Starting phenix.real_space_refine on Fri Sep 11 11:48:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m4h_30078/09_2026/6m4h_30078.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m4h_30078/09_2026/6m4h_30078.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6m4h_30078/09_2026/6m4h_30078.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m4h_30078/09_2026/6m4h_30078.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6m4h_30078/09_2026/6m4h_30078.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m4h_30078/09_2026/6m4h_30078.map" } resolution = 3.9 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= 0.005 sd= 0.063 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 206 5.49 5 S 16 5.16 5 C 5279 2.51 5 N 1735 2.21 5 O 2184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s 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: 9420 Number of models: 1 Model: "" Number of chains: 10 Chain: "I" Number of atoms: 2132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 2132 Classifications: {'DNA': 103} Link IDs: {'rna3p': 102} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 2090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 2090 Classifications: {'DNA': 103} Link IDs: {'rna3p': 102} Chain: "A" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 599 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "B" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 610 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "C" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 705 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "D" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 685 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "E" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 599 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "F" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 610 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "G" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 705 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "H" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 685 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 2, 'TRANS': 85} Time building chain proxies: 2.07, per 1000 atoms: 0.22 Number of scatterers: 9420 At special positions: 0 Unit cell: (97.76, 114.4, 113.36, 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 16 16.00 P 206 15.00 O 2184 8.00 N 1735 7.00 C 5279 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: 0.90 Conformation dependent library (CDL) restraints added in 215.2 milliseconds 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1244 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 6 sheets defined 74.7% alpha, 2.1% beta 98 base pairs and 164 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.585A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.532A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.628A pdb=" N GLY B 28 " --> pdb=" O ASN B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.635A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.647A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 25 Processing helix chain 'C' and resid 30 through 40 Processing helix chain 'C' and resid 52 through 78 removed outlier: 3.865A pdb=" N GLU C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 69 " --> pdb=" O LYS C 65 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN C 75 " --> pdb=" O GLY C 71 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASN C 76 " --> pdb=" O ASN C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 93 removed outlier: 3.786A pdb=" N HIS C 92 " --> pdb=" O ASP C 88 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN C 93 " --> pdb=" O MET C 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.703A pdb=" N TYR D 42 " --> pdb=" O SER D 38 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS D 43 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 84 removed outlier: 3.608A pdb=" N GLY D 60 " --> pdb=" O SER D 56 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.689A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 123 removed outlier: 4.028A pdb=" N LYS D 120 " --> pdb=" O LYS D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 75 Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.583A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.532A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.628A pdb=" N GLY F 28 " --> pdb=" O ASN F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.634A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.648A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 25 Processing helix chain 'G' and resid 30 through 40 Processing helix chain 'G' and resid 50 through 76 removed outlier: 3.865A pdb=" N GLU G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU G 69 " --> pdb=" O LYS G 65 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN G 75 " --> pdb=" O GLY G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 93 removed outlier: 3.788A pdb=" N HIS G 92 " --> pdb=" O ASP G 88 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN G 93 " --> pdb=" O MET G 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.702A pdb=" N TYR H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS H 43 " --> pdb=" O ILE H 39 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 84 removed outlier: 3.607A pdb=" N GLY H 60 " --> pdb=" O SER H 56 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY H 75 " --> pdb=" O GLU H 71 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.689A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 123 removed outlier: 4.027A pdb=" N LYS H 120 " --> pdb=" O LYS H 116 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.336A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 104 through 106 removed outlier: 6.729A pdb=" N THR C 105 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.123A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 316 hydrogen bonds defined for protein. 942 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 249 hydrogen bonds 486 hydrogen bond angles 0 basepair planarities 98 basepair parallelities 164 stacking parallelities Total time for adding SS restraints: 1.70 Time building geometry restraints manager: 1.17 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: 1574 1.33 - 1.45: 3361 1.45 - 1.57: 4624 1.57 - 1.69: 412 1.69 - 1.80: 28 Bond restraints: 9999 Sorted by residual: bond pdb=" C6 DG J 37 " pdb=" N1 DG J 37 " ideal model delta sigma weight residual 1.391 1.362 0.029 7.00e-03 2.04e+04 1.71e+01 bond pdb=" C3' DC I 111 " pdb=" C2' DC I 111 " ideal model delta sigma weight residual 1.516 1.548 -0.032 8.00e-03 1.56e+04 1.58e+01 bond pdb=" C3' DC J 118 " pdb=" C2' DC J 118 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.54e+01 bond pdb=" C3' DG I 39 " pdb=" O3' DG I 39 " ideal model delta sigma weight residual 1.435 1.385 0.050 1.30e-02 5.92e+03 1.48e+01 bond pdb=" C4' DA I 91 " pdb=" C3' DA I 91 " ideal model delta sigma weight residual 1.529 1.491 0.038 1.00e-02 1.00e+04 1.43e+01 ... (remaining 9994 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 14201 3.12 - 6.24: 183 6.24 - 9.36: 10 9.36 - 12.48: 0 12.48 - 15.60: 1 Bond angle restraints: 14395 Sorted by residual: angle pdb=" O4' DA I 91 " pdb=" C4' DA I 91 " pdb=" C3' DA I 91 " ideal model delta sigma weight residual 106.00 101.13 4.87 6.00e-01 2.78e+00 6.58e+01 angle pdb=" O4' DA I 100 " pdb=" C4' DA I 100 " pdb=" C3' DA I 100 " ideal model delta sigma weight residual 106.00 101.22 4.78 6.00e-01 2.78e+00 6.34e+01 angle pdb=" O4' DA I 110 " pdb=" C4' DA I 110 " pdb=" C3' DA I 110 " ideal model delta sigma weight residual 106.00 101.57 4.43 6.00e-01 2.78e+00 5.45e+01 angle pdb=" O4' DC J 81 " pdb=" C4' DC J 81 " pdb=" C3' DC J 81 " ideal model delta sigma weight residual 106.00 102.33 3.67 6.00e-01 2.78e+00 3.74e+01 angle pdb=" O4' DA J 65 " pdb=" C4' DA J 65 " pdb=" C3' DA J 65 " ideal model delta sigma weight residual 106.00 102.62 3.38 6.00e-01 2.78e+00 3.17e+01 ... (remaining 14390 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.17: 4392 35.17 - 70.34: 1018 70.34 - 105.51: 46 105.51 - 140.69: 4 140.69 - 175.86: 6 Dihedral angle restraints: 5466 sinusoidal: 3548 harmonic: 1918 Sorted by residual: dihedral pdb=" C4' DC I 34 " pdb=" C3' DC I 34 " pdb=" O3' DC I 34 " pdb=" P DT I 35 " ideal model delta sinusoidal sigma weight residual -140.00 35.86 -175.86 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT J 32 " pdb=" C3' DT J 32 " pdb=" O3' DT J 32 " pdb=" P DG J 33 " ideal model delta sinusoidal sigma weight residual -140.00 32.37 -172.37 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA HIS G 92 " pdb=" C HIS G 92 " pdb=" N ASN G 93 " pdb=" CA ASN G 93 " ideal model delta harmonic sigma weight residual 180.00 160.29 19.71 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 5463 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 973 0.038 - 0.076: 436 0.076 - 0.114: 165 0.114 - 0.152: 71 0.152 - 0.190: 21 Chirality restraints: 1666 Sorted by residual: chirality pdb=" C3' DA J 60 " pdb=" C4' DA J 60 " pdb=" O3' DA J 60 " pdb=" C2' DA J 60 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.98e-01 chirality pdb=" C1' DA I 90 " pdb=" O4' DA I 90 " pdb=" C2' DA I 90 " pdb=" N9 DA I 90 " both_signs ideal model delta sigma weight residual False 2.43 2.25 0.18 2.00e-01 2.50e+01 7.99e-01 chirality pdb=" CA GLU A 97 " pdb=" N GLU A 97 " pdb=" C GLU A 97 " pdb=" CB GLU A 97 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.76e-01 ... (remaining 1663 not shown) Planarity restraints: 1100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 51 " -0.099 5.00e-02 4.00e+02 1.53e-01 3.74e+01 pdb=" N PRO C 52 " 0.265 5.00e-02 4.00e+02 pdb=" CA PRO C 52 " -0.090 5.00e-02 4.00e+02 pdb=" CD PRO C 52 " -0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 67 " 0.020 2.00e-02 2.50e+03 4.09e-02 1.67e+01 pdb=" C ASN D 67 " -0.071 2.00e-02 2.50e+03 pdb=" O ASN D 67 " 0.026 2.00e-02 2.50e+03 pdb=" N ASP D 68 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN H 67 " -0.020 2.00e-02 2.50e+03 4.07e-02 1.66e+01 pdb=" C ASN H 67 " 0.070 2.00e-02 2.50e+03 pdb=" O ASN H 67 " -0.026 2.00e-02 2.50e+03 pdb=" N ASP H 68 " -0.024 2.00e-02 2.50e+03 ... (remaining 1097 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.36: 33 2.36 - 3.00: 4572 3.00 - 3.63: 17703 3.63 - 4.27: 25383 4.27 - 4.90: 36252 Nonbonded interactions: 83943 Sorted by model distance: nonbonded pdb=" OP1 DT J 31 " pdb=" OG SER C 20 " model vdw 1.729 3.040 nonbonded pdb=" OP1 DT J 31 " pdb=" CA SER C 20 " model vdw 1.765 3.470 nonbonded pdb=" OP2 DC I 81 " pdb=" N GLY B 48 " model vdw 1.880 3.120 nonbonded pdb=" OP2 DA J 91 " pdb=" NH2 ARG E 69 " model vdw 1.970 3.120 nonbonded pdb=" OP2 DA I 113 " pdb=" NH2 ARG C 39 " model vdw 1.974 3.120 ... (remaining 83938 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' } ncs_group { reference = chain 'D' 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 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.520 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 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 : 0.008 0.056 9999 Z= 0.754 Angle : 1.009 15.598 14395 Z= 0.829 Chirality : 0.054 0.190 1666 Planarity : 0.010 0.153 1100 Dihedral : 29.217 175.856 4222 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 27.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.12 % Favored : 96.72 % Rotamer: Outliers : 2.85 % Allowed : 2.31 % Favored : 94.84 % 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: -6.02 (0.19), residues: 640 helix: -4.08 (0.11), residues: 444 sheet: None (None), residues: 0 loop : -3.15 (0.32), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 78 TYR 0.026 0.003 TYR B 51 PHE 0.021 0.003 PHE E 67 HIS 0.011 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00821 / 0.75 ( 9999) covalent geometry : angle 1.00880 / 0.83 (14395) hydrogen bonds : bond 0.13054 / 14.23 ( 565) hydrogen bonds : angle 5.08564 / 6.77 ( 1428) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 287 time to evaluate : 0.274 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 VAL cc_start: 0.8574 (OUTLIER) cc_final: 0.8295 (m) REVERT: B 59 LYS cc_start: 0.8613 (tttt) cc_final: 0.8115 (ttmt) REVERT: B 75 HIS cc_start: 0.7843 (t-90) cc_final: 0.7519 (t-170) REVERT: B 80 THR cc_start: 0.7724 (m) cc_final: 0.7506 (p) REVERT: B 84 MET cc_start: 0.6505 (mmm) cc_final: 0.5992 (mmm) REVERT: C 68 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7579 (tm-30) REVERT: D 62 MET cc_start: 0.8518 (mmm) cc_final: 0.8317 (mmt) REVERT: D 68 ASP cc_start: 0.7408 (t70) cc_final: 0.7071 (t0) REVERT: D 70 PHE cc_start: 0.8359 (t80) cc_final: 0.8112 (t80) REVERT: D 102 LEU cc_start: 0.8193 (mp) cc_final: 0.7980 (mp) REVERT: E 101 VAL cc_start: 0.8590 (OUTLIER) cc_final: 0.8310 (m) REVERT: F 29 ILE cc_start: 0.8916 (mm) cc_final: 0.8649 (mm) REVERT: F 59 LYS cc_start: 0.8493 (tttt) cc_final: 0.8104 (tttp) REVERT: F 75 HIS cc_start: 0.7852 (t-90) cc_final: 0.7381 (t70) REVERT: F 80 THR cc_start: 0.8092 (m) cc_final: 0.7851 (p) REVERT: G 31 VAL cc_start: 0.7902 (m) cc_final: 0.7436 (p) REVERT: H 37 TYR cc_start: 0.5303 (m-10) cc_final: 0.4669 (m-80) REVERT: H 62 MET cc_start: 0.8383 (mmm) cc_final: 0.8094 (mmt) REVERT: H 68 ASP cc_start: 0.7535 (t70) cc_final: 0.7027 (t0) outliers start: 16 outliers final: 2 residues processed: 292 average time/residue: 0.1547 time to fit residues: 56.2716 Evaluate side-chains 154 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 150 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 104 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 72 ASN E 68 GLN ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.048251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.036796 restraints weight = 65252.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.037929 restraints weight = 32996.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.038643 restraints weight = 21583.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.039109 restraints weight = 16665.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.039370 restraints weight = 14248.033| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9999 Z= 0.193 Angle : 0.865 10.625 14395 Z= 0.488 Chirality : 0.054 0.291 1666 Planarity : 0.007 0.056 1100 Dihedral : 33.867 168.088 2966 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.74 % Allowed : 16.55 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.91 (0.28), residues: 640 helix: -1.60 (0.20), residues: 460 sheet: None (None), residues: 0 loop : -2.35 (0.40), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 80 TYR 0.026 0.003 TYR F 88 PHE 0.015 0.002 PHE A 78 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.19 ( 9999) covalent geometry : angle 0.86532 / 0.49 (14395) hydrogen bonds : bond 0.07919 / 8.32 ( 565) hydrogen bonds : angle 3.97001 / 5.21 ( 1428) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 182 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.9307 (tttt) cc_final: 0.8831 (tptm) REVERT: B 63 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8105 (mt-10) REVERT: B 80 THR cc_start: 0.8814 (m) cc_final: 0.8429 (p) REVERT: C 31 VAL cc_start: 0.8915 (m) cc_final: 0.8284 (p) REVERT: C 33 GLN cc_start: 0.8833 (tt0) cc_final: 0.8017 (tm-30) REVERT: C 68 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7617 (tm-30) REVERT: C 72 ASN cc_start: 0.8261 (m-40) cc_final: 0.8057 (m-40) REVERT: D 93 GLU cc_start: 0.8393 (mp0) cc_final: 0.8066 (mm-30) REVERT: F 59 LYS cc_start: 0.9257 (tttt) cc_final: 0.8878 (tptm) REVERT: F 63 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7939 (mt-10) REVERT: F 80 THR cc_start: 0.8990 (m) cc_final: 0.8593 (p) REVERT: F 88 TYR cc_start: 0.8959 (m-80) cc_final: 0.8729 (m-80) REVERT: G 31 VAL cc_start: 0.8895 (m) cc_final: 0.8360 (p) REVERT: H 80 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8338 (tp) REVERT: H 93 GLU cc_start: 0.8410 (mp0) cc_final: 0.7923 (mm-30) outliers start: 21 outliers final: 11 residues processed: 189 average time/residue: 0.1242 time to fit residues: 30.9290 Evaluate side-chains 162 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 17 optimal weight: 30.0000 chunk 78 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 7 optimal weight: 30.0000 chunk 10 optimal weight: 50.0000 chunk 25 optimal weight: 0.0470 chunk 75 optimal weight: 5.9990 chunk 0 optimal weight: 50.0000 chunk 52 optimal weight: 0.6980 overall best weight: 2.7282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS D 84 ASN F 64 ASN ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.046269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.035074 restraints weight = 66920.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.036171 restraints weight = 33091.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.036900 restraints weight = 21438.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.037298 restraints weight = 16382.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.037595 restraints weight = 14116.543| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9999 Z= 0.211 Angle : 0.822 9.711 14395 Z= 0.462 Chirality : 0.052 0.246 1666 Planarity : 0.006 0.047 1100 Dihedral : 33.709 170.066 2962 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 5.16 % Allowed : 17.79 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.31), residues: 640 helix: -0.14 (0.23), residues: 472 sheet: None (None), residues: 0 loop : -2.12 (0.42), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 80 TYR 0.029 0.002 TYR C 61 PHE 0.009 0.001 PHE A 78 HIS 0.006 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.21 ( 9999) covalent geometry : angle 0.82206 / 0.46 (14395) hydrogen bonds : bond 0.07695 / 8.00 ( 565) hydrogen bonds : angle 3.63596 / 4.69 ( 1428) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7682 (tm-30) REVERT: A 85 GLN cc_start: 0.9086 (mt0) cc_final: 0.8674 (mt0) REVERT: A 90 MET cc_start: 0.9026 (mmm) cc_final: 0.8677 (mmp) REVERT: B 59 LYS cc_start: 0.9298 (tttt) cc_final: 0.8857 (tptm) REVERT: B 63 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8068 (mt-10) REVERT: B 80 THR cc_start: 0.8936 (m) cc_final: 0.8504 (p) REVERT: C 31 VAL cc_start: 0.9057 (m) cc_final: 0.8309 (p) REVERT: C 33 GLN cc_start: 0.8928 (tt0) cc_final: 0.8155 (tm-30) REVERT: C 68 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7481 (tm-30) REVERT: C 72 ASN cc_start: 0.8354 (m-40) cc_final: 0.7635 (m-40) REVERT: D 80 LEU cc_start: 0.9062 (mp) cc_final: 0.8334 (tp) REVERT: D 83 TYR cc_start: 0.7714 (m-10) cc_final: 0.7501 (m-10) REVERT: D 93 GLU cc_start: 0.8639 (mp0) cc_final: 0.8240 (mm-30) REVERT: E 68 GLN cc_start: 0.8758 (tp-100) cc_final: 0.8226 (tp-100) REVERT: E 86 SER cc_start: 0.9061 (t) cc_final: 0.8663 (m) REVERT: E 90 MET cc_start: 0.9066 (mmm) cc_final: 0.8806 (mmp) REVERT: F 63 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8126 (mt-10) REVERT: F 80 THR cc_start: 0.9054 (m) cc_final: 0.8574 (p) REVERT: F 84 MET cc_start: 0.8780 (tpp) cc_final: 0.8218 (tpp) REVERT: F 88 TYR cc_start: 0.9012 (m-80) cc_final: 0.8704 (m-80) REVERT: G 31 VAL cc_start: 0.8961 (m) cc_final: 0.8476 (p) REVERT: G 60 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.7676 (tt0) REVERT: H 93 GLU cc_start: 0.8643 (mp0) cc_final: 0.8198 (mm-30) outliers start: 29 outliers final: 19 residues processed: 171 average time/residue: 0.1138 time to fit residues: 26.0103 Evaluate side-chains 166 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 82 HIS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 20.0000 chunk 66 optimal weight: 0.0980 chunk 38 optimal weight: 0.6980 chunk 6 optimal weight: 20.0000 chunk 25 optimal weight: 4.9990 chunk 34 optimal weight: 30.0000 chunk 52 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 4 optimal weight: 20.0000 chunk 42 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS ** G 45 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 = 0.3307 r_free = 0.3307 target = 0.046931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.035933 restraints weight = 66895.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.037067 restraints weight = 32352.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.037834 restraints weight = 20667.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.038243 restraints weight = 15600.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.038551 restraints weight = 13332.843| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9999 Z= 0.158 Angle : 0.760 8.672 14395 Z= 0.430 Chirality : 0.049 0.226 1666 Planarity : 0.005 0.038 1100 Dihedral : 33.592 173.013 2962 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.38 % Allowed : 20.46 % Favored : 76.16 % 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: -0.30 (0.32), residues: 640 helix: 0.49 (0.23), residues: 472 sheet: None (None), residues: 0 loop : -2.07 (0.42), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 72 TYR 0.033 0.002 TYR D 83 PHE 0.008 0.001 PHE E 78 HIS 0.011 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.16 ( 9999) covalent geometry : angle 0.75965 / 0.43 (14395) hydrogen bonds : bond 0.06935 / 7.08 ( 565) hydrogen bonds : angle 3.43881 / 4.38 ( 1428) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.8987 (mt) cc_final: 0.8781 (mt) REVERT: A 68 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7557 (tm-30) REVERT: A 90 MET cc_start: 0.8994 (mmm) cc_final: 0.8657 (mmp) REVERT: B 80 THR cc_start: 0.8906 (m) cc_final: 0.8449 (p) REVERT: C 31 VAL cc_start: 0.8940 (m) cc_final: 0.8533 (p) REVERT: C 33 GLN cc_start: 0.8950 (tt0) cc_final: 0.8254 (tm-30) REVERT: C 61 TYR cc_start: 0.8642 (t80) cc_final: 0.8413 (t80) REVERT: C 68 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7467 (tm-30) REVERT: C 72 ASN cc_start: 0.8335 (m-40) cc_final: 0.7590 (m-40) REVERT: C 80 ARG cc_start: 0.6887 (tpm170) cc_final: 0.5980 (tpt90) REVERT: D 40 TYR cc_start: 0.8873 (m-80) cc_final: 0.8491 (m-80) REVERT: D 80 LEU cc_start: 0.9047 (mp) cc_final: 0.8518 (tp) REVERT: D 93 GLU cc_start: 0.8567 (mp0) cc_final: 0.8239 (mm-30) REVERT: E 62 ILE cc_start: 0.8951 (mt) cc_final: 0.8745 (mt) REVERT: E 68 GLN cc_start: 0.8669 (tp-100) cc_final: 0.8149 (tp-100) REVERT: E 86 SER cc_start: 0.9014 (t) cc_final: 0.8583 (m) REVERT: E 90 MET cc_start: 0.9036 (mmm) cc_final: 0.8738 (mmp) REVERT: F 63 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8165 (mt-10) REVERT: F 84 MET cc_start: 0.8748 (tpp) cc_final: 0.8415 (tpp) REVERT: F 88 TYR cc_start: 0.8988 (m-80) cc_final: 0.8680 (m-80) REVERT: G 31 VAL cc_start: 0.8944 (m) cc_final: 0.8425 (p) REVERT: G 42 HIS cc_start: 0.8668 (m90) cc_final: 0.8448 (m90) REVERT: G 60 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.7631 (tt0) REVERT: H 80 LEU cc_start: 0.9022 (mp) cc_final: 0.8395 (tp) REVERT: H 93 GLU cc_start: 0.8563 (mp0) cc_final: 0.8253 (mm-30) outliers start: 19 outliers final: 15 residues processed: 167 average time/residue: 0.1078 time to fit residues: 24.0936 Evaluate side-chains 158 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain E residue 85 GLN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 0.9980 chunk 51 optimal weight: 0.4980 chunk 1 optimal weight: 30.0000 chunk 50 optimal weight: 7.9990 chunk 71 optimal weight: 0.6980 chunk 36 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 0.0170 overall best weight: 1.0420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.047059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.035972 restraints weight = 66302.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.037095 restraints weight = 31835.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.037823 restraints weight = 20360.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.038242 restraints weight = 15471.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.038538 restraints weight = 13227.249| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9999 Z= 0.155 Angle : 0.747 8.923 14395 Z= 0.419 Chirality : 0.048 0.232 1666 Planarity : 0.005 0.038 1100 Dihedral : 33.552 177.889 2962 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.45 % Allowed : 19.40 % Favored : 76.16 % 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: 0.32 (0.33), residues: 640 helix: 0.94 (0.24), residues: 472 sheet: None (None), residues: 0 loop : -1.80 (0.44), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 128 TYR 0.021 0.002 TYR D 121 PHE 0.007 0.001 PHE A 78 HIS 0.006 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.15 ( 9999) covalent geometry : angle 0.74665 / 0.42 (14395) hydrogen bonds : bond 0.06783 / 6.96 ( 565) hydrogen bonds : angle 3.36898 / 4.30 ( 1428) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7551 (tm-30) REVERT: A 86 SER cc_start: 0.9053 (t) cc_final: 0.8563 (m) REVERT: A 90 MET cc_start: 0.9044 (mmm) cc_final: 0.8650 (mmp) REVERT: B 80 THR cc_start: 0.8949 (m) cc_final: 0.8480 (p) REVERT: B 84 MET cc_start: 0.8299 (tpp) cc_final: 0.8025 (tpp) REVERT: B 92 ARG cc_start: 0.9031 (ttm-80) cc_final: 0.8745 (tpp80) REVERT: C 31 VAL cc_start: 0.8992 (m) cc_final: 0.8602 (p) REVERT: C 33 GLN cc_start: 0.8972 (tt0) cc_final: 0.8347 (tm-30) REVERT: C 63 THR cc_start: 0.9265 (m) cc_final: 0.8992 (p) REVERT: C 68 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7514 (tm-30) REVERT: C 72 ASN cc_start: 0.8308 (m-40) cc_final: 0.7916 (m-40) REVERT: C 80 ARG cc_start: 0.6833 (tpm170) cc_final: 0.6057 (tpt90) REVERT: D 40 TYR cc_start: 0.8844 (m-80) cc_final: 0.8452 (m-80) REVERT: D 80 LEU cc_start: 0.8954 (mp) cc_final: 0.8164 (tp) REVERT: E 68 GLN cc_start: 0.8694 (tp-100) cc_final: 0.8154 (tp-100) REVERT: E 86 SER cc_start: 0.9050 (t) cc_final: 0.8582 (m) REVERT: E 90 MET cc_start: 0.9037 (mmm) cc_final: 0.8732 (mmp) REVERT: F 63 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8144 (mt-10) REVERT: F 84 MET cc_start: 0.8785 (tpp) cc_final: 0.8363 (tpp) REVERT: F 88 TYR cc_start: 0.8979 (m-80) cc_final: 0.8665 (m-80) REVERT: G 31 VAL cc_start: 0.8981 (m) cc_final: 0.8460 (p) REVERT: G 42 HIS cc_start: 0.8636 (m90) cc_final: 0.8371 (m90) REVERT: H 80 LEU cc_start: 0.9012 (mp) cc_final: 0.8630 (mm) outliers start: 25 outliers final: 19 residues processed: 162 average time/residue: 0.1057 time to fit residues: 23.0558 Evaluate side-chains 159 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 99 ARG Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 20 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 30.0000 chunk 13 optimal weight: 20.0000 chunk 65 optimal weight: 8.9990 chunk 59 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 12 optimal weight: 20.0000 chunk 77 optimal weight: 0.9990 chunk 4 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS ** G 45 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 = 0.3291 r_free = 0.3291 target = 0.046470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.035381 restraints weight = 67206.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.036486 restraints weight = 32652.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.037207 restraints weight = 20988.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.037654 restraints weight = 15974.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.037913 restraints weight = 13564.370| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9999 Z= 0.185 Angle : 0.759 9.235 14395 Z= 0.422 Chirality : 0.048 0.234 1666 Planarity : 0.005 0.039 1100 Dihedral : 33.507 179.903 2962 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.27 % Allowed : 22.95 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.59 (0.33), residues: 640 helix: 1.10 (0.24), residues: 488 sheet: None (None), residues: 0 loop : -1.87 (0.45), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 80 TYR 0.026 0.002 TYR G 61 PHE 0.009 0.001 PHE G 101 HIS 0.004 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.18 ( 9999) covalent geometry : angle 0.75892 / 0.42 (14395) hydrogen bonds : bond 0.06919 / 7.13 ( 565) hydrogen bonds : angle 3.39489 / 4.35 ( 1428) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7670 (tm-30) REVERT: B 80 THR cc_start: 0.9053 (m) cc_final: 0.8557 (p) REVERT: C 31 VAL cc_start: 0.9190 (m) cc_final: 0.8825 (p) REVERT: C 33 GLN cc_start: 0.9012 (tt0) cc_final: 0.8452 (tm-30) REVERT: C 63 THR cc_start: 0.9349 (m) cc_final: 0.9107 (p) REVERT: C 68 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7550 (tm-30) REVERT: C 72 ASN cc_start: 0.8298 (m-40) cc_final: 0.7900 (m-40) REVERT: E 68 GLN cc_start: 0.8734 (tp-100) cc_final: 0.8262 (tp-100) REVERT: E 86 SER cc_start: 0.9083 (t) cc_final: 0.8716 (m) REVERT: E 90 MET cc_start: 0.9014 (mmm) cc_final: 0.8691 (mmp) REVERT: F 63 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8167 (mt-10) REVERT: F 84 MET cc_start: 0.8850 (tpp) cc_final: 0.8471 (tpp) REVERT: F 88 TYR cc_start: 0.8944 (m-80) cc_final: 0.8690 (m-80) REVERT: G 31 VAL cc_start: 0.9069 (m) cc_final: 0.8603 (p) REVERT: G 42 HIS cc_start: 0.8610 (m90) cc_final: 0.8372 (m90) REVERT: G 60 GLU cc_start: 0.8931 (tt0) cc_final: 0.7738 (tt0) outliers start: 24 outliers final: 15 residues processed: 152 average time/residue: 0.1057 time to fit residues: 21.8276 Evaluate side-chains 150 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 82 HIS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 1 optimal weight: 30.0000 chunk 4 optimal weight: 20.0000 chunk 42 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS ** G 45 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 = 0.3300 r_free = 0.3300 target = 0.046741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.035616 restraints weight = 67409.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.036714 restraints weight = 32948.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.037436 restraints weight = 21257.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.037866 restraints weight = 16241.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.038153 restraints weight = 13875.132| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9999 Z= 0.164 Angle : 0.746 8.846 14395 Z= 0.415 Chirality : 0.048 0.243 1666 Planarity : 0.004 0.039 1100 Dihedral : 33.461 179.025 2962 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.20 % Allowed : 25.09 % Favored : 71.71 % 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: 0.80 (0.33), residues: 640 helix: 1.24 (0.24), residues: 482 sheet: None (None), residues: 0 loop : -1.65 (0.46), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 128 TYR 0.017 0.002 TYR D 83 PHE 0.007 0.001 PHE D 70 HIS 0.014 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.16 ( 9999) covalent geometry : angle 0.74624 / 0.41 (14395) hydrogen bonds : bond 0.06647 / 6.84 ( 565) hydrogen bonds : angle 3.36896 / 4.30 ( 1428) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7540 (tm-30) REVERT: B 80 THR cc_start: 0.8924 (m) cc_final: 0.8489 (p) REVERT: C 31 VAL cc_start: 0.9182 (m) cc_final: 0.8812 (p) REVERT: C 33 GLN cc_start: 0.9038 (tt0) cc_final: 0.8487 (tm-30) REVERT: C 63 THR cc_start: 0.9367 (m) cc_final: 0.9123 (p) REVERT: C 68 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7556 (tm-30) REVERT: C 72 ASN cc_start: 0.8295 (m-40) cc_final: 0.7881 (m-40) REVERT: D 40 TYR cc_start: 0.8734 (m-80) cc_final: 0.8364 (m-80) REVERT: E 68 GLN cc_start: 0.8743 (tp-100) cc_final: 0.8005 (tp-100) REVERT: E 90 MET cc_start: 0.9011 (mmm) cc_final: 0.8689 (mmp) REVERT: F 63 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8148 (mt-10) REVERT: F 84 MET cc_start: 0.8849 (tpp) cc_final: 0.8478 (tpp) REVERT: F 88 TYR cc_start: 0.8927 (m-80) cc_final: 0.8715 (m-80) REVERT: G 42 HIS cc_start: 0.8606 (m90) cc_final: 0.8355 (m90) REVERT: G 60 GLU cc_start: 0.8927 (tt0) cc_final: 0.7762 (tt0) outliers start: 18 outliers final: 16 residues processed: 153 average time/residue: 0.1145 time to fit residues: 23.4012 Evaluate side-chains 155 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 99 ARG Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 62 optimal weight: 0.0980 chunk 35 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 19 optimal weight: 30.0000 chunk 76 optimal weight: 2.9990 chunk 12 optimal weight: 20.0000 chunk 78 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 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 = 0.3305 r_free = 0.3305 target = 0.046849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.035842 restraints weight = 66378.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.036953 restraints weight = 32078.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.037689 restraints weight = 20504.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.038148 restraints weight = 15548.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.038409 restraints weight = 13123.606| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9999 Z= 0.155 Angle : 0.746 11.902 14395 Z= 0.412 Chirality : 0.047 0.255 1666 Planarity : 0.004 0.039 1100 Dihedral : 33.409 176.734 2962 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.38 % Allowed : 25.80 % Favored : 70.82 % 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: 1.05 (0.33), residues: 640 helix: 1.43 (0.24), residues: 482 sheet: None (None), residues: 0 loop : -1.59 (0.47), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 128 TYR 0.025 0.002 TYR G 61 PHE 0.005 0.001 PHE G 29 HIS 0.003 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.16 ( 9999) covalent geometry : angle 0.74647 / 0.41 (14395) hydrogen bonds : bond 0.06511 / 6.69 ( 565) hydrogen bonds : angle 3.32641 / 4.25 ( 1428) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.7524 (tm-30) REVERT: B 75 HIS cc_start: 0.8501 (t70) cc_final: 0.8165 (t-170) REVERT: B 80 THR cc_start: 0.8995 (m) cc_final: 0.8686 (p) REVERT: C 31 VAL cc_start: 0.9204 (m) cc_final: 0.8746 (p) REVERT: C 33 GLN cc_start: 0.9074 (tt0) cc_final: 0.8520 (tm-30) REVERT: C 63 THR cc_start: 0.9366 (m) cc_final: 0.9109 (p) REVERT: C 68 GLU cc_start: 0.8299 (tm-30) cc_final: 0.7567 (tm-30) REVERT: C 72 ASN cc_start: 0.8331 (m-40) cc_final: 0.7905 (m-40) REVERT: D 40 TYR cc_start: 0.8703 (m-80) cc_final: 0.8323 (m-80) REVERT: E 68 GLN cc_start: 0.8764 (tp-100) cc_final: 0.7992 (tp-100) REVERT: E 90 MET cc_start: 0.9008 (mmm) cc_final: 0.8651 (mmp) REVERT: E 120 MET cc_start: 0.8603 (mtt) cc_final: 0.8295 (mtt) REVERT: F 63 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8174 (mt-10) REVERT: F 84 MET cc_start: 0.8837 (tpp) cc_final: 0.8450 (tpp) REVERT: G 31 VAL cc_start: 0.8942 (OUTLIER) cc_final: 0.8470 (p) REVERT: G 42 HIS cc_start: 0.8598 (m90) cc_final: 0.8342 (m90) REVERT: G 60 GLU cc_start: 0.8983 (tt0) cc_final: 0.7903 (tt0) REVERT: H 99 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.8167 (mtm180) outliers start: 19 outliers final: 15 residues processed: 157 average time/residue: 0.1045 time to fit residues: 21.9484 Evaluate side-chains 158 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 82 HIS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 99 ARG Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 76 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 17 optimal weight: 30.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 45 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 = 0.3310 r_free = 0.3310 target = 0.047027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.036119 restraints weight = 65685.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.037259 restraints weight = 30647.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.037977 restraints weight = 19174.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.038464 restraints weight = 14408.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.038718 restraints weight = 12087.291| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9999 Z= 0.152 Angle : 0.730 9.557 14395 Z= 0.406 Chirality : 0.047 0.265 1666 Planarity : 0.004 0.039 1100 Dihedral : 33.337 174.705 2962 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.31 % Allowed : 26.33 % Favored : 71.35 % 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 (0.33), residues: 640 helix: 1.57 (0.24), residues: 482 sheet: None (None), residues: 0 loop : -1.61 (0.46), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 128 TYR 0.024 0.002 TYR C 61 PHE 0.004 0.001 PHE H 70 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.15 ( 9999) covalent geometry : angle 0.72981 / 0.41 (14395) hydrogen bonds : bond 0.06439 / 6.64 ( 565) hydrogen bonds : angle 3.33912 / 4.31 ( 1428) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7519 (tm-30) REVERT: B 75 HIS cc_start: 0.8480 (t70) cc_final: 0.8172 (t-170) REVERT: B 80 THR cc_start: 0.9054 (m) cc_final: 0.8745 (p) REVERT: B 84 MET cc_start: 0.8550 (tpp) cc_final: 0.8186 (tpp) REVERT: C 31 VAL cc_start: 0.9209 (m) cc_final: 0.8754 (p) REVERT: C 33 GLN cc_start: 0.9091 (tt0) cc_final: 0.8563 (tm-30) REVERT: C 63 THR cc_start: 0.9366 (m) cc_final: 0.9109 (p) REVERT: C 68 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7861 (tm-30) REVERT: C 72 ASN cc_start: 0.8314 (m-40) cc_final: 0.7976 (m110) REVERT: D 40 TYR cc_start: 0.8740 (m-80) cc_final: 0.8355 (m-80) REVERT: E 68 GLN cc_start: 0.8775 (tp-100) cc_final: 0.8002 (tp-100) REVERT: E 90 MET cc_start: 0.9029 (mmm) cc_final: 0.8660 (mmp) REVERT: E 120 MET cc_start: 0.8572 (mtt) cc_final: 0.8265 (mtt) REVERT: F 63 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8228 (mt-10) REVERT: G 31 VAL cc_start: 0.8932 (m) cc_final: 0.8402 (p) REVERT: G 42 HIS cc_start: 0.8605 (m90) cc_final: 0.8349 (m90) REVERT: G 60 GLU cc_start: 0.8981 (tt0) cc_final: 0.7922 (tt0) REVERT: H 99 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.8141 (mtm180) outliers start: 13 outliers final: 9 residues processed: 151 average time/residue: 0.1111 time to fit residues: 22.5675 Evaluate side-chains 150 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain D residue 82 HIS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 99 ARG Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 53 optimal weight: 0.9990 chunk 4 optimal weight: 20.0000 chunk 75 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 5 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 45 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 = 0.3299 r_free = 0.3299 target = 0.046714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.035681 restraints weight = 66379.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.036764 restraints weight = 32344.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.037494 restraints weight = 20791.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.037941 restraints weight = 15825.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.038198 restraints weight = 13428.011| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.4923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9999 Z= 0.170 Angle : 0.749 9.649 14395 Z= 0.412 Chirality : 0.047 0.269 1666 Planarity : 0.004 0.040 1100 Dihedral : 33.288 173.229 2962 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.31 % Allowed : 27.05 % Favored : 70.64 % 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: 1.15 (0.33), residues: 640 helix: 1.58 (0.24), residues: 488 sheet: None (None), residues: 0 loop : -1.98 (0.42), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 79 TYR 0.024 0.002 TYR G 61 PHE 0.005 0.001 PHE E 84 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.17 ( 9999) covalent geometry : angle 0.74897 / 0.41 (14395) hydrogen bonds : bond 0.06619 / 6.86 ( 565) hydrogen bonds : angle 3.42559 / 4.46 ( 1428) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.7564 (tm-30) REVERT: A 90 MET cc_start: 0.9028 (tpp) cc_final: 0.8770 (mmp) REVERT: B 75 HIS cc_start: 0.8477 (t70) cc_final: 0.8116 (t-170) REVERT: B 80 THR cc_start: 0.9075 (m) cc_final: 0.8742 (p) REVERT: B 84 MET cc_start: 0.8592 (tpp) cc_final: 0.8305 (tpp) REVERT: C 31 VAL cc_start: 0.9309 (m) cc_final: 0.8878 (p) REVERT: C 33 GLN cc_start: 0.9099 (tt0) cc_final: 0.8597 (tm-30) REVERT: C 63 THR cc_start: 0.9395 (m) cc_final: 0.9152 (p) REVERT: C 68 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7812 (tm-30) REVERT: C 72 ASN cc_start: 0.8344 (m-40) cc_final: 0.8124 (m110) REVERT: D 40 TYR cc_start: 0.8686 (m-80) cc_final: 0.8327 (m-80) REVERT: D 99 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8231 (mpp80) REVERT: E 68 GLN cc_start: 0.8773 (tp-100) cc_final: 0.8312 (tp-100) REVERT: E 90 MET cc_start: 0.8978 (mmm) cc_final: 0.8617 (mmp) REVERT: E 120 MET cc_start: 0.8722 (mtt) cc_final: 0.8450 (mtt) REVERT: F 63 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8275 (mt-10) REVERT: F 84 MET cc_start: 0.8593 (tpp) cc_final: 0.8259 (tpp) REVERT: G 27 LEU cc_start: 0.8072 (mm) cc_final: 0.7783 (mp) REVERT: G 31 VAL cc_start: 0.9063 (m) cc_final: 0.8571 (p) REVERT: G 42 HIS cc_start: 0.8577 (m90) cc_final: 0.8335 (m90) REVERT: G 60 GLU cc_start: 0.9028 (tt0) cc_final: 0.7915 (tt0) REVERT: H 99 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.8131 (mtm180) outliers start: 13 outliers final: 7 residues processed: 140 average time/residue: 0.1065 time to fit residues: 20.2577 Evaluate side-chains 140 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain D residue 82 HIS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain H residue 99 ARG Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 27 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 76 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 2 optimal weight: 20.0000 chunk 25 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 8 optimal weight: 30.0000 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 45 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 = 0.3281 r_free = 0.3281 target = 0.046411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.035201 restraints weight = 65521.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.036268 restraints weight = 32247.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.036987 restraints weight = 20821.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.037434 restraints weight = 15907.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.037638 restraints weight = 13523.188| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.4969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9999 Z= 0.174 Angle : 0.750 9.299 14395 Z= 0.414 Chirality : 0.048 0.271 1666 Planarity : 0.004 0.039 1100 Dihedral : 33.247 173.177 2962 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.96 % Allowed : 26.69 % Favored : 71.35 % 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: 1.00 (0.33), residues: 640 helix: 1.43 (0.23), residues: 490 sheet: None (None), residues: 0 loop : -1.94 (0.43), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 128 TYR 0.061 0.003 TYR D 83 PHE 0.006 0.001 PHE E 78 HIS 0.011 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.17 ( 9999) covalent geometry : angle 0.74983 / 0.41 (14395) hydrogen bonds : bond 0.06560 / 6.81 ( 565) hydrogen bonds : angle 3.46856 / 4.48 ( 1428) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1545.75 seconds wall clock time: 28 minutes 14.76 seconds (1694.76 seconds total)