc_start: 0.8164 (mmt-90) cc_final: 0.7817 (mmm-85) REVERT: D 41 TYR cc_start: 0.9010 (m-80) cc_final: 0.8797 (m-80) REVERT: D 60 MET cc_start: 0.8784 (tpp) cc_final: 0.8318 (tpp) REVERT: D 94 GLU cc_start: 0.8972 (mp0) cc_final: 0.8769 (mp0) REVERT: E 74 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8295 (tm-30) REVERT: E 121 MET cc_start: 0.8438 (mmm) cc_final: 0.8025 (mmm) REVERT: F 45 LYS cc_start: 0.9220 (tttt) cc_final: 0.8825 (tptp) REVERT: F 51 ILE cc_start: 0.8826 (mm) cc_final: 0.8129 (mm) REVERT: F 55 THR cc_start: 0.9589 (m) cc_final: 0.9369 (p) REVERT: F 64 GLU cc_start: 0.9172 (mt-10) cc_final: 0.8914 (mt-10) REVERT: F 94 GLN cc_start: 0.8789 (mm-40) cc_final: 0.8521 (mm-40) REVERT: G 14 LYS cc_start: 0.7377 (ttpt) cc_final: 0.7149 (tptt) REVERT: G 18 ARG cc_start: 0.8527 (mtm-85) cc_final: 0.8240 (mtm110) REVERT: G 26 PHE cc_start: 0.9045 (m-80) cc_final: 0.8623 (m-80) REVERT: G 62 GLU cc_start: 0.8234 (tp30) cc_final: 0.7993 (tp30) REVERT: G 65 GLU cc_start: 0.8251 (pp20) cc_final: 0.8032 (pp20) REVERT: G 91 ASP cc_start: 0.8973 (t70) cc_final: 0.8686 (t0) REVERT: G 93 GLU cc_start: 0.9020 (mp0) cc_final: 0.8074 (mt-10) REVERT: G 111 ASN cc_start: 0.8853 (t0) cc_final: 0.8646 (t0) REVERT: H 52 ASP cc_start: 0.9035 (p0) cc_final: 0.8679 (p0) REVERT: H 63 MET cc_start: 0.8808 (mmt) cc_final: 0.8147 (mmm) REVERT: H 83 HIS cc_start: 0.8049 (t70) cc_final: 0.7694 (t70) REVERT: H 90 ILE cc_start: 0.9348 (mm) cc_final: 0.9057 (mm) REVERT: H 94 GLU cc_start: 0.9049 (mp0) cc_final: 0.8620 (mp0) REVERT: H 107 LEU cc_start: 0.8991 (mt) cc_final: 0.8636 (mt) REVERT: H 114 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8399 (mm-30) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.1076 time to fit residues: 36.2770 Evaluate side-chains 185 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 89 optimal weight: 30.0000 chunk 177 optimal weight: 50.0000 chunk 158 optimal weight: 50.0000 chunk 168 optimal weight: 40.0000 chunk 125 optimal weight: 5.9990 chunk 106 optimal weight: 30.0000 chunk 47 optimal weight: 2.9990 chunk 143 optimal weight: 40.0000 chunk 140 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 175 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 85 ASN ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 HIS H 110 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.111053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.071630 restraints weight = 70736.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.073341 restraints weight = 33104.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.074442 restraints weight = 21623.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.075121 restraints weight = 17256.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.075460 restraints weight = 15363.510| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.166 16699 Z= 0.343 Angle : 0.852 9.943 23978 Z= 0.469 Chirality : 0.050 0.278 2816 Planarity : 0.006 0.067 2173 Dihedral : 28.743 87.974 4750 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % 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 are not related in a simple way. whole: 1.11 (0.21), residues: 1528 helix: 0.94 (0.20), residues: 622 sheet: 0.72 (0.29), residues: 324 loop : 0.78 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 130 TYR 0.026 0.003 TYR G 51 PHE 0.019 0.002 PHE D 71 TRP 0.000 0.000 TRP K 146 HIS 0.019 0.003 HIS G 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00694 / 0.34 (16699) covalent geometry : angle 0.85214 / 0.47 (23978) hydrogen bonds : bond 0.07749 / 5.42 ( 977) hydrogen bonds : angle 4.59550 / 3.39 ( 2466) *********************** 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 206 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.9171 (tp) cc_final: 0.8912 (tp) REVERT: A 107 ASP cc_start: 0.8240 (m-30) cc_final: 0.8029 (m-30) REVERT: B 45 LYS cc_start: 0.9399 (tttt) cc_final: 0.9146 (ttpp) REVERT: B 64 GLU cc_start: 0.8702 (pt0) cc_final: 0.8490 (pt0) REVERT: C 57 GLU cc_start: 0.8719 (pp20) cc_final: 0.8437 (pp20) REVERT: C 93 GLU cc_start: 0.8548 (mp0) cc_final: 0.8291 (mp0) REVERT: D 40 ILE cc_start: 0.9481 (mp) cc_final: 0.9254 (tp) REVERT: D 41 TYR cc_start: 0.8837 (m-80) cc_final: 0.8605 (m-80) REVERT: D 60 MET cc_start: 0.8894 (tpp) cc_final: 0.8313 (tpp) REVERT: E 60 GLU cc_start: 0.8675 (pm20) cc_final: 0.8106 (pp20) REVERT: E 61 LEU cc_start: 0.8654 (mm) cc_final: 0.8134 (tt) REVERT: E 74 GLU cc_start: 0.8902 (tm-30) cc_final: 0.8462 (tm-30) REVERT: E 121 MET cc_start: 0.8832 (mmm) cc_final: 0.8212 (mmm) REVERT: F 45 LYS cc_start: 0.9191 (tttt) cc_final: 0.8938 (tptp) REVERT: F 51 ILE cc_start: 0.9228 (mm) cc_final: 0.8807 (mm) REVERT: F 65 ASN cc_start: 0.8605 (t0) cc_final: 0.8130 (t0) REVERT: F 94 GLN cc_start: 0.8685 (mm-40) cc_final: 0.8266 (mm-40) REVERT: G 91 ASP cc_start: 0.9113 (t70) cc_final: 0.8684 (t0) REVERT: G 93 GLU cc_start: 0.8911 (mp0) cc_final: 0.8373 (mt-10) REVERT: H 52 ASP cc_start: 0.9009 (p0) cc_final: 0.8612 (p0) REVERT: H 63 MET cc_start: 0.8908 (mmt) cc_final: 0.8243 (mmm) REVERT: H 83 HIS cc_start: 0.8144 (t70) cc_final: 0.7830 (t70) REVERT: H 90 ILE cc_start: 0.9469 (mm) cc_final: 0.9255 (mm) REVERT: H 94 GLU cc_start: 0.9068 (mp0) cc_final: 0.8742 (mp0) REVERT: H 106 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7498 (tm-30) REVERT: H 114 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8214 (mm-30) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.1059 time to fit residues: 33.5876 Evaluate side-chains 176 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 20 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 105 optimal weight: 30.0000 chunk 36 optimal weight: 20.0000 chunk 112 optimal weight: 50.0000 chunk 24 optimal weight: 0.9990 chunk 111 optimal weight: 30.0000 chunk 110 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 88 optimal weight: 50.0000 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 HIS D 85 ASN D 110 HIS ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.115326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.075875 restraints weight = 68600.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.077756 restraints weight = 30991.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.078957 restraints weight = 19823.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.079680 restraints weight = 15615.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.080005 restraints weight = 13786.429| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16699 Z= 0.146 Angle : 0.660 7.252 23978 Z= 0.376 Chirality : 0.045 0.222 2816 Planarity : 0.004 0.046 2173 Dihedral : 28.455 81.091 4750 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % 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 are not related in a simple way. whole: 1.84 (0.21), residues: 1528 helix: 1.95 (0.21), residues: 618 sheet: 0.76 (0.29), residues: 324 loop : 0.88 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 18 TYR 0.032 0.002 TYR H 43 PHE 0.022 0.002 PHE E 105 TRP 0.000 0.000 TRP K 146 HIS 0.005 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.15 (16699) covalent geometry : angle 0.66040 / 0.38 (23978) hydrogen bonds : bond 0.04930 / 3.43 ( 977) hydrogen bonds : angle 3.82379 / 2.82 ( 2466) *********************** 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 234 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 PHE cc_start: 0.8643 (m-80) cc_final: 0.8434 (m-10) REVERT: A 95 GLU cc_start: 0.8934 (tp30) cc_final: 0.8599 (tp30) REVERT: B 45 LYS cc_start: 0.9341 (tttt) cc_final: 0.8894 (ttmt) REVERT: B 54 GLU cc_start: 0.9013 (tp30) cc_final: 0.8722 (tp30) REVERT: B 63 LEU cc_start: 0.9626 (tp) cc_final: 0.9393 (tt) REVERT: B 64 GLU cc_start: 0.8747 (pt0) cc_final: 0.8197 (pt0) REVERT: B 67 ILE cc_start: 0.9606 (mt) cc_final: 0.9292 (mt) REVERT: C 39 ASN cc_start: 0.8153 (m-40) cc_final: 0.7916 (m-40) REVERT: C 96 LYS cc_start: 0.9338 (tttp) cc_final: 0.9013 (tptt) REVERT: D 40 ILE cc_start: 0.9490 (mp) cc_final: 0.9289 (tp) REVERT: D 60 MET cc_start: 0.8861 (tpp) cc_final: 0.8501 (tpp) REVERT: E 74 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8417 (tm-30) REVERT: E 121 MET cc_start: 0.8500 (mmm) cc_final: 0.8121 (mmm) REVERT: F 45 LYS cc_start: 0.9204 (tttt) cc_final: 0.8747 (tptp) REVERT: F 64 GLU cc_start: 0.9103 (mt-10) cc_final: 0.8804 (mt-10) REVERT: F 65 ASN cc_start: 0.8628 (t0) cc_final: 0.8210 (t0) REVERT: F 94 GLN cc_start: 0.8726 (mm-40) cc_final: 0.8376 (mm-40) REVERT: G 62 GLU cc_start: 0.8332 (tp30) cc_final: 0.8028 (tp30) REVERT: G 91 ASP cc_start: 0.9179 (t70) cc_final: 0.8906 (t0) REVERT: G 93 GLU cc_start: 0.8828 (mp0) cc_final: 0.8039 (mt-10) REVERT: H 52 ASP cc_start: 0.8993 (p0) cc_final: 0.8551 (p0) REVERT: H 63 MET cc_start: 0.8915 (mmt) cc_final: 0.8637 (mmp) REVERT: H 83 HIS cc_start: 0.8176 (t70) cc_final: 0.7839 (t70) REVERT: H 94 GLU cc_start: 0.8985 (mp0) cc_final: 0.8647 (mp0) REVERT: H 103 LEU cc_start: 0.9603 (mp) cc_final: 0.9386 (mp) REVERT: H 106 GLU cc_start: 0.8344 (tm-30) cc_final: 0.7504 (tm-30) REVERT: H 107 LEU cc_start: 0.9050 (mt) cc_final: 0.7887 (mt) REVERT: H 114 GLU cc_start: 0.8652 (mm-30) cc_final: 0.7984 (mm-30) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.0962 time to fit residues: 34.8171 Evaluate side-chains 189 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 74 optimal weight: 30.0000 chunk 105 optimal weight: 50.0000 chunk 106 optimal weight: 50.0000 chunk 151 optimal weight: 0.0060 chunk 139 optimal weight: 20.0000 chunk 173 optimal weight: 50.0000 chunk 15 optimal weight: 0.0670 chunk 68 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 100 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 overall best weight: 2.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 25 GLN H 48 GLN H 50 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.113690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.074604 restraints weight = 68881.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.076418 restraints weight = 31617.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.077543 restraints weight = 20482.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.078194 restraints weight = 16229.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.078530 restraints weight = 14442.385| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.125 16699 Z= 0.190 Angle : 0.677 10.545 23978 Z= 0.384 Chirality : 0.043 0.262 2816 Planarity : 0.004 0.045 2173 Dihedral : 28.272 79.064 4750 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % 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 are not related in a simple way. whole: 1.89 (0.21), residues: 1528 helix: 2.00 (0.21), residues: 624 sheet: 0.76 (0.29), residues: 324 loop : 0.88 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 100 TYR 0.024 0.002 TYR H 41 PHE 0.016 0.002 PHE F 101 TRP 0.000 0.000 TRP K 146 HIS 0.008 0.002 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.19 (16699) covalent geometry : angle 0.67685 / 0.38 (23978) hydrogen bonds : bond 0.05415 / 3.76 ( 977) hydrogen bonds : angle 3.82179 / 2.81 ( 2466) *********************** 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 215 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 PHE cc_start: 0.8685 (m-80) cc_final: 0.8431 (m-10) REVERT: B 63 LEU cc_start: 0.9641 (tp) cc_final: 0.9384 (tp) REVERT: B 64 GLU cc_start: 0.8757 (pt0) cc_final: 0.8451 (pt0) REVERT: C 39 ASN cc_start: 0.8104 (m-40) cc_final: 0.7314 (m-40) REVERT: C 96 LYS cc_start: 0.9299 (tttp) cc_final: 0.9018 (tptt) REVERT: D 60 MET cc_start: 0.8840 (tpp) cc_final: 0.8399 (tpp) REVERT: E 74 GLU cc_start: 0.8903 (tm-30) cc_final: 0.8443 (tm-30) REVERT: F 45 LYS cc_start: 0.9185 (tttt) cc_final: 0.8773 (tptp) REVERT: F 64 GLU cc_start: 0.9158 (mt-10) cc_final: 0.8820 (mt-10) REVERT: F 94 GLN cc_start: 0.8653 (mm-40) cc_final: 0.8276 (mm-40) REVERT: G 88 ILE cc_start: 0.9320 (mt) cc_final: 0.9048 (mm) REVERT: G 111 ASN cc_start: 0.8971 (t0) cc_final: 0.8717 (t0) REVERT: H 63 MET cc_start: 0.8955 (mmt) cc_final: 0.8484 (mmm) REVERT: H 69 ASP cc_start: 0.8979 (t70) cc_final: 0.8611 (t70) REVERT: H 83 HIS cc_start: 0.8133 (t70) cc_final: 0.7752 (t70) REVERT: H 94 GLU cc_start: 0.9111 (mp0) cc_final: 0.8724 (mp0) REVERT: H 96 GLN cc_start: 0.9205 (tt0) cc_final: 0.8782 (pt0) REVERT: H 107 LEU cc_start: 0.9033 (mt) cc_final: 0.8363 (mt) REVERT: H 114 GLU cc_start: 0.8692 (mm-30) cc_final: 0.7997 (mm-30) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1138 time to fit residues: 38.1574 Evaluate side-chains 184 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 43 optimal weight: 9.9990 chunk 69 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 126 optimal weight: 40.0000 chunk 100 optimal weight: 0.0000 chunk 71 optimal weight: 3.9990 chunk 83 optimal weight: 40.0000 chunk 175 optimal weight: 0.2980 chunk 116 optimal weight: 30.0000 chunk 48 optimal weight: 0.8980 chunk 170 optimal weight: 8.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 110 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.116032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.076663 restraints weight = 68488.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.078490 restraints weight = 31373.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.079700 restraints weight = 20300.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.080350 restraints weight = 16072.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.080477 restraints weight = 14286.085| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 16699 Z= 0.136 Angle : 0.629 7.343 23978 Z= 0.363 Chirality : 0.043 0.233 2816 Planarity : 0.004 0.041 2173 Dihedral : 28.019 76.536 4750 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % 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 are not related in a simple way. whole: 2.09 (0.21), residues: 1528 helix: 2.21 (0.21), residues: 619 sheet: 0.87 (0.29), residues: 324 loop : 0.95 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 30 TYR 0.024 0.002 TYR B 89 PHE 0.010 0.001 PHE F 101 TRP 0.000 0.000 TRP K 146 HIS 0.005 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.14 (16699) covalent geometry : angle 0.62931 / 0.36 (23978) hydrogen bonds : bond 0.04374 / 3.02 ( 977) hydrogen bonds : angle 3.53121 / 2.60 ( 2466) *********************** 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 227 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 PHE cc_start: 0.8620 (m-80) cc_final: 0.8374 (m-10) REVERT: B 32 LYS cc_start: 0.8778 (ttpp) cc_final: 0.8577 (mttp) REVERT: B 44 VAL cc_start: 0.9070 (t) cc_final: 0.8792 (p) REVERT: B 51 ILE cc_start: 0.9268 (mt) cc_final: 0.9066 (mt) REVERT: B 63 LEU cc_start: 0.9514 (tp) cc_final: 0.9181 (tt) REVERT: B 64 GLU cc_start: 0.8748 (pt0) cc_final: 0.8416 (pt0) REVERT: B 67 ILE cc_start: 0.9629 (mt) cc_final: 0.9288 (mt) REVERT: B 87 VAL cc_start: 0.9093 (t) cc_final: 0.8802 (p) REVERT: C 39 ASN cc_start: 0.7500 (m-40) cc_final: 0.7232 (m-40) REVERT: C 96 LYS cc_start: 0.9332 (tttp) cc_final: 0.8992 (tptt) REVERT: D 60 MET cc_start: 0.8818 (tpp) cc_final: 0.8384 (tpp) REVERT: E 74 GLU cc_start: 0.8865 (tm-30) cc_final: 0.8440 (tm-30) REVERT: F 32 LYS cc_start: 0.9037 (pptt) cc_final: 0.8803 (ptpp) REVERT: F 45 LYS cc_start: 0.9140 (tttt) cc_final: 0.8715 (tptp) REVERT: G 14 LYS cc_start: 0.7339 (ttpt) cc_final: 0.7139 (tptp) REVERT: H 52 ASP cc_start: 0.8980 (p0) cc_final: 0.8494 (p0) REVERT: H 63 MET cc_start: 0.8875 (mmt) cc_final: 0.8436 (mmm) REVERT: H 69 ASP cc_start: 0.8847 (t70) cc_final: 0.8470 (t70) REVERT: H 83 HIS cc_start: 0.8048 (t70) cc_final: 0.7705 (t70) REVERT: H 94 GLU cc_start: 0.8984 (mp0) cc_final: 0.8646 (mp0) REVERT: H 107 LEU cc_start: 0.9001 (mt) cc_final: 0.8629 (mt) REVERT: H 114 GLU cc_start: 0.8672 (mm-30) cc_final: 0.7837 (mm-30) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.1147 time to fit residues: 40.1353 Evaluate side-chains 191 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 57 optimal weight: 2.9990 chunk 96 optimal weight: 20.0000 chunk 16 optimal weight: 0.7980 chunk 122 optimal weight: 30.0000 chunk 156 optimal weight: 50.0000 chunk 43 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 123 optimal weight: 30.0000 chunk 118 optimal weight: 40.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.114606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.074986 restraints weight = 68478.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.076863 restraints weight = 31374.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.078045 restraints weight = 20278.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.078720 restraints weight = 16073.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.079068 restraints weight = 14263.923| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 16699 Z= 0.164 Angle : 0.640 7.453 23978 Z= 0.368 Chirality : 0.042 0.283 2816 Planarity : 0.004 0.042 2173 Dihedral : 27.924 75.022 4750 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % 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 are not related in a simple way. whole: 2.05 (0.22), residues: 1528 helix: 2.16 (0.21), residues: 623 sheet: 0.80 (0.29), residues: 336 loop : 0.97 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 78 TYR 0.020 0.001 TYR H 41 PHE 0.011 0.001 PHE F 62 TRP 0.000 0.000 TRP K 146 HIS 0.006 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.16 (16699) covalent geometry : angle 0.63970 / 0.37 (23978) hydrogen bonds : bond 0.04858 / 3.36 ( 977) hydrogen bonds : angle 3.64027 / 2.69 ( 2466) *********************** 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 216 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8681 (mp0) cc_final: 0.8140 (mp0) REVERT: A 85 PHE cc_start: 0.8616 (m-80) cc_final: 0.8414 (m-10) REVERT: B 32 LYS cc_start: 0.8819 (ttpp) cc_final: 0.8601 (mttp) REVERT: B 44 VAL cc_start: 0.9022 (t) cc_final: 0.8730 (p) REVERT: B 50 LEU cc_start: 0.8771 (mp) cc_final: 0.8381 (mp) REVERT: B 63 LEU cc_start: 0.9559 (tp) cc_final: 0.9227 (tt) REVERT: B 64 GLU cc_start: 0.8768 (pt0) cc_final: 0.8201 (pt0) REVERT: B 67 ILE cc_start: 0.9630 (mt) cc_final: 0.9283 (mt) REVERT: C 96 LYS cc_start: 0.9311 (tttp) cc_final: 0.9011 (tptt) REVERT: D 60 MET cc_start: 0.8881 (tpp) cc_final: 0.8420 (tpp) REVERT: D 85 ASN cc_start: 0.8908 (t0) cc_final: 0.8629 (t0) REVERT: D 94 GLU cc_start: 0.8551 (mm-30) cc_final: 0.7786 (mm-30) REVERT: E 74 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8433 (tm-30) REVERT: F 45 LYS cc_start: 0.9127 (tttt) cc_final: 0.8714 (tptp) REVERT: F 64 GLU cc_start: 0.9005 (mp0) cc_final: 0.8676 (mp0) REVERT: G 88 ILE cc_start: 0.9263 (mt) cc_final: 0.9018 (mm) REVERT: H 63 MET cc_start: 0.8822 (mmt) cc_final: 0.8328 (mmm) REVERT: H 69 ASP cc_start: 0.8881 (t70) cc_final: 0.8509 (t70) REVERT: H 83 HIS cc_start: 0.8093 (t70) cc_final: 0.7707 (t70) REVERT: H 94 GLU cc_start: 0.9063 (mp0) cc_final: 0.8648 (mp0) REVERT: H 96 GLN cc_start: 0.9191 (tt0) cc_final: 0.8775 (pt0) REVERT: H 114 GLU cc_start: 0.8679 (mm-30) cc_final: 0.7933 (mm-30) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.1049 time to fit residues: 35.3523 Evaluate side-chains 185 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 15 optimal weight: 0.6980 chunk 135 optimal weight: 50.0000 chunk 142 optimal weight: 0.0050 chunk 123 optimal weight: 40.0000 chunk 36 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 166 optimal weight: 8.9990 chunk 102 optimal weight: 9.9990 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 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 = 0.4218 r_free = 0.4218 target = 0.115914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.076115 restraints weight = 67705.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.077968 restraints weight = 31083.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.079135 restraints weight = 20199.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.079793 restraints weight = 16081.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.080126 restraints weight = 14358.073| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 16699 Z= 0.137 Angle : 0.609 7.788 23978 Z= 0.354 Chirality : 0.042 0.303 2816 Planarity : 0.004 0.040 2173 Dihedral : 27.777 74.902 4750 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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 are not related in a simple way. whole: 2.09 (0.22), residues: 1528 helix: 2.15 (0.21), residues: 623 sheet: 0.87 (0.29), residues: 336 loop : 1.02 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 78 TYR 0.017 0.001 TYR H 41 PHE 0.008 0.001 PHE E 68 TRP 0.000 0.000 TRP K 146 HIS 0.005 0.001 HIS E 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.14 (16699) covalent geometry : angle 0.60926 / 0.35 (23978) hydrogen bonds : bond 0.04228 / 2.93 ( 977) hydrogen bonds : angle 3.51472 / 2.60 ( 2466) *********************** 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 216 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 PHE cc_start: 0.8703 (m-80) cc_final: 0.8468 (m-10) REVERT: B 32 LYS cc_start: 0.8793 (ttpp) cc_final: 0.8589 (mttp) REVERT: B 44 VAL cc_start: 0.9073 (t) cc_final: 0.8786 (p) REVERT: B 63 LEU cc_start: 0.9519 (tp) cc_final: 0.9155 (tt) REVERT: B 64 GLU cc_start: 0.8765 (pt0) cc_final: 0.8231 (pt0) REVERT: B 67 ILE cc_start: 0.9634 (mt) cc_final: 0.9299 (mt) REVERT: C 96 LYS cc_start: 0.9309 (tttp) cc_final: 0.8979 (tptt) REVERT: D 60 MET cc_start: 0.8845 (tpp) cc_final: 0.8405 (tpp) REVERT: D 85 ASN cc_start: 0.8887 (t0) cc_final: 0.8591 (t0) REVERT: D 94 GLU cc_start: 0.8468 (mm-30) cc_final: 0.7708 (mm-30) REVERT: D 107 LEU cc_start: 0.9185 (mm) cc_final: 0.8332 (mm) REVERT: E 74 GLU cc_start: 0.8935 (tm-30) cc_final: 0.8538 (tm-30) REVERT: E 107 ASP cc_start: 0.8746 (m-30) cc_final: 0.8538 (m-30) REVERT: F 32 LYS cc_start: 0.9054 (pptt) cc_final: 0.8776 (ptpp) REVERT: F 45 LYS cc_start: 0.9125 (tttt) cc_final: 0.8684 (tptp) REVERT: F 64 GLU cc_start: 0.8836 (mp0) cc_final: 0.8502 (mp0) REVERT: H 63 MET cc_start: 0.8842 (mmt) cc_final: 0.8382 (mmm) REVERT: H 69 ASP cc_start: 0.8892 (t70) cc_final: 0.8506 (t70) REVERT: H 83 HIS cc_start: 0.8059 (t70) cc_final: 0.7691 (t70) REVERT: H 94 GLU cc_start: 0.8951 (mp0) cc_final: 0.8579 (mp0) REVERT: H 96 GLN cc_start: 0.9169 (tt0) cc_final: 0.8767 (pt0) REVERT: H 114 GLU cc_start: 0.8634 (mm-30) cc_final: 0.7874 (mm-30) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.1062 time to fit residues: 36.1055 Evaluate side-chains 186 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 45 optimal weight: 0.9980 chunk 94 optimal weight: 20.0000 chunk 104 optimal weight: 50.0000 chunk 95 optimal weight: 20.0000 chunk 166 optimal weight: 5.9990 chunk 175 optimal weight: 0.0670 chunk 102 optimal weight: 30.0000 chunk 157 optimal weight: 20.0000 chunk 30 optimal weight: 0.6980 chunk 82 optimal weight: 20.0000 chunk 150 optimal weight: 30.0000 overall best weight: 5.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 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 = 0.4136 r_free = 0.4136 target = 0.111215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.072065 restraints weight = 70251.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.073825 restraints weight = 32576.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.074954 restraints weight = 21255.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.075625 restraints weight = 17002.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.075734 restraints weight = 15170.803| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.5316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.133 16699 Z= 0.295 Angle : 0.759 9.497 23978 Z= 0.424 Chirality : 0.046 0.326 2816 Planarity : 0.005 0.057 2173 Dihedral : 28.057 77.508 4750 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % 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 are not related in a simple way. whole: 1.67 (0.21), residues: 1528 helix: 1.62 (0.20), residues: 628 sheet: 0.78 (0.29), residues: 336 loop : 0.95 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 78 TYR 0.033 0.003 TYR H 41 PHE 0.022 0.002 PHE D 71 TRP 0.000 0.000 TRP K 146 HIS 0.009 0.002 HIS E 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.29 (16699) covalent geometry : angle 0.75948 / 0.42 (23978) hydrogen bonds : bond 0.07336 / 5.08 ( 977) hydrogen bonds : angle 4.09156 / 3.00 ( 2466) *********************** 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 195 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 PHE cc_start: 0.8706 (m-80) cc_final: 0.8398 (m-10) REVERT: B 63 LEU cc_start: 0.9681 (tp) cc_final: 0.9439 (tp) REVERT: B 64 GLU cc_start: 0.8661 (pt0) cc_final: 0.8199 (pt0) REVERT: C 39 ASN cc_start: 0.7658 (m-40) cc_final: 0.7067 (m-40) REVERT: C 57 GLU cc_start: 0.8701 (pp20) cc_final: 0.8408 (pp20) REVERT: C 96 LYS cc_start: 0.9304 (tttp) cc_final: 0.9025 (tptt) REVERT: D 60 MET cc_start: 0.8878 (tpp) cc_final: 0.8435 (tpp) REVERT: D 85 ASN cc_start: 0.8911 (t0) cc_final: 0.8655 (t0) REVERT: D 94 GLU cc_start: 0.8577 (mm-30) cc_final: 0.7901 (mm-30) REVERT: E 60 GLU cc_start: 0.8481 (pp20) cc_final: 0.7618 (pp20) REVERT: E 74 GLU cc_start: 0.8928 (tm-30) cc_final: 0.8343 (tm-30) REVERT: E 102 VAL cc_start: 0.9204 (p) cc_final: 0.9002 (p) REVERT: E 107 ASP cc_start: 0.8948 (m-30) cc_final: 0.8499 (m-30) REVERT: F 45 LYS cc_start: 0.9072 (tttt) cc_final: 0.8755 (tptp) REVERT: F 64 GLU cc_start: 0.8906 (mp0) cc_final: 0.8411 (mp0) REVERT: G 39 ASN cc_start: 0.7867 (t0) cc_final: 0.7488 (t0) REVERT: H 63 MET cc_start: 0.8775 (mmt) cc_final: 0.8382 (mmm) REVERT: H 69 ASP cc_start: 0.8947 (t70) cc_final: 0.8590 (t70) REVERT: H 83 HIS cc_start: 0.8051 (t70) cc_final: 0.7688 (t70) REVERT: H 96 GLN cc_start: 0.9172 (tt0) cc_final: 0.8838 (pt0) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.1060 time to fit residues: 32.2604 Evaluate side-chains 167 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 131 optimal weight: 4.9990 chunk 139 optimal weight: 0.6980 chunk 78 optimal weight: 20.0000 chunk 90 optimal weight: 20.0000 chunk 92 optimal weight: 9.9990 chunk 179 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 93 optimal weight: 20.0000 chunk 126 optimal weight: 40.0000 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 20.0000 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 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 = 0.4146 r_free = 0.4146 target = 0.111931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.074972 restraints weight = 67658.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.076679 restraints weight = 31135.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.077783 restraints weight = 20043.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.078385 restraints weight = 15854.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.078501 restraints weight = 14088.342| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.5463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 16699 Z= 0.206 Angle : 0.674 7.937 23978 Z= 0.386 Chirality : 0.043 0.354 2816 Planarity : 0.004 0.052 2173 Dihedral : 28.082 76.926 4750 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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 are not related in a simple way. whole: 1.73 (0.21), residues: 1528 helix: 1.73 (0.20), residues: 628 sheet: 0.78 (0.29), residues: 336 loop : 0.92 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 78 TYR 0.034 0.002 TYR H 41 PHE 0.023 0.002 PHE A 68 TRP 0.000 0.000 TRP K 146 HIS 0.007 0.002 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.21 (16699) covalent geometry : angle 0.67390 / 0.39 (23978) hydrogen bonds : bond 0.05232 / 3.65 ( 977) hydrogen bonds : angle 3.89798 / 2.88 ( 2466) ********************** 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 200 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 PHE cc_start: 0.8652 (m-80) cc_final: 0.8406 (m-10) REVERT: B 63 LEU cc_start: 0.9589 (tp) cc_final: 0.9261 (tt) REVERT: B 64 GLU cc_start: 0.8668 (pt0) cc_final: 0.8384 (pt0) REVERT: B 67 ILE cc_start: 0.9688 (mt) cc_final: 0.9382 (mt) REVERT: C 57 GLU cc_start: 0.8640 (pp20) cc_final: 0.8423 (pp20) REVERT: C 96 LYS cc_start: 0.9351 (tttp) cc_final: 0.9069 (tptt) REVERT: D 60 MET cc_start: 0.8873 (tpp) cc_final: 0.8365 (tpp) REVERT: D 85 ASN cc_start: 0.8933 (t0) cc_final: 0.8629 (t0) REVERT: D 94 GLU cc_start: 0.8573 (mm-30) cc_final: 0.7923 (mm-30) REVERT: E 74 GLU cc_start: 0.8912 (tm-30) cc_final: 0.8426 (tm-30) REVERT: E 106 GLU cc_start: 0.8808 (pt0) cc_final: 0.8514 (pt0) REVERT: E 107 ASP cc_start: 0.8881 (m-30) cc_final: 0.8656 (m-30) REVERT: F 45 LYS cc_start: 0.8997 (tttt) cc_final: 0.8709 (tptp) REVERT: G 39 ASN cc_start: 0.7903 (t0) cc_final: 0.7419 (t0) REVERT: H 63 MET cc_start: 0.8867 (mmt) cc_final: 0.8501 (mmm) REVERT: H 69 ASP cc_start: 0.8938 (t70) cc_final: 0.8529 (t70) REVERT: H 83 HIS cc_start: 0.8047 (t70) cc_final: 0.7728 (t70) REVERT: H 94 GLU cc_start: 0.9048 (mp0) cc_final: 0.8698 (mp0) REVERT: H 96 GLN cc_start: 0.9176 (tt0) cc_final: 0.8774 (pt0) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.1073 time to fit residues: 33.5835 Evaluate side-chains 167 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 164 optimal weight: 30.0000 chunk 62 optimal weight: 2.9990 chunk 84 optimal weight: 50.0000 chunk 65 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 159 optimal weight: 30.0000 chunk 82 optimal weight: 30.0000 chunk 146 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 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 = 0.4191 r_free = 0.4191 target = 0.114150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.074688 restraints weight = 69373.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.076501 restraints weight = 31885.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.077656 restraints weight = 20632.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.078356 restraints weight = 16486.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.078629 restraints weight = 14681.665| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.5555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16699 Z= 0.149 Angle : 0.639 10.460 23978 Z= 0.369 Chirality : 0.043 0.369 2816 Planarity : 0.004 0.045 2173 Dihedral : 27.932 75.185 4750 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 are not related in a simple way. whole: 1.89 (0.22), residues: 1528 helix: 1.92 (0.21), residues: 625 sheet: 0.82 (0.29), residues: 336 loop : 0.95 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 100 TYR 0.031 0.002 TYR H 41 PHE 0.025 0.001 PHE A 68 TRP 0.000 0.000 TRP K 146 HIS 0.005 0.001 HIS E 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.15 (16699) covalent geometry : angle 0.63872 / 0.37 (23978) hydrogen bonds : bond 0.04515 / 3.14 ( 977) hydrogen bonds : angle 3.72583 / 2.75 ( 2466) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3031.31 seconds wall clock time: 52 minutes 34.40 seconds (3154.40 seconds total)