Starting phenix.real_space_refine on Sat Sep 12 11:52:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r04_53478/09_2026/9r04_53478.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r04_53478/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9r04_53478/09_2026/9r04_53478.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r04_53478/09_2026/9r04_53478.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9r04_53478/09_2026/9r04_53478.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r04_53478/09_2026/9r04_53478.map" } 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-2.2.1-6174/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: 3.69, 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: 1.35 Conformation dependent library (CDL) restraints added in 607.7 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: 2.30 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: 3.18 Time building geometry restraints manager: 1.84 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: 21421 1.85 - 3.70: 2039 3.70 - 5.56: 385 5.56 - 7.41: 98 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=" C3' DA I 120 " pdb=" O3' DA I 120 " pdb=" P DG I 121 " ideal model delta sigma weight residual 119.70 126.29 -6.59 1.20e+00 6.94e-01 3.02e+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 ... (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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 17.740 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.700 ------------------------------------------------------------------------------- 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= 0.824 Angle : 1.235 9.261 23978 Z= 0.846 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 1.23490 / 0.85 (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 : 0.468 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: symmetry clash REVERT: A 61 LEU cc_start: 0.8893 (mt) cc_final: 0.7603 (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: 0.7956 (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: 0.9047 (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: 0.8575 (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: 0.7249 (p) REVERT: E 121 MET cc_start: 0.8069 (mmm) cc_final: 0.7735 (mmm) REVERT: F 45 LYS cc_start: 0.9200 (tttt) cc_final: 0.8565 (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: 0.8754 (mm110) REVERT: F 101 PHE cc_start: 0.8363 (m-80) cc_final: 0.8126 (m-80) REVERT: G 26 PHE cc_start: 0.8826 (m-80) cc_final: 0.8167 (m-80) REVERT: G 51 TYR cc_start: 0.9132 (t80) cc_final: 0.8907 (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: 0.8171 (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: 0.8684 (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: 0.8519 (mt) outliers start: 4 outliers final: 2 residues processed: 305 average time/residue: 0.1433 time to fit residues: 62.5494 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 : 0.464 ------------------------------------------------------------------------------- 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: 20.0000 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 30.0000 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 50.0000 overall best weight: 6.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 76 HIS D 85 ASN E 69 GLN E 86 GLN ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 25 GLN G 32 HIS G 39 ASN H 96 GLN H 110 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.112977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.075395 restraints weight = 67546.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.077146 restraints weight = 31313.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.078216 restraints weight = 20263.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.078885 restraints weight = 16046.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.079228 restraints weight = 14214.908| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.198 16699 Z= 0.345 Angle : 0.953 11.355 23978 Z= 0.502 Chirality : 0.054 0.269 2816 Planarity : 0.007 0.065 2173 Dihedral : 29.732 89.379 4750 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 0.15 % Allowed : 3.06 % Favored : 96.79 % 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: 0.89 (0.21), residues: 1528 helix: 0.55 (0.20), residues: 615 sheet: 0.84 (0.30), residues: 320 loop : 0.75 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG G 21 TYR 0.025 0.003 TYR D 41 PHE 0.015 0.003 PHE C 26 TRP 0.000 0.000 TRP K 146 HIS 0.013 0.003 HIS E 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00702 / 0.34 (16699) covalent geometry : angle 0.95335 / 0.50 (23978) hydrogen bonds : bond 0.09085 / 6.25 ( 977) hydrogen bonds : angle 4.81126 / 3.57 ( 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 220 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 219 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8646 (mt) cc_final: 0.8417 (mt) REVERT: A 94 GLN cc_start: 0.8817 (tm-30) cc_final: 0.7742 (tm-30) REVERT: A 107 ASP cc_start: 0.8278 (m-30) cc_final: 0.8063 (m-30) REVERT: B 45 LYS cc_start: 0.9376 (tttt) cc_final: 0.8891 (ttmt) REVERT: B 67 ILE cc_start: 0.9610 (mt) cc_final: 0.9409 (mt) REVERT: C 39 ASN cc_start: 0.6891 (m-40) cc_final: 0.6327 (t0) REVERT: C 57 GLU cc_start: 0.8825 (pp20) cc_final: 0.8480 (pp20) REVERT: C 100 ARG cc_start: 0.8237 (mmt-90) cc_final: 0.7890 (mmm-85) REVERT: D 60 MET cc_start: 0.8806 (tpp) cc_final: 0.8263 (tpp) REVERT: D 94 GLU cc_start: 0.9036 (mp0) cc_final: 0.8758 (mp0) REVERT: E 74 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8345 (tm-30) REVERT: E 121 MET cc_start: 0.8516 (mmm) cc_final: 0.7970 (mmm) REVERT: F 45 LYS cc_start: 0.9223 (tttt) cc_final: 0.8855 (pttm) REVERT: F 55 THR cc_start: 0.9589 (m) cc_final: 0.9378 (p) REVERT: F 64 GLU cc_start: 0.9188 (mt-10) cc_final: 0.8939 (mt-10) REVERT: F 65 ASN cc_start: 0.8681 (t0) cc_final: 0.8223 (t0) REVERT: F 94 GLN cc_start: 0.8887 (mm-40) cc_final: 0.8559 (mm-40) REVERT: G 91 ASP cc_start: 0.8971 (t70) cc_final: 0.8545 (t0) REVERT: G 93 GLU cc_start: 0.9080 (mp0) cc_final: 0.8210 (mt-10) REVERT: H 52 ASP cc_start: 0.9070 (p0) cc_final: 0.8676 (p0) REVERT: H 63 MET cc_start: 0.8752 (mmt) cc_final: 0.8135 (mmm) REVERT: H 83 HIS cc_start: 0.8082 (t70) cc_final: 0.7737 (t70) REVERT: H 90 ILE cc_start: 0.9427 (mm) cc_final: 0.9143 (mm) REVERT: H 94 GLU cc_start: 0.9018 (mp0) cc_final: 0.8564 (mp0) REVERT: H 107 LEU cc_start: 0.8958 (mt) cc_final: 0.8445 (mt) REVERT: H 114 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8515 (mm-30) outliers start: 1 outliers final: 0 residues processed: 219 average time/residue: 0.1173 time to fit residues: 39.3493 Evaluate side-chains 177 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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: 0.4980 chunk 158 optimal weight: 10.0000 chunk 168 optimal weight: 4.9990 chunk 125 optimal weight: 0.4980 chunk 106 optimal weight: 8.9990 chunk 47 optimal weight: 0.8980 chunk 143 optimal weight: 40.0000 chunk 140 optimal weight: 0.0770 chunk 25 optimal weight: 0.0040 chunk 175 optimal weight: 2.9990 overall best weight: 0.3950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 85 ASN E 94 GLN G 25 GLN H 48 GLN H 96 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.117949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.078902 restraints weight = 68898.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.080850 restraints weight = 30896.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.082058 restraints weight = 19728.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.082790 restraints weight = 15494.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.083146 restraints weight = 13683.501| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 16699 Z= 0.142 Angle : 0.673 7.081 23978 Z= 0.375 Chirality : 0.045 0.361 2816 Planarity : 0.005 0.052 2173 Dihedral : 28.390 83.578 4750 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % 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: 1.90 (0.21), residues: 619 sheet: 0.95 (0.29), residues: 324 loop : 0.91 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 36 TYR 0.031 0.002 TYR G 51 PHE 0.013 0.001 PHE F 101 TRP 0.000 0.000 TRP K 146 HIS 0.018 0.002 HIS G 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.14 (16699) covalent geometry : angle 0.67343 / 0.37 (23978) hydrogen bonds : bond 0.05022 / 3.49 ( 977) hydrogen bonds : angle 3.75978 / 2.79 ( 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 240 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.459 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: symmetry clash REVERT: A 51 GLU cc_start: 0.8585 (mp0) cc_final: 0.8127 (mp0) REVERT: A 85 PHE cc_start: 0.8770 (m-80) cc_final: 0.8552 (m-10) REVERT: A 121 MET cc_start: 0.7465 (mtm) cc_final: 0.7004 (mtt) REVERT: B 45 LYS cc_start: 0.9235 (tttt) cc_final: 0.8779 (ttmt) REVERT: B 54 GLU cc_start: 0.8902 (tp30) cc_final: 0.8688 (tp30) REVERT: B 63 LEU cc_start: 0.9516 (tp) cc_final: 0.9220 (tt) REVERT: B 67 ILE cc_start: 0.9610 (mt) cc_final: 0.9079 (mt) REVERT: B 87 VAL cc_start: 0.9136 (t) cc_final: 0.8882 (p) REVERT: C 39 ASN cc_start: 0.6711 (m-40) cc_final: 0.6170 (t0) REVERT: C 79 ILE cc_start: 0.8980 (mm) cc_final: 0.8748 (mm) REVERT: C 85 GLN cc_start: 0.8766 (tp40) cc_final: 0.8505 (tm-30) REVERT: C 96 LYS cc_start: 0.9384 (tttp) cc_final: 0.8789 (ttpt) REVERT: D 60 MET cc_start: 0.8895 (tpp) cc_final: 0.8407 (tpp) REVERT: E 55 TYR cc_start: 0.8133 (m-80) cc_final: 0.7658 (m-80) REVERT: E 74 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8341 (tm-30) REVERT: F 45 LYS cc_start: 0.9227 (tttt) cc_final: 0.8841 (tptp) REVERT: F 65 ASN cc_start: 0.8625 (t0) cc_final: 0.8079 (t0) REVERT: F 86 ASP cc_start: 0.8688 (m-30) cc_final: 0.8415 (m-30) REVERT: F 89 TYR cc_start: 0.8654 (m-10) cc_final: 0.8154 (m-10) REVERT: F 94 GLN cc_start: 0.8674 (mm-40) cc_final: 0.8240 (mm-40) REVERT: G 26 PHE cc_start: 0.8826 (m-80) cc_final: 0.8505 (m-80) REVERT: G 91 ASP cc_start: 0.9181 (t70) cc_final: 0.8868 (t0) REVERT: G 93 GLU cc_start: 0.8818 (mp0) cc_final: 0.8048 (mt-10) REVERT: H 43 TYR cc_start: 0.8194 (p90) cc_final: 0.7880 (p90) REVERT: H 52 ASP cc_start: 0.8955 (p0) cc_final: 0.8481 (p0) REVERT: H 63 MET cc_start: 0.8882 (mmt) cc_final: 0.8210 (mmm) REVERT: H 83 HIS cc_start: 0.8100 (t70) cc_final: 0.7741 (t70) REVERT: H 94 GLU cc_start: 0.8966 (mp0) cc_final: 0.8702 (mp0) REVERT: H 103 LEU cc_start: 0.9588 (mp) cc_final: 0.9379 (mp) REVERT: H 107 LEU cc_start: 0.9051 (mt) cc_final: 0.8587 (mt) REVERT: H 114 GLU cc_start: 0.8416 (mm-30) cc_final: 0.7868 (mm-30) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.1135 time to fit residues: 42.0737 Evaluate side-chains 198 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.463 ------------------------------------------------------------------------------- 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: 0.6980 chunk 65 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 105 optimal weight: 30.0000 chunk 36 optimal weight: 20.0000 chunk 112 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 110 optimal weight: 50.0000 chunk 41 optimal weight: 1.9990 chunk 88 optimal weight: 50.0000 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 39 ASN H 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.115963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.076849 restraints weight = 68478.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.078738 restraints weight = 31347.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.079927 restraints weight = 20252.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.080620 restraints weight = 16095.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.080982 restraints weight = 14247.325| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.135 16699 Z= 0.171 Angle : 0.682 7.197 23978 Z= 0.377 Chirality : 0.043 0.220 2816 Planarity : 0.004 0.040 2173 Dihedral : 28.126 88.074 4750 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 0.15 % Allowed : 2.77 % Favored : 97.08 % 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: 2.00 (0.21), residues: 1528 helix: 2.03 (0.21), residues: 619 sheet: 0.96 (0.30), residues: 324 loop : 0.95 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 72 TYR 0.023 0.002 TYR D 41 PHE 0.012 0.001 PHE A 68 TRP 0.000 0.000 TRP K 146 HIS 0.006 0.002 HIS E 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.17 (16699) covalent geometry : angle 0.68170 / 0.38 (23978) hydrogen bonds : bond 0.05490 / 3.78 ( 977) hydrogen bonds : angle 3.72959 / 2.76 ( 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 225 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 224 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8696 (mp0) cc_final: 0.8357 (mp0) REVERT: A 85 PHE cc_start: 0.8764 (m-80) cc_final: 0.8489 (m-10) REVERT: A 94 GLN cc_start: 0.7771 (tm-30) cc_final: 0.7468 (tm-30) REVERT: B 45 LYS cc_start: 0.9347 (tttt) cc_final: 0.8911 (ttmt) REVERT: B 51 ILE cc_start: 0.9255 (mt) cc_final: 0.9049 (mt) REVERT: B 61 VAL cc_start: 0.9559 (t) cc_final: 0.9111 (t) REVERT: B 63 LEU cc_start: 0.9588 (tp) cc_final: 0.9368 (tt) REVERT: B 67 ILE cc_start: 0.9621 (mt) cc_final: 0.9339 (mt) REVERT: C 39 ASN cc_start: 0.7058 (m-40) cc_final: 0.6315 (t0) REVERT: C 79 ILE cc_start: 0.8997 (mm) cc_final: 0.8739 (mm) REVERT: C 91 ASP cc_start: 0.8838 (t0) cc_final: 0.8438 (t0) REVERT: C 92 GLU cc_start: 0.8979 (tm-30) cc_final: 0.8770 (tm-30) REVERT: C 96 LYS cc_start: 0.9325 (tttp) cc_final: 0.8806 (ttpt) REVERT: D 40 ILE cc_start: 0.9466 (pt) cc_final: 0.9222 (pt) REVERT: D 60 MET cc_start: 0.8848 (tpp) cc_final: 0.8461 (tpp) REVERT: E 74 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8446 (tm-30) REVERT: F 45 LYS cc_start: 0.9182 (tttt) cc_final: 0.8851 (tmtt) REVERT: F 65 ASN cc_start: 0.8202 (t0) cc_final: 0.7973 (t0) REVERT: F 75 GLU cc_start: 0.9022 (tm-30) cc_final: 0.8816 (tm-30) REVERT: F 86 ASP cc_start: 0.8653 (m-30) cc_final: 0.8384 (m-30) REVERT: F 94 GLN cc_start: 0.8588 (mm-40) cc_final: 0.8312 (mm-40) REVERT: G 26 PHE cc_start: 0.8900 (m-80) cc_final: 0.8475 (m-80) REVERT: G 91 ASP cc_start: 0.9277 (t70) cc_final: 0.8967 (t0) REVERT: G 93 GLU cc_start: 0.8822 (mp0) cc_final: 0.8144 (mt-10) REVERT: G 111 ASN cc_start: 0.8939 (t0) cc_final: 0.8679 (t0) REVERT: H 52 ASP cc_start: 0.8973 (p0) cc_final: 0.8500 (p0) REVERT: H 63 MET cc_start: 0.8821 (mmt) cc_final: 0.8167 (mmm) REVERT: H 83 HIS cc_start: 0.8091 (t70) cc_final: 0.7742 (t70) REVERT: H 90 ILE cc_start: 0.9615 (mt) cc_final: 0.9249 (mt) REVERT: H 94 GLU cc_start: 0.8989 (mp0) cc_final: 0.8626 (mp0) REVERT: H 107 LEU cc_start: 0.8980 (mt) cc_final: 0.8578 (mt) REVERT: H 114 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8057 (mm-30) outliers start: 1 outliers final: 0 residues processed: 225 average time/residue: 0.1035 time to fit residues: 36.8857 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 : 0.466 ------------------------------------------------------------------------------- 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: 20.0000 chunk 106 optimal weight: 8.9990 chunk 151 optimal weight: 0.5980 chunk 139 optimal weight: 9.9990 chunk 173 optimal weight: 40.0000 chunk 15 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 100 optimal weight: 0.0370 chunk 25 optimal weight: 7.9990 overall best weight: 3.5264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 HIS G 25 GLN H 48 GLN H 50 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.114541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.075436 restraints weight = 68577.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.077258 restraints weight = 31480.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.078412 restraints weight = 20594.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.079054 restraints weight = 16352.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.079340 restraints weight = 14557.906| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 16699 Z= 0.206 Angle : 0.672 6.097 23978 Z= 0.380 Chirality : 0.043 0.232 2816 Planarity : 0.004 0.043 2173 Dihedral : 28.013 82.489 4750 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.98 (0.21), residues: 1528 helix: 2.01 (0.20), residues: 623 sheet: 0.91 (0.29), residues: 324 loop : 0.96 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 129 TYR 0.019 0.002 TYR G 51 PHE 0.026 0.002 PHE E 105 TRP 0.000 0.000 TRP K 146 HIS 0.008 0.002 HIS G 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.21 (16699) covalent geometry : angle 0.67225 / 0.38 (23978) hydrogen bonds : bond 0.05270 / 3.67 ( 977) hydrogen bonds : angle 3.75203 / 2.77 ( 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 206 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8757 (mp0) cc_final: 0.8487 (mt-10) REVERT: A 85 PHE cc_start: 0.8734 (m-80) cc_final: 0.8467 (m-10) REVERT: A 94 GLN cc_start: 0.7781 (tm-30) cc_final: 0.7412 (tm-30) REVERT: A 121 MET cc_start: 0.7953 (mtm) cc_final: 0.7666 (mtm) REVERT: B 45 LYS cc_start: 0.9348 (tttt) cc_final: 0.8922 (ttmt) REVERT: B 63 LEU cc_start: 0.9619 (tp) cc_final: 0.9378 (tt) REVERT: B 64 GLU cc_start: 0.8803 (pt0) cc_final: 0.8459 (pt0) REVERT: B 67 ILE cc_start: 0.9631 (mt) cc_final: 0.9311 (mt) REVERT: C 79 ILE cc_start: 0.8957 (mm) cc_final: 0.8677 (mm) REVERT: C 92 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8678 (tm-30) REVERT: C 96 LYS cc_start: 0.9307 (tttp) cc_final: 0.9038 (tptt) REVERT: D 60 MET cc_start: 0.8831 (tpp) cc_final: 0.8360 (tpp) REVERT: D 85 ASN cc_start: 0.8937 (t0) cc_final: 0.8620 (t0) REVERT: E 74 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8458 (tm-30) REVERT: E 121 MET cc_start: 0.8676 (mmm) cc_final: 0.8352 (mmm) REVERT: F 45 LYS cc_start: 0.9164 (tttt) cc_final: 0.8728 (tptp) REVERT: F 65 ASN cc_start: 0.8322 (t0) cc_final: 0.8111 (t0) REVERT: F 75 GLU cc_start: 0.9083 (tm-30) cc_final: 0.8810 (tm-30) REVERT: F 86 ASP cc_start: 0.8514 (m-30) cc_final: 0.8275 (m-30) REVERT: F 94 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8303 (mm-40) REVERT: G 62 GLU cc_start: 0.8327 (tp30) cc_final: 0.8108 (tp30) REVERT: G 111 ASN cc_start: 0.8964 (t0) cc_final: 0.8738 (t0) REVERT: H 52 ASP cc_start: 0.9006 (p0) cc_final: 0.8574 (p0) REVERT: H 63 MET cc_start: 0.8787 (mmt) cc_final: 0.8372 (mmm) REVERT: H 83 HIS cc_start: 0.8151 (t70) cc_final: 0.7769 (t70) REVERT: H 90 ILE cc_start: 0.9627 (mt) cc_final: 0.9246 (mt) REVERT: H 94 GLU cc_start: 0.9028 (mp0) cc_final: 0.8696 (mp0) REVERT: H 103 LEU cc_start: 0.9614 (mp) cc_final: 0.9411 (mp) REVERT: H 106 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7455 (tm-30) REVERT: H 107 LEU cc_start: 0.8950 (mt) cc_final: 0.7792 (mt) REVERT: H 114 GLU cc_start: 0.8614 (mm-30) cc_final: 0.7972 (mm-30) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.1120 time to fit residues: 35.9703 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 : 0.478 ------------------------------------------------------------------------------- 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: 7.9990 chunk 69 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 126 optimal weight: 50.0000 chunk 100 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 83 optimal weight: 40.0000 chunk 175 optimal weight: 20.0000 chunk 116 optimal weight: 40.0000 chunk 48 optimal weight: 0.7980 chunk 170 optimal weight: 50.0000 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 48 GLN G 25 GLN ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 GLN H 50 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.115438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.075971 restraints weight = 67087.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.077834 restraints weight = 30797.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.079018 restraints weight = 19972.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.079676 restraints weight = 15890.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.080040 restraints weight = 14167.192| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 16699 Z= 0.155 Angle : 0.628 7.154 23978 Z= 0.357 Chirality : 0.042 0.267 2816 Planarity : 0.004 0.041 2173 Dihedral : 27.904 81.722 4750 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: 2.16 (0.21), residues: 1528 helix: 2.21 (0.20), residues: 624 sheet: 0.93 (0.29), residues: 324 loop : 1.03 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 100 TYR 0.012 0.001 TYR D 41 PHE 0.014 0.001 PHE E 105 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 0.00299 / 0.15 (16699) covalent geometry : angle 0.62760 / 0.36 (23978) hydrogen bonds : bond 0.04743 / 3.30 ( 977) hydrogen bonds : angle 3.58237 / 2.64 ( 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 209 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8633 (mp0) cc_final: 0.7970 (mp0) REVERT: A 85 PHE cc_start: 0.8709 (m-80) cc_final: 0.8442 (m-10) REVERT: B 50 LEU cc_start: 0.8701 (mp) cc_final: 0.8202 (mp) REVERT: B 64 GLU cc_start: 0.8773 (pt0) cc_final: 0.8405 (pt0) REVERT: C 39 ASN cc_start: 0.7967 (m-40) cc_final: 0.7763 (m-40) REVERT: C 79 ILE cc_start: 0.8941 (mm) cc_final: 0.8698 (mm) REVERT: C 96 LYS cc_start: 0.9305 (tttp) cc_final: 0.9027 (tptt) REVERT: D 60 MET cc_start: 0.8885 (tpp) cc_final: 0.8471 (tpp) REVERT: D 85 ASN cc_start: 0.8941 (t0) cc_final: 0.8640 (t0) REVERT: E 74 GLU cc_start: 0.8958 (tm-30) cc_final: 0.8473 (tm-30) REVERT: E 121 MET cc_start: 0.8647 (mmm) cc_final: 0.8406 (mmm) REVERT: F 45 LYS cc_start: 0.9136 (tttt) cc_final: 0.8671 (tptp) REVERT: F 86 ASP cc_start: 0.8535 (m-30) cc_final: 0.8269 (m-30) REVERT: H 52 ASP cc_start: 0.8980 (p0) cc_final: 0.8551 (p0) REVERT: H 63 MET cc_start: 0.8831 (mmt) cc_final: 0.8422 (mmm) REVERT: H 83 HIS cc_start: 0.8100 (t70) cc_final: 0.7716 (t70) REVERT: H 90 ILE cc_start: 0.9566 (mt) cc_final: 0.9186 (mt) REVERT: H 94 GLU cc_start: 0.8974 (mp0) cc_final: 0.8644 (mp0) REVERT: H 103 LEU cc_start: 0.9572 (mp) cc_final: 0.9347 (mp) REVERT: H 114 GLU cc_start: 0.8520 (mm-30) cc_final: 0.7835 (mm-30) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.1021 time to fit residues: 34.2904 Evaluate side-chains 179 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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: 0.6980 chunk 52 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 96 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 156 optimal weight: 50.0000 chunk 43 optimal weight: 9.9990 chunk 49 optimal weight: 0.7980 chunk 123 optimal weight: 0.9980 chunk 118 optimal weight: 50.0000 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4204 r_free = 0.4204 target = 0.114969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.075495 restraints weight = 68950.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.077369 restraints weight = 31303.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.078602 restraints weight = 20308.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.079246 restraints weight = 16029.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.079609 restraints weight = 14269.855| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.128 16699 Z= 0.174 Angle : 0.648 7.712 23978 Z= 0.371 Chirality : 0.042 0.281 2816 Planarity : 0.004 0.042 2173 Dihedral : 27.804 76.609 4750 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.11 (0.21), residues: 1528 helix: 2.15 (0.21), residues: 617 sheet: 0.95 (0.29), residues: 320 loop : 1.02 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 87 TYR 0.013 0.001 TYR G 51 PHE 0.012 0.001 PHE E 105 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 0.00349 / 0.17 (16699) covalent geometry : angle 0.64818 / 0.37 (23978) hydrogen bonds : bond 0.04941 / 3.42 ( 977) hydrogen bonds : angle 3.59427 / 2.64 ( 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 205 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 PHE cc_start: 0.8697 (m-80) cc_final: 0.8420 (m-10) REVERT: B 64 GLU cc_start: 0.8782 (pt0) cc_final: 0.8396 (pt0) REVERT: B 85 MET cc_start: 0.8743 (mmm) cc_final: 0.8459 (mmt) REVERT: C 39 ASN cc_start: 0.8221 (m-40) cc_final: 0.6926 (m-40) REVERT: C 79 ILE cc_start: 0.8854 (mm) cc_final: 0.8620 (mm) REVERT: C 96 LYS cc_start: 0.9330 (tttp) cc_final: 0.8805 (tmmt) REVERT: D 60 MET cc_start: 0.8847 (tpp) cc_final: 0.8376 (tpp) REVERT: D 85 ASN cc_start: 0.9000 (t0) cc_final: 0.8717 (t0) REVERT: E 74 GLU cc_start: 0.8936 (tm-30) cc_final: 0.8503 (tm-30) REVERT: E 107 ASP cc_start: 0.8879 (m-30) cc_final: 0.8675 (m-30) REVERT: E 121 MET cc_start: 0.8695 (mmm) cc_final: 0.8434 (mmm) REVERT: F 45 LYS cc_start: 0.9120 (tttt) cc_final: 0.8671 (tptp) REVERT: G 111 ASN cc_start: 0.8927 (t0) cc_final: 0.8717 (t0) REVERT: H 63 MET cc_start: 0.8799 (mmt) cc_final: 0.8376 (mmm) REVERT: H 83 HIS cc_start: 0.7996 (t70) cc_final: 0.7649 (t70) REVERT: H 90 ILE cc_start: 0.9490 (mt) cc_final: 0.9147 (mt) REVERT: H 94 GLU cc_start: 0.8966 (mp0) cc_final: 0.8665 (mp0) REVERT: H 103 LEU cc_start: 0.9511 (mp) cc_final: 0.9284 (mp) REVERT: H 114 GLU cc_start: 0.8574 (mm-30) cc_final: 0.7781 (mm-30) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.1075 time to fit residues: 34.9018 Evaluate side-chains 177 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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: 0.9990 chunk 135 optimal weight: 30.0000 chunk 142 optimal weight: 10.0000 chunk 123 optimal weight: 40.0000 chunk 36 optimal weight: 20.0000 chunk 27 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 166 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.115979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.076951 restraints weight = 68517.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.078848 restraints weight = 31310.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.080026 restraints weight = 20094.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.080711 restraints weight = 15944.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.081078 restraints weight = 14187.617| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 16699 Z= 0.138 Angle : 0.600 6.987 23978 Z= 0.348 Chirality : 0.041 0.270 2816 Planarity : 0.004 0.040 2173 Dihedral : 27.663 76.023 4750 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % 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: 2.27 (0.22), residues: 1528 helix: 2.34 (0.21), residues: 615 sheet: 0.96 (0.29), residues: 336 loop : 1.10 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 100 TYR 0.012 0.001 TYR A 42 PHE 0.009 0.001 PHE E 105 TRP 0.000 0.000 TRP K 146 HIS 0.008 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.14 (16699) covalent geometry : angle 0.60004 / 0.35 (23978) hydrogen bonds : bond 0.04289 / 2.96 ( 977) hydrogen bonds : angle 3.45702 / 2.55 ( 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 214 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 PHE cc_start: 0.8724 (m-80) cc_final: 0.8456 (m-10) REVERT: B 44 VAL cc_start: 0.9089 (t) cc_final: 0.8802 (p) REVERT: B 64 GLU cc_start: 0.8769 (pt0) cc_final: 0.8369 (pt0) REVERT: B 85 MET cc_start: 0.8698 (mmm) cc_final: 0.8362 (mmt) REVERT: C 79 ILE cc_start: 0.8850 (mm) cc_final: 0.8602 (mm) REVERT: C 96 LYS cc_start: 0.9318 (tttp) cc_final: 0.8788 (ttpt) REVERT: D 60 MET cc_start: 0.8894 (tpp) cc_final: 0.8526 (tpp) REVERT: D 85 ASN cc_start: 0.9006 (t0) cc_final: 0.8717 (t0) REVERT: E 74 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8531 (tm-30) REVERT: E 121 MET cc_start: 0.8629 (mmm) cc_final: 0.8389 (mmm) REVERT: F 45 LYS cc_start: 0.9134 (tttt) cc_final: 0.8696 (tptp) REVERT: G 42 GLU cc_start: 0.8520 (tp30) cc_final: 0.8308 (tp30) REVERT: G 88 ILE cc_start: 0.9268 (mt) cc_final: 0.9028 (mm) REVERT: H 63 MET cc_start: 0.8771 (mmt) cc_final: 0.8350 (mmm) REVERT: H 83 HIS cc_start: 0.7967 (t70) cc_final: 0.7589 (t70) REVERT: H 90 ILE cc_start: 0.9348 (mt) cc_final: 0.9008 (mt) REVERT: H 94 GLU cc_start: 0.8843 (mp0) cc_final: 0.8530 (mp0) REVERT: H 103 LEU cc_start: 0.9518 (mp) cc_final: 0.9288 (mp) REVERT: H 114 GLU cc_start: 0.8542 (mm-30) cc_final: 0.7700 (mm-30) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.1017 time to fit residues: 34.9939 Evaluate side-chains 180 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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: 0.8980 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: 0.6980 chunk 102 optimal weight: 3.9990 chunk 157 optimal weight: 50.0000 chunk 30 optimal weight: 1.9990 chunk 82 optimal weight: 30.0000 chunk 150 optimal weight: 50.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 110 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.114539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.075649 restraints weight = 68592.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.077479 restraints weight = 31522.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.078673 restraints weight = 20411.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.079345 restraints weight = 16190.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.079617 restraints weight = 14418.325| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.4924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 16699 Z= 0.179 Angle : 0.641 10.723 23978 Z= 0.366 Chirality : 0.042 0.309 2816 Planarity : 0.004 0.041 2173 Dihedral : 27.654 73.289 4750 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % 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: 2.12 (0.22), residues: 1528 helix: 2.09 (0.20), residues: 627 sheet: 0.92 (0.29), residues: 332 loop : 1.12 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 100 TYR 0.012 0.002 TYR H 41 PHE 0.012 0.001 PHE D 71 TRP 0.000 0.000 TRP K 146 HIS 0.008 0.002 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.18 (16699) covalent geometry : angle 0.64114 / 0.37 (23978) hydrogen bonds : bond 0.05041 / 3.50 ( 977) hydrogen bonds : angle 3.60755 / 2.65 ( 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 198 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.568 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: 0.8693 (m-80) cc_final: 0.8442 (m-10) REVERT: B 63 LEU cc_start: 0.9573 (tp) cc_final: 0.9269 (tt) REVERT: B 64 GLU cc_start: 0.8803 (pt0) cc_final: 0.8382 (pt0) REVERT: B 67 ILE cc_start: 0.9616 (mt) cc_final: 0.9307 (mt) REVERT: C 79 ILE cc_start: 0.8873 (mm) cc_final: 0.8631 (mm) REVERT: C 96 LYS cc_start: 0.9351 (tttp) cc_final: 0.9055 (tptt) REVERT: D 60 MET cc_start: 0.8824 (tpp) cc_final: 0.8505 (tpp) REVERT: D 85 ASN cc_start: 0.9125 (t0) cc_final: 0.8829 (t0) REVERT: E 74 GLU cc_start: 0.8934 (tm-30) cc_final: 0.8457 (tm-30) REVERT: E 121 MET cc_start: 0.8667 (mmm) cc_final: 0.8386 (mmm) REVERT: F 45 LYS cc_start: 0.9152 (tttt) cc_final: 0.8704 (tptp) REVERT: G 42 GLU cc_start: 0.8657 (tp30) cc_final: 0.8375 (tp30) REVERT: G 88 ILE cc_start: 0.9266 (mt) cc_final: 0.9030 (mm) REVERT: H 63 MET cc_start: 0.8808 (mmt) cc_final: 0.8357 (mmm) REVERT: H 83 HIS cc_start: 0.7992 (t70) cc_final: 0.7641 (t70) REVERT: H 90 ILE cc_start: 0.9368 (mt) cc_final: 0.9111 (mt) REVERT: H 94 GLU cc_start: 0.8961 (mp0) cc_final: 0.8656 (mp0) REVERT: H 103 LEU cc_start: 0.9553 (mp) cc_final: 0.9351 (mp) REVERT: H 114 GLU cc_start: 0.8541 (mm-30) cc_final: 0.7741 (mm-30) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.1068 time to fit residues: 33.8050 Evaluate side-chains 169 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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: 30.0000 chunk 139 optimal weight: 40.0000 chunk 78 optimal weight: 20.0000 chunk 90 optimal weight: 20.0000 chunk 92 optimal weight: 20.0000 chunk 179 optimal weight: 30.0000 chunk 4 optimal weight: 3.9990 chunk 93 optimal weight: 20.0000 chunk 126 optimal weight: 30.0000 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 20.0000 overall best weight: 12.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 HIS ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.104268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.067580 restraints weight = 71382.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.069096 restraints weight = 34848.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.070040 restraints weight = 23268.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.070591 restraints weight = 18754.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.070884 restraints weight = 16788.187| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.6137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.286 16699 Z= 0.624 Angle : 1.194 17.485 23978 Z= 0.634 Chirality : 0.065 0.333 2816 Planarity : 0.009 0.101 2173 Dihedral : 28.586 82.440 4750 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 23.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.21 % Favored : 96.73 % 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: 0.13 (0.21), residues: 1528 helix: -0.07 (0.19), residues: 622 sheet: 0.27 (0.29), residues: 336 loop : 0.46 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG E 70 TYR 0.038 0.005 TYR C 58 PHE 0.048 0.006 PHE D 71 TRP 0.000 0.000 TRP K 146 HIS 0.026 0.005 HIS G 32 Details of bonding type rmsd/Z covalent geometry : bond 0.01301 / 0.62 (16699) covalent geometry : angle 1.19448 / 0.63 (23978) hydrogen bonds : bond 0.13568 / 9.46 ( 977) hydrogen bonds : angle 5.56776 / 4.08 ( 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 163 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 LEU cc_start: 0.9627 (tp) cc_final: 0.9241 (tt) REVERT: B 64 GLU cc_start: 0.8839 (pt0) cc_final: 0.8499 (pt0) REVERT: B 67 ILE cc_start: 0.9687 (mt) cc_final: 0.9392 (mt) REVERT: C 39 ASN cc_start: 0.8062 (m-40) cc_final: 0.7746 (m-40) REVERT: D 85 ASN cc_start: 0.9204 (t0) cc_final: 0.8907 (t0) REVERT: E 60 GLU cc_start: 0.8447 (pp20) cc_final: 0.7620 (pp20) REVERT: E 74 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8356 (tm-30) REVERT: E 78 ASP cc_start: 0.8812 (m-30) cc_final: 0.8329 (m-30) REVERT: E 107 ASP cc_start: 0.9094 (m-30) cc_final: 0.8884 (m-30) REVERT: E 121 MET cc_start: 0.8717 (mmm) cc_final: 0.8462 (mmm) REVERT: F 54 GLU cc_start: 0.8754 (mp0) cc_final: 0.8525 (mp0) REVERT: G 39 ASN cc_start: 0.8537 (t0) cc_final: 0.8200 (t0) REVERT: G 62 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8482 (tm-30) REVERT: G 88 ILE cc_start: 0.9363 (mt) cc_final: 0.9155 (mm) REVERT: H 63 MET cc_start: 0.8600 (mmt) cc_final: 0.8144 (mmm) REVERT: H 94 GLU cc_start: 0.9170 (mp0) cc_final: 0.8875 (mp0) REVERT: H 114 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8160 (mm-30) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.1092 time to fit residues: 28.0123 Evaluate side-chains 135 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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: 20.0000 chunk 62 optimal weight: 0.0070 chunk 84 optimal weight: 50.0000 chunk 65 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 159 optimal weight: 8.9990 chunk 82 optimal weight: 20.0000 chunk 146 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 94 GLN ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.111299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.074600 restraints weight = 68156.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.076229 restraints weight = 32324.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.077271 restraints weight = 21234.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.077839 restraints weight = 17131.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.078087 restraints weight = 15279.300| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.5969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16699 Z= 0.165 Angle : 0.714 9.974 23978 Z= 0.401 Chirality : 0.046 0.317 2816 Planarity : 0.005 0.050 2173 Dihedral : 28.523 85.143 4750 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % 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: 1.21 (0.21), residues: 1528 helix: 1.32 (0.20), residues: 625 sheet: 0.38 (0.29), residues: 336 loop : 0.71 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 100 TYR 0.018 0.002 TYR B 89 PHE 0.034 0.002 PHE A 68 TRP 0.000 0.000 TRP K 146 HIS 0.008 0.002 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.17 (16699) covalent geometry : angle 0.71414 / 0.40 (23978) hydrogen bonds : bond 0.05314 / 3.70 ( 977) hydrogen bonds : angle 4.13088 / 3.04 ( 2466) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3157.60 seconds wall clock time: 54 minutes 45.97 seconds (3285.97 seconds total)