Starting phenix.real_space_refine on Thu Jul 31 11:53:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d20_30552/07_2025/7d20_30552.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d20_30552/07_2025/7d20_30552.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7d20_30552/07_2025/7d20_30552.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d20_30552/07_2025/7d20_30552.map" model { file = "/net/cci-nas-00/data/ceres_data/7d20_30552/07_2025/7d20_30552.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d20_30552/07_2025/7d20_30552.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1358 atoms to isotropic. 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 272 5.49 5 S 14 5.16 5 C 7237 2.51 5 N 2397 2.21 5 O 2916 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12836 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 732 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "E" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 749 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "B" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 729 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "F" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 699 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "I" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2768 Classifications: {'DNA': 136} Link IDs: {'rna3p': 135} Chain: "J" Number of atoms: 2808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2808 Classifications: {'DNA': 136} Link IDs: {'rna3p': 135} Chain: "K" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1330 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 3, 'TRANS': 162} Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Time building chain proxies: 8.21, per 1000 atoms: 0.64 Number of scatterers: 12836 At special positions: 0 Unit cell: (118.65, 99.75, 116.55, 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 272 15.00 O 2916 8.00 N 2397 7.00 C 7237 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: 3.44 Conformation dependent library (CDL) restraints added in 1.1 seconds 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1694 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 12 sheets defined 61.9% alpha, 6.0% beta 132 base pairs and 237 stacking pairs defined. Time for finding SS restraints: 6.44 Creating SS restraints... Processing helix chain 'A' and resid 47 through 56 removed outlier: 3.758A pdb=" N LYS A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 87 through 114 removed outlier: 4.010A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.854A pdb=" N VAL A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 132 removed outlier: 3.592A pdb=" N ARG A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 63 through 78 removed outlier: 3.575A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 110 removed outlier: 3.833A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 134 removed outlier: 3.620A pdb=" N ARG E 133 " --> pdb=" O ALA E 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.581A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.606A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.397A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.569A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.616A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 124 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.618A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.524A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.568A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'K' and resid 194 through 213 Processing helix chain 'K' and resid 254 through 264 removed outlier: 3.885A pdb=" N GLU K 259 " --> pdb=" O ALA K 255 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ALA K 260 " --> pdb=" O LYS K 256 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN K 264 " --> pdb=" O ALA K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 340 through 347 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 Processing sheet with id=AA1, first strand: chain 'A' and resid 120 through 121 Processing sheet with id=AA2, first strand: chain 'E' and resid 85 through 86 removed outlier: 7.260A pdb=" N ASN E 85 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'E' and resid 120 through 121 Processing sheet with id=AA4, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA5, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.401A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA7, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.913A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.034A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'K' and resid 218 through 223 removed outlier: 3.931A pdb=" N GLY K 227 " --> pdb=" O ILE K 223 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 241 through 244 removed outlier: 7.160A pdb=" N LEU K 320 " --> pdb=" O VAL K 242 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N GLU K 244 " --> pdb=" O LEU K 318 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N LEU K 318 " --> pdb=" O GLU K 244 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL K 315 " --> pdb=" O ILE K 312 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 248 through 250 removed outlier: 3.685A pdb=" N CYS K 283 " --> pdb=" O ILE K 250 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE K 275 " --> pdb=" O TYR K 282 " (cutoff:3.500A) 423 hydrogen bonds defined for protein. 1248 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 341 hydrogen bonds 682 hydrogen bond angles 0 basepair planarities 132 basepair parallelities 237 stacking parallelities Total time for adding SS restraints: 6.38 Time building geometry restraints manager: 4.05 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: 2145 1.33 - 1.45: 4532 1.45 - 1.57: 6382 1.57 - 1.69: 542 1.69 - 1.81: 22 Bond restraints: 13623 Sorted by residual: bond pdb=" CA ALA B 76 " pdb=" C ALA B 76 " ideal model delta sigma weight residual 1.523 1.468 0.055 1.80e-02 3.09e+03 9.40e+00 bond pdb=" CB ILE F 46 " pdb=" CG2 ILE F 46 " ideal model delta sigma weight residual 1.521 1.450 0.071 3.30e-02 9.18e+02 4.68e+00 bond pdb=" CB THR E 113 " pdb=" CG2 THR E 113 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.09e+00 bond pdb=" CB VAL B 70 " pdb=" CG1 VAL B 70 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.66e+00 bond pdb=" CB ILE B 50 " pdb=" CG2 ILE B 50 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.43e+00 ... (remaining 13618 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.49: 19534 5.49 - 10.97: 18 10.97 - 16.46: 0 16.46 - 21.95: 1 21.95 - 27.43: 1 Bond angle restraints: 19554 Sorted by residual: angle pdb=" O3' DG J 20 " pdb=" P DG J 21 " pdb=" OP1 DG J 21 " ideal model delta sigma weight residual 108.00 80.57 27.43 3.00e+00 1.11e-01 8.36e+01 angle pdb=" N VAL E 119 " pdb=" CA VAL E 119 " pdb=" C VAL E 119 " ideal model delta sigma weight residual 113.71 106.10 7.61 9.50e-01 1.11e+00 6.41e+01 angle pdb=" O3' DG J 20 " pdb=" P DG J 21 " pdb=" OP2 DG J 21 " ideal model delta sigma weight residual 108.00 87.00 21.00 3.00e+00 1.11e-01 4.90e+01 angle pdb=" O3' DG J 20 " pdb=" P DG J 21 " pdb=" O5' DG J 21 " ideal model delta sigma weight residual 104.00 98.12 5.88 1.50e+00 4.44e-01 1.54e+01 angle pdb=" OP1 DG J 21 " pdb=" P DG J 21 " pdb=" OP2 DG J 21 " ideal model delta sigma weight residual 120.00 130.43 -10.43 3.00e+00 1.11e-01 1.21e+01 ... (remaining 19549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.94: 5845 32.94 - 65.88: 1564 65.88 - 98.82: 53 98.82 - 131.76: 1 131.76 - 164.71: 1 Dihedral angle restraints: 7464 sinusoidal: 4830 harmonic: 2634 Sorted by residual: dihedral pdb=" CA THR E 113 " pdb=" C THR E 113 " pdb=" N LEU E 114 " pdb=" CA LEU E 114 " ideal model delta harmonic sigma weight residual 180.00 150.65 29.35 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ILE F 29 " pdb=" C ILE F 29 " pdb=" N THR F 30 " pdb=" CA THR F 30 " ideal model delta harmonic sigma weight residual -180.00 -160.25 -19.75 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual 180.00 -160.33 -19.67 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 7461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.405: 2211 0.405 - 0.809: 0 0.809 - 1.214: 0 1.214 - 1.619: 0 1.619 - 2.023: 1 Chirality restraints: 2212 Sorted by residual: chirality pdb=" P DG J 21 " pdb=" OP1 DG J 21 " pdb=" OP2 DG J 21 " pdb=" O5' DG J 21 " both_signs ideal model delta sigma weight residual True 2.35 0.32 2.02 2.00e-01 2.50e+01 1.02e+02 chirality pdb=" CB ILE D 54 " pdb=" CA ILE D 54 " pdb=" CG1 ILE D 54 " pdb=" CG2 ILE D 54 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.27e-01 chirality pdb=" CA ILE F 29 " pdb=" N ILE F 29 " pdb=" C ILE F 29 " pdb=" CB ILE F 29 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.74e-01 ... (remaining 2209 not shown) Planarity restraints: 1531 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 26 " 0.029 2.00e-02 2.50e+03 1.24e-02 4.61e+00 pdb=" N9 DG I 26 " -0.026 2.00e-02 2.50e+03 pdb=" C8 DG I 26 " -0.006 2.00e-02 2.50e+03 pdb=" N7 DG I 26 " -0.007 2.00e-02 2.50e+03 pdb=" C5 DG I 26 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DG I 26 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 26 " 0.011 2.00e-02 2.50e+03 pdb=" N1 DG I 26 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 26 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 26 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DG I 26 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DG I 26 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -35 " 0.030 2.00e-02 2.50e+03 1.29e-02 4.55e+00 pdb=" N9 DA I -35 " -0.027 2.00e-02 2.50e+03 pdb=" C8 DA I -35 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DA I -35 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA I -35 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA I -35 " 0.003 2.00e-02 2.50e+03 pdb=" N6 DA I -35 " 0.011 2.00e-02 2.50e+03 pdb=" N1 DA I -35 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I -35 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DA I -35 " -0.007 2.00e-02 2.50e+03 pdb=" C4 DA I -35 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 24 " -0.002 2.00e-02 2.50e+03 1.32e-02 3.91e+00 pdb=" N1 DC J 24 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DC J 24 " -0.031 2.00e-02 2.50e+03 pdb=" O2 DC J 24 " 0.018 2.00e-02 2.50e+03 pdb=" N3 DC J 24 " 0.008 2.00e-02 2.50e+03 pdb=" C4 DC J 24 " -0.012 2.00e-02 2.50e+03 pdb=" N4 DC J 24 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DC J 24 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DC J 24 " 0.005 2.00e-02 2.50e+03 ... (remaining 1528 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 38 2.38 - 3.01: 6761 3.01 - 3.64: 21719 3.64 - 4.27: 34416 4.27 - 4.90: 50373 Nonbonded interactions: 113307 Sorted by model distance: nonbonded pdb=" OXT GLY B 102 " pdb=" ND2 ASN H 67 " model vdw 1.752 3.120 nonbonded pdb=" OG1 THR A 79 " pdb=" O VAL A 82 " model vdw 2.039 3.040 nonbonded pdb=" O ALA K 255 " pdb=" OH TYR K 274 " model vdw 2.088 3.040 nonbonded pdb=" OD2 ASP D 68 " pdb=" OH TYR F 98 " model vdw 2.121 3.040 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 68 " model vdw 2.132 3.040 ... (remaining 113302 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' and resid 46 through 134) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 23 through 102) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 12 through 118) } ncs_group { reference = (chain 'D' and resid 33 through 124) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 19.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 37.840 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.150 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:202.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 261.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 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 0.071 13623 Z= 0.397 Angle : 0.811 27.433 19554 Z= 0.464 Chirality : 0.061 2.023 2212 Planarity : 0.004 0.039 1531 Dihedral : 28.627 164.706 5770 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.23), residues: 896 helix: -1.58 (0.18), residues: 561 sheet: -3.38 (0.76), residues: 26 loop : -3.03 (0.29), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP K 349 HIS 0.006 0.001 HIS F 75 PHE 0.027 0.002 PHE G 25 TYR 0.015 0.002 TYR K 274 ARG 0.007 0.001 ARG A 118 Details of bonding type rmsd hydrogen bonds : bond 0.10803 ( 764) hydrogen bonds : angle 4.82231 ( 1930) covalent geometry : bond 0.00926 (13623) covalent geometry : angle 0.81094 (19554) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.8397 (tttt) cc_final: 0.7808 (tttp) REVERT: E 53 LYS cc_start: 0.8337 (ttmt) cc_final: 0.7983 (ttmm) REVERT: E 59 HIS cc_start: 0.7451 (m-70) cc_final: 0.6808 (m170) REVERT: E 131 ARG cc_start: 0.8275 (tmt-80) cc_final: 0.8042 (ttp80) REVERT: B 44 LYS cc_start: 0.8510 (tttt) cc_final: 0.8292 (tttt) REVERT: C 15 LYS cc_start: 0.8510 (pttm) cc_final: 0.8252 (pttt) REVERT: C 36 LYS cc_start: 0.8870 (ptmm) cc_final: 0.8542 (ptpt) REVERT: C 50 TYR cc_start: 0.8890 (t80) cc_final: 0.8543 (t80) REVERT: C 75 LYS cc_start: 0.8255 (mttp) cc_final: 0.8021 (mtpp) REVERT: C 90 ASP cc_start: 0.7868 (t0) cc_final: 0.7547 (t0) REVERT: C 95 LYS cc_start: 0.8820 (ttmt) cc_final: 0.8407 (mtpp) REVERT: C 104 GLN cc_start: 0.8798 (mm-40) cc_final: 0.8291 (mm110) REVERT: D 51 ASP cc_start: 0.7960 (p0) cc_final: 0.7621 (p0) REVERT: D 76 GLU cc_start: 0.8022 (tp30) cc_final: 0.7530 (tp30) REVERT: D 85 LYS cc_start: 0.9043 (mtpt) cc_final: 0.8761 (mtmm) REVERT: G 19 SER cc_start: 0.9475 (t) cc_final: 0.9121 (p) REVERT: K 218 MET cc_start: 0.5989 (mpp) cc_final: 0.5753 (mpp) REVERT: K 310 HIS cc_start: 0.7529 (t70) cc_final: 0.6996 (t70) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 1.8582 time to fit residues: 316.9925 Evaluate side-chains 119 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.0670 chunk 85 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 65 optimal weight: 8.9990 chunk 102 optimal weight: 30.0000 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS E 59 HIS E 95 GLN E 115 HIS B 27 GLN D 47 GLN D 49 HIS D 84 ASN D 95 GLN F 18 HIS F 75 HIS F 93 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.162861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.098773 restraints weight = 20492.822| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.44 r_work: 0.2978 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13623 Z= 0.155 Angle : 0.663 26.905 19554 Z= 0.367 Chirality : 0.056 2.029 2212 Planarity : 0.004 0.035 1531 Dihedral : 31.084 164.483 3983 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.12 % Allowed : 14.95 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.26), residues: 896 helix: 0.33 (0.21), residues: 574 sheet: -2.71 (0.68), residues: 41 loop : -2.09 (0.33), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 86 HIS 0.005 0.001 HIS F 75 PHE 0.010 0.001 PHE K 275 TYR 0.014 0.002 TYR D 40 ARG 0.009 0.001 ARG H 92 Details of bonding type rmsd hydrogen bonds : bond 0.03640 ( 764) hydrogen bonds : angle 3.29008 ( 1930) covalent geometry : bond 0.00336 (13623) covalent geometry : angle 0.66350 (19554) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 1.057 Fit side-chains REVERT: A 53 LYS cc_start: 0.7546 (tttt) cc_final: 0.7062 (tttm) REVERT: E 53 LYS cc_start: 0.7475 (ttmt) cc_final: 0.7265 (ttmm) REVERT: E 59 HIS cc_start: 0.7085 (m90) cc_final: 0.6348 (m90) REVERT: E 120 THR cc_start: 0.8106 (m) cc_final: 0.7863 (p) REVERT: E 131 ARG cc_start: 0.8241 (ttt-90) cc_final: 0.7684 (ttp-110) REVERT: B 77 LYS cc_start: 0.8794 (mttt) cc_final: 0.8505 (mtmt) REVERT: C 15 LYS cc_start: 0.7538 (pttm) cc_final: 0.7313 (pttt) REVERT: C 19 SER cc_start: 0.9021 (t) cc_final: 0.8546 (p) REVERT: C 36 LYS cc_start: 0.8075 (ptmm) cc_final: 0.7803 (ptpt) REVERT: C 75 LYS cc_start: 0.7531 (mttp) cc_final: 0.7292 (mtpp) REVERT: C 92 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7059 (mt-10) REVERT: C 95 LYS cc_start: 0.8162 (ttmt) cc_final: 0.7832 (mtpp) REVERT: C 99 ARG cc_start: 0.7638 (mtt180) cc_final: 0.6648 (mmt-90) REVERT: C 104 GLN cc_start: 0.8367 (mm-40) cc_final: 0.7616 (mm110) REVERT: D 47 GLN cc_start: 0.8309 (mt0) cc_final: 0.8050 (mt0) REVERT: D 85 LYS cc_start: 0.8723 (mtpt) cc_final: 0.8385 (mtmm) REVERT: F 84 MET cc_start: 0.7390 (mmm) cc_final: 0.6929 (mmt) REVERT: G 19 SER cc_start: 0.9235 (t) cc_final: 0.9004 (p) REVERT: G 36 LYS cc_start: 0.8531 (pptt) cc_final: 0.7982 (pttt) REVERT: K 310 HIS cc_start: 0.7154 (t70) cc_final: 0.6552 (t-90) outliers start: 16 outliers final: 5 residues processed: 144 average time/residue: 1.5579 time to fit residues: 240.0351 Evaluate side-chains 123 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 118 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain D residue 113 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 21 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 chunk 20 optimal weight: 0.6980 chunk 88 optimal weight: 20.0000 chunk 100 optimal weight: 20.0000 chunk 1 optimal weight: 6.9990 chunk 23 optimal weight: 0.6980 chunk 103 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 127 GLN B 27 GLN C 24 GLN F 25 ASN F 27 GLN F 93 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.162570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.098272 restraints weight = 20584.870| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.39 r_work: 0.2997 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13623 Z= 0.163 Angle : 0.645 26.958 19554 Z= 0.356 Chirality : 0.055 2.003 2212 Planarity : 0.004 0.037 1531 Dihedral : 30.837 166.717 3983 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.91 % Allowed : 17.33 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.28), residues: 896 helix: 1.20 (0.21), residues: 574 sheet: -2.52 (0.67), residues: 44 loop : -1.41 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 349 HIS 0.005 0.001 HIS B 75 PHE 0.009 0.001 PHE G 25 TYR 0.015 0.001 TYR D 40 ARG 0.012 0.001 ARG C 35 Details of bonding type rmsd hydrogen bonds : bond 0.03426 ( 764) hydrogen bonds : angle 3.04372 ( 1930) covalent geometry : bond 0.00361 (13623) covalent geometry : angle 0.64452 (19554) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.971 Fit side-chains revert: symmetry clash REVERT: A 53 LYS cc_start: 0.7498 (tttt) cc_final: 0.7002 (tttp) REVERT: E 59 HIS cc_start: 0.7123 (m90) cc_final: 0.6407 (m90) REVERT: E 83 ASP cc_start: 0.8828 (m-30) cc_final: 0.7610 (p0) REVERT: E 125 ASP cc_start: 0.8692 (m-30) cc_final: 0.8356 (m-30) REVERT: E 131 ARG cc_start: 0.8226 (ttt-90) cc_final: 0.7679 (ttp-110) REVERT: B 74 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8176 (mt-10) REVERT: C 19 SER cc_start: 0.9095 (t) cc_final: 0.8621 (p) REVERT: C 36 LYS cc_start: 0.8094 (ptmm) cc_final: 0.7848 (ptpt) REVERT: C 38 ASN cc_start: 0.8180 (OUTLIER) cc_final: 0.7319 (t0) REVERT: C 90 ASP cc_start: 0.6881 (t0) cc_final: 0.6290 (t0) REVERT: C 92 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7168 (mt-10) REVERT: C 95 LYS cc_start: 0.8265 (ttmt) cc_final: 0.7917 (mtpp) REVERT: D 42 TYR cc_start: 0.7386 (t80) cc_final: 0.7067 (t80) REVERT: D 85 LYS cc_start: 0.8737 (mtpt) cc_final: 0.8376 (mtmm) REVERT: F 21 VAL cc_start: 0.5834 (OUTLIER) cc_final: 0.5473 (p) REVERT: F 84 MET cc_start: 0.7395 (mmm) cc_final: 0.6963 (mmt) REVERT: G 19 SER cc_start: 0.9244 (t) cc_final: 0.9020 (p) REVERT: G 36 LYS cc_start: 0.8281 (pptt) cc_final: 0.7898 (pttt) REVERT: G 41 GLU cc_start: 0.9136 (tt0) cc_final: 0.8504 (mp0) REVERT: G 90 ASP cc_start: 0.7899 (t0) cc_final: 0.7503 (t0) REVERT: G 92 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7826 (mt-10) REVERT: K 310 HIS cc_start: 0.7407 (t70) cc_final: 0.6709 (t-90) REVERT: H 105 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7137 (mm-30) outliers start: 22 outliers final: 11 residues processed: 145 average time/residue: 1.5037 time to fit residues: 234.1668 Evaluate side-chains 129 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain K residue 307 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 51 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 62 optimal weight: 50.0000 chunk 5 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 74 optimal weight: 20.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 127 GLN B 27 GLN B 93 GLN F 25 ASN F 27 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN H 109 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.163695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.099317 restraints weight = 20505.757| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.45 r_work: 0.2997 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13623 Z= 0.152 Angle : 0.631 26.734 19554 Z= 0.346 Chirality : 0.055 1.995 2212 Planarity : 0.003 0.044 1531 Dihedral : 30.648 167.982 3983 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.57 % Allowed : 18.65 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.28), residues: 896 helix: 1.57 (0.21), residues: 584 sheet: -2.43 (0.68), residues: 44 loop : -1.05 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 349 HIS 0.003 0.001 HIS B 75 PHE 0.008 0.001 PHE A 78 TYR 0.016 0.001 TYR D 40 ARG 0.012 0.000 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.03323 ( 764) hydrogen bonds : angle 2.92365 ( 1930) covalent geometry : bond 0.00334 (13623) covalent geometry : angle 0.63115 (19554) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.968 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.6978 (tt0) cc_final: 0.6755 (tt0) REVERT: A 53 LYS cc_start: 0.7347 (tttt) cc_final: 0.6933 (tttp) REVERT: A 92 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6694 (tp) REVERT: E 59 HIS cc_start: 0.6988 (m90) cc_final: 0.6291 (m90) REVERT: E 60 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7904 (mt) REVERT: E 83 ASP cc_start: 0.8808 (m-30) cc_final: 0.7665 (p0) REVERT: E 131 ARG cc_start: 0.8281 (ttt-90) cc_final: 0.7728 (ttp-110) REVERT: B 74 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8113 (mt-10) REVERT: C 15 LYS cc_start: 0.7177 (pttt) cc_final: 0.6957 (pmtt) REVERT: C 19 SER cc_start: 0.9090 (t) cc_final: 0.8622 (p) REVERT: C 36 LYS cc_start: 0.8071 (ptmm) cc_final: 0.7845 (ptpt) REVERT: C 90 ASP cc_start: 0.6871 (t0) cc_final: 0.6251 (t0) REVERT: C 92 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7226 (mt-10) REVERT: C 95 LYS cc_start: 0.8283 (ttmt) cc_final: 0.7917 (mtpp) REVERT: C 104 GLN cc_start: 0.8172 (tp40) cc_final: 0.7421 (mm110) REVERT: D 85 LYS cc_start: 0.8680 (mtpt) cc_final: 0.8370 (mtmm) REVERT: D 86 ARG cc_start: 0.6950 (mtt-85) cc_final: 0.6639 (mtt-85) REVERT: F 21 VAL cc_start: 0.6132 (OUTLIER) cc_final: 0.5827 (p) REVERT: F 84 MET cc_start: 0.7287 (mmm) cc_final: 0.6883 (mmt) REVERT: G 19 SER cc_start: 0.9243 (t) cc_final: 0.9024 (p) REVERT: G 36 LYS cc_start: 0.8082 (pptt) cc_final: 0.7816 (pttt) REVERT: G 90 ASP cc_start: 0.8005 (t0) cc_final: 0.7512 (t0) REVERT: G 92 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7713 (mt-10) REVERT: H 99 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7609 (ttp80) REVERT: H 105 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7235 (mm-30) outliers start: 27 outliers final: 10 residues processed: 143 average time/residue: 1.4271 time to fit residues: 219.9168 Evaluate side-chains 127 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 99 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 40.0000 chunk 82 optimal weight: 7.9990 chunk 70 optimal weight: 7.9990 chunk 96 optimal weight: 50.0000 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 95 GLN E 127 GLN B 27 GLN D 47 GLN F 25 ASN F 27 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN G 104 GLN ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 310 HIS H 49 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.160476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.095089 restraints weight = 20461.236| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.40 r_work: 0.2958 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 13623 Z= 0.249 Angle : 0.681 26.944 19554 Z= 0.368 Chirality : 0.056 1.969 2212 Planarity : 0.004 0.046 1531 Dihedral : 31.160 170.124 3983 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.57 % Allowed : 19.71 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.28), residues: 896 helix: 1.51 (0.21), residues: 577 sheet: -2.23 (0.71), residues: 44 loop : -1.02 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 349 HIS 0.004 0.001 HIS B 75 PHE 0.015 0.002 PHE G 25 TYR 0.026 0.002 TYR H 121 ARG 0.014 0.001 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.03803 ( 764) hydrogen bonds : angle 3.11135 ( 1930) covalent geometry : bond 0.00577 (13623) covalent geometry : angle 0.68074 (19554) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 1.164 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7029 (tt0) cc_final: 0.6817 (tt0) REVERT: A 53 LYS cc_start: 0.7317 (tttt) cc_final: 0.6925 (tttp) REVERT: A 92 LEU cc_start: 0.6989 (OUTLIER) cc_final: 0.6782 (tp) REVERT: E 59 HIS cc_start: 0.7210 (m90) cc_final: 0.6603 (m90) REVERT: E 63 ARG cc_start: 0.6984 (mmp-170) cc_final: 0.6663 (mmp80) REVERT: E 83 ASP cc_start: 0.8803 (m-30) cc_final: 0.7698 (p0) REVERT: E 131 ARG cc_start: 0.8237 (ttt-90) cc_final: 0.7644 (ttp-110) REVERT: B 44 LYS cc_start: 0.8231 (tttt) cc_final: 0.8009 (tttp) REVERT: C 19 SER cc_start: 0.9046 (t) cc_final: 0.8574 (p) REVERT: C 36 LYS cc_start: 0.8106 (ptmm) cc_final: 0.7818 (ptpt) REVERT: C 90 ASP cc_start: 0.6790 (t0) cc_final: 0.6172 (t0) REVERT: C 92 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7147 (mt-10) REVERT: C 95 LYS cc_start: 0.8183 (ttmt) cc_final: 0.7840 (mtpp) REVERT: D 85 LYS cc_start: 0.8665 (mtpt) cc_final: 0.8345 (mtmm) REVERT: D 93 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6681 (mm-30) REVERT: D 105 GLU cc_start: 0.7859 (tp30) cc_final: 0.7596 (tp30) REVERT: D 108 LYS cc_start: 0.6731 (mmtt) cc_final: 0.6318 (mmtt) REVERT: F 21 VAL cc_start: 0.6093 (OUTLIER) cc_final: 0.5801 (p) REVERT: G 19 SER cc_start: 0.9231 (t) cc_final: 0.8988 (p) REVERT: G 36 LYS cc_start: 0.8086 (pptt) cc_final: 0.7788 (pttt) REVERT: G 90 ASP cc_start: 0.7889 (t0) cc_final: 0.7684 (t0) REVERT: G 92 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7913 (mt-10) REVERT: K 310 HIS cc_start: 0.7429 (t70) cc_final: 0.6742 (t70) REVERT: H 105 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7395 (mm-30) outliers start: 27 outliers final: 14 residues processed: 142 average time/residue: 1.7346 time to fit residues: 262.6658 Evaluate side-chains 130 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain H residue 99 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 26 optimal weight: 0.7980 chunk 66 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 99 optimal weight: 50.0000 chunk 112 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 95 optimal weight: 40.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN E 127 GLN B 27 GLN F 25 ASN F 27 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.161251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.095885 restraints weight = 20758.240| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.41 r_work: 0.2976 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13623 Z= 0.211 Angle : 0.655 27.096 19554 Z= 0.355 Chirality : 0.056 1.986 2212 Planarity : 0.004 0.049 1531 Dihedral : 31.035 170.616 3983 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.17 % Allowed : 21.03 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.28), residues: 896 helix: 1.60 (0.21), residues: 577 sheet: -2.03 (0.73), residues: 44 loop : -0.89 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 349 HIS 0.005 0.001 HIS B 75 PHE 0.012 0.001 PHE G 25 TYR 0.015 0.001 TYR H 121 ARG 0.011 0.001 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.03584 ( 764) hydrogen bonds : angle 2.99660 ( 1930) covalent geometry : bond 0.00485 (13623) covalent geometry : angle 0.65484 (19554) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 1.090 Fit side-chains REVERT: A 50 GLU cc_start: 0.7033 (tt0) cc_final: 0.6798 (tt0) REVERT: A 53 LYS cc_start: 0.7302 (tttt) cc_final: 0.6911 (tttp) REVERT: A 92 LEU cc_start: 0.6916 (OUTLIER) cc_final: 0.6707 (tp) REVERT: E 59 HIS cc_start: 0.7049 (m90) cc_final: 0.6396 (m90) REVERT: E 63 ARG cc_start: 0.6895 (mmp-170) cc_final: 0.6597 (mmp80) REVERT: E 83 ASP cc_start: 0.8797 (m-30) cc_final: 0.7752 (p0) REVERT: E 131 ARG cc_start: 0.8258 (ttt-90) cc_final: 0.7678 (ttp-110) REVERT: C 15 LYS cc_start: 0.7111 (pttt) cc_final: 0.6880 (pttm) REVERT: C 19 SER cc_start: 0.9058 (t) cc_final: 0.8582 (p) REVERT: C 36 LYS cc_start: 0.8027 (ptmm) cc_final: 0.7787 (ptpt) REVERT: C 90 ASP cc_start: 0.6747 (t0) cc_final: 0.6124 (t0) REVERT: C 92 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7195 (mt-10) REVERT: C 95 LYS cc_start: 0.8290 (ttmt) cc_final: 0.7989 (mtpp) REVERT: D 85 LYS cc_start: 0.8696 (mtpt) cc_final: 0.8362 (mtmm) REVERT: D 105 GLU cc_start: 0.7763 (tp30) cc_final: 0.7505 (tp30) REVERT: D 108 LYS cc_start: 0.6685 (mmtt) cc_final: 0.6293 (mmtt) REVERT: F 21 VAL cc_start: 0.6116 (OUTLIER) cc_final: 0.5814 (p) REVERT: G 19 SER cc_start: 0.9229 (t) cc_final: 0.8984 (p) REVERT: G 36 LYS cc_start: 0.8070 (pptt) cc_final: 0.7761 (pttt) REVERT: G 90 ASP cc_start: 0.7885 (t0) cc_final: 0.7660 (t0) REVERT: G 92 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7833 (mt-10) REVERT: K 218 MET cc_start: 0.3861 (pmm) cc_final: 0.3621 (pmm) REVERT: K 310 HIS cc_start: 0.7363 (t70) cc_final: 0.6668 (t70) REVERT: H 105 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7340 (mm-30) outliers start: 24 outliers final: 14 residues processed: 131 average time/residue: 1.6400 time to fit residues: 230.0448 Evaluate side-chains 125 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain H residue 113 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 104 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 87 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 108 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 67 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 127 GLN B 27 GLN C 24 GLN F 25 ASN F 27 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.161798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.096505 restraints weight = 20607.823| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.40 r_work: 0.2959 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13623 Z= 0.183 Angle : 0.647 27.184 19554 Z= 0.348 Chirality : 0.055 1.998 2212 Planarity : 0.004 0.052 1531 Dihedral : 30.917 171.995 3983 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.17 % Allowed : 22.09 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.28), residues: 896 helix: 1.77 (0.21), residues: 576 sheet: -2.09 (0.72), residues: 44 loop : -0.81 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 349 HIS 0.004 0.001 HIS B 75 PHE 0.010 0.001 PHE G 25 TYR 0.018 0.001 TYR D 83 ARG 0.011 0.001 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.03462 ( 764) hydrogen bonds : angle 2.94381 ( 1930) covalent geometry : bond 0.00417 (13623) covalent geometry : angle 0.64652 (19554) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 1.842 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7049 (tt0) cc_final: 0.6797 (tt0) REVERT: A 53 LYS cc_start: 0.7297 (tttt) cc_final: 0.6917 (tttp) REVERT: A 92 LEU cc_start: 0.6906 (OUTLIER) cc_final: 0.6695 (tp) REVERT: E 59 HIS cc_start: 0.7177 (m90) cc_final: 0.6536 (m90) REVERT: E 60 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7957 (mt) REVERT: E 63 ARG cc_start: 0.6894 (mmp-170) cc_final: 0.6595 (mmp80) REVERT: E 83 ASP cc_start: 0.8770 (m-30) cc_final: 0.7804 (p0) REVERT: E 131 ARG cc_start: 0.8262 (ttt-90) cc_final: 0.7680 (ttp-110) REVERT: C 19 SER cc_start: 0.9063 (t) cc_final: 0.8605 (p) REVERT: C 36 LYS cc_start: 0.8025 (ptmm) cc_final: 0.7781 (ptpt) REVERT: C 90 ASP cc_start: 0.6768 (t0) cc_final: 0.6145 (t0) REVERT: C 92 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7239 (mt-10) REVERT: C 95 LYS cc_start: 0.8322 (ttmt) cc_final: 0.8015 (mtpp) REVERT: D 85 LYS cc_start: 0.8735 (mtpt) cc_final: 0.8409 (mtmm) REVERT: D 105 GLU cc_start: 0.7774 (tp30) cc_final: 0.7521 (tp30) REVERT: D 108 LYS cc_start: 0.6722 (mmtt) cc_final: 0.6304 (mmtt) REVERT: F 21 VAL cc_start: 0.6026 (OUTLIER) cc_final: 0.5721 (p) REVERT: G 19 SER cc_start: 0.9225 (t) cc_final: 0.8981 (p) REVERT: G 36 LYS cc_start: 0.7981 (pptt) cc_final: 0.7707 (pttt) REVERT: G 90 ASP cc_start: 0.7856 (t0) cc_final: 0.7619 (t0) REVERT: G 92 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7777 (mt-10) REVERT: K 310 HIS cc_start: 0.7299 (t70) cc_final: 0.6627 (t70) REVERT: H 105 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7368 (mm-30) outliers start: 24 outliers final: 16 residues processed: 134 average time/residue: 2.3567 time to fit residues: 339.8126 Evaluate side-chains 126 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain H residue 99 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 110 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 55 optimal weight: 0.0270 chunk 19 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 overall best weight: 0.7838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 89 GLN B 25 ASN B 27 GLN C 24 GLN D 47 GLN F 25 ASN F 27 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.165336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.101086 restraints weight = 20603.161| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.38 r_work: 0.3048 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13623 Z= 0.140 Angle : 0.622 27.052 19554 Z= 0.337 Chirality : 0.054 2.001 2212 Planarity : 0.004 0.046 1531 Dihedral : 30.446 173.045 3983 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.91 % Allowed : 23.02 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.28), residues: 896 helix: 2.01 (0.21), residues: 584 sheet: -2.13 (0.71), residues: 44 loop : -0.65 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 86 HIS 0.004 0.001 HIS B 75 PHE 0.009 0.001 PHE A 78 TYR 0.020 0.001 TYR D 83 ARG 0.010 0.000 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.03288 ( 764) hydrogen bonds : angle 2.76829 ( 1930) covalent geometry : bond 0.00303 (13623) covalent geometry : angle 0.62216 (19554) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 1.204 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7125 (tt0) cc_final: 0.6905 (tt0) REVERT: A 53 LYS cc_start: 0.7323 (tttt) cc_final: 0.6953 (tttp) REVERT: A 92 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6688 (tp) REVERT: E 59 HIS cc_start: 0.6979 (m90) cc_final: 0.6761 (m-70) REVERT: E 60 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8220 (mt) REVERT: E 83 ASP cc_start: 0.8702 (m-30) cc_final: 0.7963 (p0) REVERT: E 131 ARG cc_start: 0.8122 (ttt-90) cc_final: 0.7644 (ttp-110) REVERT: C 19 SER cc_start: 0.9128 (t) cc_final: 0.8661 (p) REVERT: C 36 LYS cc_start: 0.8051 (ptmm) cc_final: 0.7793 (ptpt) REVERT: C 90 ASP cc_start: 0.6946 (t0) cc_final: 0.6287 (t0) REVERT: C 92 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7399 (mt-10) REVERT: C 95 LYS cc_start: 0.8382 (ttmt) cc_final: 0.8051 (mtpp) REVERT: C 104 GLN cc_start: 0.8291 (tp40) cc_final: 0.7546 (mm110) REVERT: D 85 LYS cc_start: 0.8778 (mtpt) cc_final: 0.8501 (mtmm) REVERT: D 108 LYS cc_start: 0.6738 (mmtt) cc_final: 0.6309 (mmtt) REVERT: F 21 VAL cc_start: 0.6004 (OUTLIER) cc_final: 0.5697 (p) REVERT: G 19 SER cc_start: 0.9250 (t) cc_final: 0.9027 (p) REVERT: G 36 LYS cc_start: 0.8022 (pptt) cc_final: 0.7771 (pttt) REVERT: G 90 ASP cc_start: 0.7980 (t0) cc_final: 0.7430 (t0) REVERT: K 218 MET cc_start: 0.3528 (pmm) cc_final: 0.3297 (pmm) REVERT: K 310 HIS cc_start: 0.7289 (t70) cc_final: 0.6619 (t70) REVERT: H 99 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7387 (mtt-85) REVERT: H 105 GLU cc_start: 0.7457 (mm-30) cc_final: 0.6806 (mm-30) outliers start: 22 outliers final: 9 residues processed: 142 average time/residue: 2.1773 time to fit residues: 335.6872 Evaluate side-chains 127 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain H residue 99 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 77 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 85 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 74 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 89 GLN E 95 GLN B 27 GLN F 25 ASN F 27 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.160394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.094564 restraints weight = 20458.682| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.40 r_work: 0.2915 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 13623 Z= 0.290 Angle : 0.712 27.426 19554 Z= 0.376 Chirality : 0.058 1.988 2212 Planarity : 0.004 0.055 1531 Dihedral : 31.063 174.584 3983 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.38 % Allowed : 24.74 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.28), residues: 896 helix: 1.69 (0.21), residues: 576 sheet: -2.12 (0.70), residues: 44 loop : -0.76 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 349 HIS 0.004 0.001 HIS B 75 PHE 0.015 0.002 PHE G 25 TYR 0.031 0.002 TYR B 88 ARG 0.013 0.001 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.03960 ( 764) hydrogen bonds : angle 3.10862 ( 1930) covalent geometry : bond 0.00676 (13623) covalent geometry : angle 0.71166 (19554) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 1.286 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7023 (tt0) cc_final: 0.6813 (tt0) REVERT: A 53 LYS cc_start: 0.7316 (tttt) cc_final: 0.6933 (tttp) REVERT: A 92 LEU cc_start: 0.6985 (OUTLIER) cc_final: 0.6778 (tp) REVERT: E 59 HIS cc_start: 0.7181 (m90) cc_final: 0.6605 (m90) REVERT: E 63 ARG cc_start: 0.7038 (mmp-170) cc_final: 0.6718 (mmp80) REVERT: E 83 ASP cc_start: 0.8803 (m-30) cc_final: 0.7972 (p0) REVERT: E 131 ARG cc_start: 0.8190 (ttt-90) cc_final: 0.7610 (ttp-110) REVERT: B 44 LYS cc_start: 0.8339 (pttt) cc_final: 0.8124 (pttp) REVERT: C 19 SER cc_start: 0.9034 (t) cc_final: 0.8513 (p) REVERT: C 36 LYS cc_start: 0.8076 (ptmm) cc_final: 0.7839 (ptpt) REVERT: C 90 ASP cc_start: 0.6783 (t0) cc_final: 0.6180 (t0) REVERT: C 92 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7252 (mt-10) REVERT: C 95 LYS cc_start: 0.8281 (ttmt) cc_final: 0.7986 (mtpp) REVERT: D 85 LYS cc_start: 0.8734 (mtpt) cc_final: 0.8414 (mtmm) REVERT: D 105 GLU cc_start: 0.7801 (tp30) cc_final: 0.7556 (tp30) REVERT: D 108 LYS cc_start: 0.6801 (mmtt) cc_final: 0.6360 (mmtt) REVERT: F 21 VAL cc_start: 0.6045 (OUTLIER) cc_final: 0.5746 (p) REVERT: G 19 SER cc_start: 0.9225 (t) cc_final: 0.8963 (p) REVERT: G 36 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7724 (pttt) REVERT: G 61 GLU cc_start: 0.7858 (tp30) cc_final: 0.7645 (tt0) REVERT: G 90 ASP cc_start: 0.7790 (t0) cc_final: 0.7470 (t0) REVERT: K 310 HIS cc_start: 0.7231 (t70) cc_final: 0.6561 (t70) outliers start: 18 outliers final: 10 residues processed: 133 average time/residue: 2.6107 time to fit residues: 372.8347 Evaluate side-chains 125 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 40.0000 chunk 23 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 127 GLN B 25 ASN B 27 GLN F 25 ASN F 27 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.163871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.099187 restraints weight = 20470.242| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.37 r_work: 0.3001 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13623 Z= 0.152 Angle : 0.647 27.152 19554 Z= 0.345 Chirality : 0.055 2.003 2212 Planarity : 0.004 0.057 1531 Dihedral : 30.546 173.691 3983 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.91 % Allowed : 24.60 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.28), residues: 896 helix: 1.94 (0.21), residues: 583 sheet: -1.97 (0.71), residues: 44 loop : -0.62 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 86 HIS 0.005 0.001 HIS B 75 PHE 0.008 0.001 PHE F 100 TYR 0.021 0.002 TYR D 83 ARG 0.014 0.001 ARG C 35 Details of bonding type rmsd hydrogen bonds : bond 0.03332 ( 764) hydrogen bonds : angle 2.89362 ( 1930) covalent geometry : bond 0.00338 (13623) covalent geometry : angle 0.64655 (19554) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 1.302 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7068 (tt0) cc_final: 0.6845 (tt0) REVERT: A 53 LYS cc_start: 0.7302 (tttt) cc_final: 0.6933 (tttp) REVERT: A 92 LEU cc_start: 0.6905 (OUTLIER) cc_final: 0.6669 (tp) REVERT: E 59 HIS cc_start: 0.6953 (m90) cc_final: 0.6289 (m90) REVERT: E 63 ARG cc_start: 0.6910 (mmp-170) cc_final: 0.6628 (mmp80) REVERT: E 73 GLU cc_start: 0.7863 (tt0) cc_final: 0.7643 (tt0) REVERT: E 83 ASP cc_start: 0.8673 (m-30) cc_final: 0.7999 (p0) REVERT: E 131 ARG cc_start: 0.8118 (ttt-90) cc_final: 0.7618 (ttp-110) REVERT: C 19 SER cc_start: 0.9079 (t) cc_final: 0.8618 (p) REVERT: C 24 GLN cc_start: 0.8327 (mm110) cc_final: 0.7921 (mp-120) REVERT: C 36 LYS cc_start: 0.8030 (ptmm) cc_final: 0.7778 (ptpt) REVERT: C 90 ASP cc_start: 0.6833 (t0) cc_final: 0.6187 (t0) REVERT: C 92 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7357 (mt-10) REVERT: C 95 LYS cc_start: 0.8347 (ttmt) cc_final: 0.8027 (mtpp) REVERT: D 47 GLN cc_start: 0.8551 (mt0) cc_final: 0.8274 (mt0) REVERT: D 85 LYS cc_start: 0.8808 (mtpt) cc_final: 0.8527 (mtmm) REVERT: D 105 GLU cc_start: 0.7742 (tp30) cc_final: 0.7513 (tp30) REVERT: D 108 LYS cc_start: 0.6749 (mmtt) cc_final: 0.6302 (mmtt) REVERT: G 19 SER cc_start: 0.9264 (t) cc_final: 0.9018 (p) REVERT: G 36 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7780 (pttt) REVERT: G 90 ASP cc_start: 0.7860 (t0) cc_final: 0.7535 (t0) REVERT: K 310 HIS cc_start: 0.7265 (t70) cc_final: 0.6601 (t70) REVERT: H 99 ARG cc_start: 0.8002 (ttp80) cc_final: 0.7593 (mtt-85) REVERT: H 105 GLU cc_start: 0.7374 (mm-30) cc_final: 0.6847 (mm-30) outliers start: 22 outliers final: 10 residues processed: 134 average time/residue: 1.7931 time to fit residues: 258.7083 Evaluate side-chains 125 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 36 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 94 optimal weight: 20.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 89 GLN B 27 GLN C 24 GLN D 47 GLN F 25 ASN F 27 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 246 HIS ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.162825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.097383 restraints weight = 20542.526| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.41 r_work: 0.2976 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13623 Z= 0.183 Angle : 0.662 27.210 19554 Z= 0.352 Chirality : 0.056 1.998 2212 Planarity : 0.004 0.061 1531 Dihedral : 30.642 174.690 3983 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.98 % Allowed : 25.93 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.28), residues: 896 helix: 1.91 (0.21), residues: 583 sheet: -1.85 (0.72), residues: 44 loop : -0.63 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 47 HIS 0.005 0.001 HIS B 75 PHE 0.010 0.001 PHE G 25 TYR 0.028 0.002 TYR B 88 ARG 0.014 0.000 ARG C 35 Details of bonding type rmsd hydrogen bonds : bond 0.03491 ( 764) hydrogen bonds : angle 2.93656 ( 1930) covalent geometry : bond 0.00416 (13623) covalent geometry : angle 0.66158 (19554) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11076.69 seconds wall clock time: 202 minutes 35.79 seconds (12155.79 seconds total)