Starting phenix.real_space_refine on Sat Aug 23 15:07:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pnv_17786/08_2025/8pnv_17786.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pnv_17786/08_2025/8pnv_17786.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.048 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pnv_17786/08_2025/8pnv_17786.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pnv_17786/08_2025/8pnv_17786.map" model { file = "/net/cci-nas-00/data/ceres_data/8pnv_17786/08_2025/8pnv_17786.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pnv_17786/08_2025/8pnv_17786.cif" } resolution = 2.048 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 6 7.16 5 S 60 5.16 5 C 8202 2.51 5 N 2106 2.21 5 O 2724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13098 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1170 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 9, 'TRANS': 145} Chain: "D" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 883 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "E" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "F" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "G" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "H" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "I" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "J" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "K" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "L" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Restraints were copied for chains: B, C, G, H, I, E, F, J, K, L Time building chain proxies: 2.19, per 1000 atoms: 0.17 Number of scatterers: 13098 At special positions: 0 Unit cell: (79.2, 81.18, 168.3, 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) Fe 6 26.01 S 60 16.00 O 2724 8.00 N 2106 7.00 C 8202 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 495.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2796 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 24 sheets defined 47.2% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 3 through 33 removed outlier: 3.543A pdb=" N GLY A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 75 Proline residue: A 61 - end of helix Processing helix chain 'A' and resid 76 through 79 removed outlier: 4.021A pdb=" N GLY A 79 " --> pdb=" O PRO A 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 76 through 79' Processing helix chain 'A' and resid 81 through 107 removed outlier: 3.906A pdb=" N ASN A 107 " --> pdb=" O TYR A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 155 Proline residue: A 134 - end of helix removed outlier: 3.654A pdb=" N LEU A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 33 removed outlier: 3.543A pdb=" N GLY B 26 " --> pdb=" O LEU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 75 Proline residue: B 61 - end of helix Processing helix chain 'B' and resid 76 through 79 removed outlier: 4.021A pdb=" N GLY B 79 " --> pdb=" O PRO B 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 76 through 79' Processing helix chain 'B' and resid 81 through 107 removed outlier: 3.906A pdb=" N ASN B 107 " --> pdb=" O TYR B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 155 Proline residue: B 134 - end of helix removed outlier: 3.654A pdb=" N LEU B 141 " --> pdb=" O LEU B 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 33 removed outlier: 3.543A pdb=" N GLY C 26 " --> pdb=" O LEU C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 75 Proline residue: C 61 - end of helix Processing helix chain 'C' and resid 76 through 79 removed outlier: 4.021A pdb=" N GLY C 79 " --> pdb=" O PRO C 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 76 through 79' Processing helix chain 'C' and resid 81 through 107 removed outlier: 3.906A pdb=" N ASN C 107 " --> pdb=" O TYR C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 155 Proline residue: C 134 - end of helix removed outlier: 3.654A pdb=" N LEU C 141 " --> pdb=" O LEU C 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 66 Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'E' and resid 63 through 66 Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'F' and resid 63 through 66 Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'G' and resid 3 through 33 removed outlier: 3.543A pdb=" N GLY G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 75 Proline residue: G 61 - end of helix Processing helix chain 'G' and resid 76 through 79 removed outlier: 4.021A pdb=" N GLY G 79 " --> pdb=" O PRO G 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 76 through 79' Processing helix chain 'G' and resid 81 through 107 removed outlier: 3.906A pdb=" N ASN G 107 " --> pdb=" O TYR G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 155 Proline residue: G 134 - end of helix removed outlier: 3.654A pdb=" N LEU G 141 " --> pdb=" O LEU G 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 33 removed outlier: 3.543A pdb=" N GLY H 26 " --> pdb=" O LEU H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 75 Proline residue: H 61 - end of helix Processing helix chain 'H' and resid 76 through 79 removed outlier: 4.021A pdb=" N GLY H 79 " --> pdb=" O PRO H 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 76 through 79' Processing helix chain 'H' and resid 81 through 107 removed outlier: 3.906A pdb=" N ASN H 107 " --> pdb=" O TYR H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 155 Proline residue: H 134 - end of helix removed outlier: 3.654A pdb=" N LEU H 141 " --> pdb=" O LEU H 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 33 removed outlier: 3.543A pdb=" N GLY I 26 " --> pdb=" O LEU I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 75 Proline residue: I 61 - end of helix Processing helix chain 'I' and resid 76 through 79 removed outlier: 4.021A pdb=" N GLY I 79 " --> pdb=" O PRO I 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 76 through 79' Processing helix chain 'I' and resid 81 through 107 removed outlier: 3.906A pdb=" N ASN I 107 " --> pdb=" O TYR I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 155 Proline residue: I 134 - end of helix removed outlier: 3.655A pdb=" N LEU I 141 " --> pdb=" O LEU I 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 66 Processing helix chain 'J' and resid 88 through 92 Processing helix chain 'K' and resid 63 through 66 Processing helix chain 'K' and resid 88 through 92 Processing helix chain 'L' and resid 63 through 66 Processing helix chain 'L' and resid 88 through 92 Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 38 removed outlier: 5.580A pdb=" N GLU A 36 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE A 43 " --> pdb=" O GLU A 36 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE A 38 " --> pdb=" O TYR A 41 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 34 through 38 removed outlier: 5.580A pdb=" N GLU B 36 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE B 43 " --> pdb=" O GLU B 36 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE B 38 " --> pdb=" O TYR B 41 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 34 through 38 removed outlier: 5.579A pdb=" N GLU C 36 " --> pdb=" O ILE C 43 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE C 43 " --> pdb=" O GLU C 36 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE C 38 " --> pdb=" O TYR C 41 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 6 through 8 Processing sheet with id=AA5, first strand: chain 'D' and resid 12 through 14 removed outlier: 6.795A pdb=" N VAL D 35 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N THR D 51 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP D 37 " --> pdb=" O VAL D 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 12 through 14 Processing sheet with id=AA7, first strand: chain 'E' and resid 6 through 8 Processing sheet with id=AA8, first strand: chain 'E' and resid 12 through 14 removed outlier: 6.795A pdb=" N VAL E 35 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N THR E 51 " --> pdb=" O VAL E 35 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP E 37 " --> pdb=" O VAL E 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 12 through 14 Processing sheet with id=AB1, first strand: chain 'F' and resid 6 through 8 Processing sheet with id=AB2, first strand: chain 'F' and resid 12 through 14 removed outlier: 6.795A pdb=" N VAL F 35 " --> pdb=" O THR F 51 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N THR F 51 " --> pdb=" O VAL F 35 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP F 37 " --> pdb=" O VAL F 49 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 12 through 14 Processing sheet with id=AB4, first strand: chain 'G' and resid 34 through 38 removed outlier: 5.580A pdb=" N GLU G 36 " --> pdb=" O ILE G 43 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE G 43 " --> pdb=" O GLU G 36 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE G 38 " --> pdb=" O TYR G 41 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 34 through 38 removed outlier: 5.580A pdb=" N GLU H 36 " --> pdb=" O ILE H 43 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE H 43 " --> pdb=" O GLU H 36 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE H 38 " --> pdb=" O TYR H 41 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 34 through 38 removed outlier: 5.579A pdb=" N GLU I 36 " --> pdb=" O ILE I 43 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE I 43 " --> pdb=" O GLU I 36 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE I 38 " --> pdb=" O TYR I 41 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 6 through 8 Processing sheet with id=AB8, first strand: chain 'J' and resid 12 through 14 removed outlier: 6.795A pdb=" N VAL J 35 " --> pdb=" O THR J 51 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N THR J 51 " --> pdb=" O VAL J 35 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP J 37 " --> pdb=" O VAL J 49 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 12 through 14 Processing sheet with id=AC1, first strand: chain 'K' and resid 6 through 8 Processing sheet with id=AC2, first strand: chain 'K' and resid 12 through 14 removed outlier: 6.795A pdb=" N VAL K 35 " --> pdb=" O THR K 51 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N THR K 51 " --> pdb=" O VAL K 35 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP K 37 " --> pdb=" O VAL K 49 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 12 through 14 Processing sheet with id=AC4, first strand: chain 'L' and resid 6 through 8 Processing sheet with id=AC5, first strand: chain 'L' and resid 12 through 14 removed outlier: 6.795A pdb=" N VAL L 35 " --> pdb=" O THR L 51 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N THR L 51 " --> pdb=" O VAL L 35 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP L 37 " --> pdb=" O VAL L 49 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 12 through 14 810 hydrogen bonds defined for protein. 2196 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.23 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 5428 1.39 - 1.55: 7412 1.55 - 1.72: 0 1.72 - 1.88: 102 1.88 - 2.05: 24 Bond restraints: 12966 Sorted by residual: bond pdb=" CB ASN L 53 " pdb=" CG ASN L 53 " ideal model delta sigma weight residual 1.516 1.476 0.040 2.50e-02 1.60e+03 2.58e+00 bond pdb=" CB ASN F 53 " pdb=" CG ASN F 53 " ideal model delta sigma weight residual 1.516 1.476 0.040 2.50e-02 1.60e+03 2.55e+00 bond pdb=" CB ASN K 53 " pdb=" CG ASN K 53 " ideal model delta sigma weight residual 1.516 1.477 0.039 2.50e-02 1.60e+03 2.49e+00 bond pdb=" CB ASN E 53 " pdb=" CG ASN E 53 " ideal model delta sigma weight residual 1.516 1.477 0.039 2.50e-02 1.60e+03 2.48e+00 bond pdb=" CB ASN D 53 " pdb=" CG ASN D 53 " ideal model delta sigma weight residual 1.516 1.477 0.039 2.50e-02 1.60e+03 2.44e+00 ... (remaining 12961 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 17009 1.39 - 2.78: 495 2.78 - 4.17: 112 4.17 - 5.56: 36 5.56 - 6.95: 18 Bond angle restraints: 17670 Sorted by residual: angle pdb=" C ILE J 52 " pdb=" N ASN J 53 " pdb=" CA ASN J 53 " ideal model delta sigma weight residual 121.06 128.01 -6.95 1.88e+00 2.83e-01 1.37e+01 angle pdb=" C ILE D 52 " pdb=" N ASN D 53 " pdb=" CA ASN D 53 " ideal model delta sigma weight residual 121.06 128.01 -6.95 1.88e+00 2.83e-01 1.36e+01 angle pdb=" C ILE K 52 " pdb=" N ASN K 53 " pdb=" CA ASN K 53 " ideal model delta sigma weight residual 121.06 127.97 -6.91 1.88e+00 2.83e-01 1.35e+01 angle pdb=" C ILE E 52 " pdb=" N ASN E 53 " pdb=" CA ASN E 53 " ideal model delta sigma weight residual 121.06 127.97 -6.91 1.88e+00 2.83e-01 1.35e+01 angle pdb=" C ILE L 52 " pdb=" N ASN L 53 " pdb=" CA ASN L 53 " ideal model delta sigma weight residual 121.06 127.96 -6.90 1.88e+00 2.83e-01 1.35e+01 ... (remaining 17665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 6192 17.03 - 34.07: 756 34.07 - 51.10: 138 51.10 - 68.14: 108 68.14 - 85.17: 30 Dihedral angle restraints: 7224 sinusoidal: 2754 harmonic: 4470 Sorted by residual: dihedral pdb=" CA ASP L 74 " pdb=" CB ASP L 74 " pdb=" CG ASP L 74 " pdb=" OD1 ASP L 74 " ideal model delta sinusoidal sigma weight residual -30.00 -89.11 59.11 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP F 74 " pdb=" CB ASP F 74 " pdb=" CG ASP F 74 " pdb=" OD1 ASP F 74 " ideal model delta sinusoidal sigma weight residual -30.00 -89.10 59.10 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP J 74 " pdb=" CB ASP J 74 " pdb=" CG ASP J 74 " pdb=" OD1 ASP J 74 " ideal model delta sinusoidal sigma weight residual -30.00 -89.10 59.10 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 7221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1075 0.030 - 0.059: 444 0.059 - 0.089: 200 0.089 - 0.119: 84 0.119 - 0.148: 21 Chirality restraints: 1824 Sorted by residual: chirality pdb=" CA ILE H 43 " pdb=" N ILE H 43 " pdb=" C ILE H 43 " pdb=" CB ILE H 43 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CA ILE A 43 " pdb=" N ILE A 43 " pdb=" C ILE A 43 " pdb=" CB ILE A 43 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CA ILE G 43 " pdb=" N ILE G 43 " pdb=" C ILE G 43 " pdb=" CB ILE G 43 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.51e-01 ... (remaining 1821 not shown) Planarity restraints: 2244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP L 63 " 0.044 5.00e-02 4.00e+02 6.67e-02 7.12e+00 pdb=" N PRO L 64 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO L 64 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO L 64 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 63 " -0.044 5.00e-02 4.00e+02 6.67e-02 7.11e+00 pdb=" N PRO D 64 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO D 64 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 64 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 63 " 0.044 5.00e-02 4.00e+02 6.66e-02 7.11e+00 pdb=" N PRO E 64 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO E 64 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 64 " 0.037 5.00e-02 4.00e+02 ... (remaining 2241 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 210 2.61 - 3.18: 11100 3.18 - 3.76: 22159 3.76 - 4.33: 30704 4.33 - 4.90: 49905 Nonbonded interactions: 114078 Sorted by model distance: nonbonded pdb=" SG CYS F 23 " pdb=" SG CYS F 97 " model vdw 2.040 3.760 nonbonded pdb=" SG CYS J 23 " pdb=" SG CYS J 97 " model vdw 2.040 3.760 nonbonded pdb=" SG CYS L 23 " pdb=" SG CYS L 97 " model vdw 2.040 3.760 nonbonded pdb=" SG CYS E 23 " pdb=" SG CYS E 97 " model vdw 2.040 3.760 nonbonded pdb=" SG CYS D 23 " pdb=" SG CYS D 97 " model vdw 2.040 3.760 ... (remaining 114073 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 12.130 Find NCS groups from input model: 0.130 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:6.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 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 : 0.004 0.044 12972 Z= 0.187 Angle : 0.662 6.948 17670 Z= 0.340 Chirality : 0.043 0.148 1824 Planarity : 0.006 0.067 2244 Dihedral : 17.458 85.170 4428 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.87 % Allowed : 19.62 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.57 (0.20), residues: 1602 helix: 3.28 (0.19), residues: 678 sheet: 0.89 (0.31), residues: 228 loop : 0.43 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 112 TYR 0.013 0.002 TYR A 103 PHE 0.016 0.002 PHE L 48 TRP 0.008 0.002 TRP C 28 HIS 0.002 0.001 HIS I 12 Details of bonding type rmsd covalent geometry : bond 0.00397 (12966) covalent geometry : angle 0.66177 (17670) hydrogen bonds : bond 0.11184 ( 774) hydrogen bonds : angle 5.22320 ( 2196) Misc. bond : bond 0.00155 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 260 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: F 107 GLU cc_start: 0.6856 (tt0) cc_final: 0.6574 (tt0) REVERT: J 107 GLU cc_start: 0.6895 (tt0) cc_final: 0.6589 (tt0) outliers start: 36 outliers final: 32 residues processed: 296 average time/residue: 0.5842 time to fit residues: 188.5631 Evaluate side-chains 286 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 254 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 66 LYS Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 118 SER Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 66 LYS Chi-restraints excluded: chain L residue 118 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.0870 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 ASN D 86 ASN G 30 ASN K 86 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.147726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.121023 restraints weight = 10753.234| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 0.94 r_work: 0.3239 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.0876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12972 Z= 0.166 Angle : 0.604 6.042 17670 Z= 0.307 Chirality : 0.042 0.133 1824 Planarity : 0.004 0.041 2244 Dihedral : 10.307 79.668 1850 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.79 % Allowed : 17.78 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.52 (0.20), residues: 1602 helix: 3.39 (0.19), residues: 678 sheet: 0.68 (0.29), residues: 228 loop : 0.29 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 112 TYR 0.008 0.002 TYR L 96 PHE 0.016 0.002 PHE D 48 TRP 0.005 0.001 TRP J 54 HIS 0.002 0.001 HIS J 58 Details of bonding type rmsd covalent geometry : bond 0.00348 (12966) covalent geometry : angle 0.60410 (17670) hydrogen bonds : bond 0.07347 ( 774) hydrogen bonds : angle 4.75955 ( 2196) Misc. bond : bond 0.02307 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 251 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: B 86 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.7242 (mtt-85) REVERT: F 107 GLU cc_start: 0.7125 (tt0) cc_final: 0.6790 (tt0) REVERT: I 86 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.7314 (mtt-85) REVERT: J 107 GLU cc_start: 0.7087 (tt0) cc_final: 0.6795 (tt0) outliers start: 35 outliers final: 24 residues processed: 280 average time/residue: 0.6052 time to fit residues: 183.9987 Evaluate side-chains 268 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 242 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 86 ARG Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 86 ARG Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 116 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 127 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 105 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 86 ASN F 53 ASN J 53 ASN K 86 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.147554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.120567 restraints weight = 10785.437| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 0.95 r_work: 0.3224 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 2.20 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12972 Z= 0.161 Angle : 0.597 6.033 17670 Z= 0.302 Chirality : 0.041 0.134 1824 Planarity : 0.004 0.033 2244 Dihedral : 9.257 79.764 1824 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.43 % Allowed : 17.46 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.42 (0.20), residues: 1602 helix: 3.39 (0.18), residues: 678 sheet: 0.60 (0.28), residues: 228 loop : 0.16 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 28 TYR 0.010 0.002 TYR J 96 PHE 0.017 0.002 PHE K 48 TRP 0.005 0.001 TRP A 28 HIS 0.001 0.001 HIS I 58 Details of bonding type rmsd covalent geometry : bond 0.00341 (12966) covalent geometry : angle 0.59655 (17670) hydrogen bonds : bond 0.07177 ( 774) hydrogen bonds : angle 4.71616 ( 2196) Misc. bond : bond 0.02226 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 245 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: A 86 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.7267 (mtt-85) REVERT: B 86 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.7243 (mtt-85) REVERT: D 93 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7358 (p0) REVERT: E 93 ASP cc_start: 0.7486 (OUTLIER) cc_final: 0.7119 (p0) REVERT: F 93 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.7138 (p0) REVERT: F 107 GLU cc_start: 0.7063 (tt0) cc_final: 0.6749 (tt0) REVERT: I 86 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.7247 (mtt-85) REVERT: J 93 ASP cc_start: 0.7486 (OUTLIER) cc_final: 0.7135 (p0) REVERT: J 107 GLU cc_start: 0.6960 (tt0) cc_final: 0.6711 (tt0) REVERT: K 93 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.7369 (p0) REVERT: L 93 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.7126 (p0) outliers start: 43 outliers final: 21 residues processed: 273 average time/residue: 0.6026 time to fit residues: 178.9284 Evaluate side-chains 267 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 237 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 86 ARG Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 86 ARG Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 116 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 59 optimal weight: 3.9990 chunk 131 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 151 optimal weight: 0.5980 chunk 132 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 86 ASN F 53 ASN J 53 ASN K 86 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.145840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.119069 restraints weight = 10824.123| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 0.94 r_work: 0.3208 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12972 Z= 0.191 Angle : 0.646 5.962 17670 Z= 0.331 Chirality : 0.043 0.138 1824 Planarity : 0.005 0.035 2244 Dihedral : 9.008 81.161 1816 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 4.78 % Allowed : 14.83 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.22 (0.20), residues: 1602 helix: 3.22 (0.19), residues: 678 sheet: 0.52 (0.28), residues: 228 loop : 0.04 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 28 TYR 0.011 0.002 TYR J 96 PHE 0.018 0.002 PHE K 48 TRP 0.005 0.001 TRP A 28 HIS 0.002 0.001 HIS I 58 Details of bonding type rmsd covalent geometry : bond 0.00403 (12966) covalent geometry : angle 0.64611 (17670) hydrogen bonds : bond 0.08089 ( 774) hydrogen bonds : angle 4.89378 ( 2196) Misc. bond : bond 0.02511 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 242 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 86 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.7281 (mtt-85) REVERT: B 86 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.7321 (mtt-85) REVERT: D 93 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.7424 (p0) REVERT: E 93 ASP cc_start: 0.7582 (OUTLIER) cc_final: 0.7206 (p0) REVERT: F 93 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.7190 (p0) REVERT: F 107 GLU cc_start: 0.7214 (tt0) cc_final: 0.6897 (tt0) REVERT: J 93 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.7193 (p0) REVERT: J 107 GLU cc_start: 0.7108 (tt0) cc_final: 0.6847 (tt0) REVERT: K 93 ASP cc_start: 0.7663 (OUTLIER) cc_final: 0.7430 (p0) REVERT: L 93 ASP cc_start: 0.7582 (OUTLIER) cc_final: 0.7206 (p0) outliers start: 60 outliers final: 32 residues processed: 289 average time/residue: 0.4986 time to fit residues: 157.2154 Evaluate side-chains 277 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 237 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 86 ARG Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 156 SER Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 116 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 34 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 86 ASN F 53 ASN J 53 ASN K 86 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.145377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.118838 restraints weight = 10796.144| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 0.93 r_work: 0.3209 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 2.24 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12972 Z= 0.197 Angle : 0.660 6.934 17670 Z= 0.338 Chirality : 0.043 0.138 1824 Planarity : 0.005 0.037 2244 Dihedral : 8.976 81.467 1812 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.35 % Allowed : 15.47 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.08 (0.20), residues: 1602 helix: 3.14 (0.19), residues: 678 sheet: 0.51 (0.28), residues: 228 loop : -0.10 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG K 28 TYR 0.013 0.002 TYR J 96 PHE 0.018 0.002 PHE K 48 TRP 0.005 0.001 TRP A 28 HIS 0.002 0.001 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00418 (12966) covalent geometry : angle 0.66015 (17670) hydrogen bonds : bond 0.08165 ( 774) hydrogen bonds : angle 4.92624 ( 2196) Misc. bond : bond 0.02627 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 238 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: A 86 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.7306 (mtt-85) REVERT: D 93 ASP cc_start: 0.7661 (OUTLIER) cc_final: 0.7426 (p0) REVERT: E 93 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7213 (p0) REVERT: F 93 ASP cc_start: 0.7553 (OUTLIER) cc_final: 0.7192 (p0) REVERT: F 107 GLU cc_start: 0.7165 (tt0) cc_final: 0.6858 (tt0) REVERT: J 93 ASP cc_start: 0.7556 (OUTLIER) cc_final: 0.7179 (p0) REVERT: K 93 ASP cc_start: 0.7661 (OUTLIER) cc_final: 0.7427 (p0) REVERT: L 93 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7215 (p0) outliers start: 42 outliers final: 31 residues processed: 266 average time/residue: 0.5080 time to fit residues: 147.2296 Evaluate side-chains 273 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 235 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 86 ARG Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 156 SER Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 116 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 53 optimal weight: 0.1980 chunk 13 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 86 ASN F 53 ASN J 53 ASN K 86 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.146183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.119718 restraints weight = 10654.971| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 0.93 r_work: 0.3220 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 2.14 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12972 Z= 0.172 Angle : 0.626 7.617 17670 Z= 0.316 Chirality : 0.042 0.136 1824 Planarity : 0.004 0.033 2244 Dihedral : 8.714 80.247 1807 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.27 % Allowed : 15.63 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.14 (0.20), residues: 1602 helix: 3.25 (0.19), residues: 678 sheet: 0.39 (0.28), residues: 234 loop : -0.09 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 112 TYR 0.010 0.002 TYR J 96 PHE 0.018 0.002 PHE K 48 TRP 0.005 0.001 TRP J 54 HIS 0.001 0.001 HIS J 58 Details of bonding type rmsd covalent geometry : bond 0.00367 (12966) covalent geometry : angle 0.62559 (17670) hydrogen bonds : bond 0.07475 ( 774) hydrogen bonds : angle 4.78126 ( 2196) Misc. bond : bond 0.02441 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 234 time to evaluate : 0.484 Fit side-chains REVERT: A 86 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.7276 (mtt-85) REVERT: A 156 SER cc_start: 0.4605 (OUTLIER) cc_final: 0.4386 (m) REVERT: B 156 SER cc_start: 0.4664 (OUTLIER) cc_final: 0.4363 (m) REVERT: C 156 SER cc_start: 0.4633 (OUTLIER) cc_final: 0.4398 (m) REVERT: D 93 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7393 (p0) REVERT: E 93 ASP cc_start: 0.7504 (OUTLIER) cc_final: 0.7132 (p0) REVERT: F 93 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.7132 (p0) REVERT: F 107 GLU cc_start: 0.7055 (tt0) cc_final: 0.6769 (tt0) REVERT: G 86 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.7292 (mtt-85) REVERT: G 156 SER cc_start: 0.4699 (OUTLIER) cc_final: 0.4461 (m) REVERT: H 156 SER cc_start: 0.4724 (OUTLIER) cc_final: 0.4454 (m) REVERT: I 156 SER cc_start: 0.4662 (OUTLIER) cc_final: 0.4362 (m) REVERT: J 93 ASP cc_start: 0.7493 (OUTLIER) cc_final: 0.7132 (p0) REVERT: K 93 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7415 (p0) REVERT: L 93 ASP cc_start: 0.7507 (OUTLIER) cc_final: 0.7138 (p0) outliers start: 41 outliers final: 20 residues processed: 264 average time/residue: 0.5280 time to fit residues: 151.8287 Evaluate side-chains 265 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 231 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 86 ARG Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 156 SER Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 116 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 69 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 78 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 136 optimal weight: 0.4980 chunk 79 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 86 ASN F 53 ASN J 53 ASN K 86 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.146664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.120499 restraints weight = 10804.760| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 0.92 r_work: 0.3221 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 2.24 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12972 Z= 0.176 Angle : 0.627 6.587 17670 Z= 0.318 Chirality : 0.042 0.136 1824 Planarity : 0.004 0.031 2244 Dihedral : 8.715 80.577 1806 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.51 % Allowed : 15.31 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.08 (0.20), residues: 1602 helix: 3.21 (0.19), residues: 678 sheet: 0.37 (0.28), residues: 234 loop : -0.13 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 28 TYR 0.012 0.002 TYR J 96 PHE 0.017 0.002 PHE K 48 TRP 0.005 0.001 TRP K 54 HIS 0.002 0.001 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00374 (12966) covalent geometry : angle 0.62659 (17670) hydrogen bonds : bond 0.07669 ( 774) hydrogen bonds : angle 4.82825 ( 2196) Misc. bond : bond 0.02485 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 236 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: A 86 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.7258 (mtt-85) REVERT: C 156 SER cc_start: 0.4716 (OUTLIER) cc_final: 0.4456 (m) REVERT: D 93 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.7423 (p0) REVERT: E 93 ASP cc_start: 0.7549 (OUTLIER) cc_final: 0.7174 (p0) REVERT: F 93 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.7180 (p0) REVERT: F 107 GLU cc_start: 0.7068 (tt0) cc_final: 0.6782 (tt0) REVERT: G 156 SER cc_start: 0.4810 (OUTLIER) cc_final: 0.4539 (m) REVERT: H 156 SER cc_start: 0.4782 (OUTLIER) cc_final: 0.4456 (m) REVERT: J 93 ASP cc_start: 0.7549 (OUTLIER) cc_final: 0.7201 (p0) REVERT: K 93 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7418 (p0) REVERT: L 93 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7181 (p0) outliers start: 44 outliers final: 25 residues processed: 267 average time/residue: 0.5502 time to fit residues: 159.7366 Evaluate side-chains 268 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 233 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 86 ARG Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 116 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 150 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 133 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 86 ASN F 53 ASN J 53 ASN K 86 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.148214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.122224 restraints weight = 10791.138| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 0.91 r_work: 0.3245 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 2.25 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12972 Z= 0.158 Angle : 0.599 6.043 17670 Z= 0.301 Chirality : 0.042 0.134 1824 Planarity : 0.004 0.030 2244 Dihedral : 8.581 79.406 1806 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.95 % Allowed : 15.47 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.20 (0.20), residues: 1602 helix: 3.34 (0.18), residues: 678 sheet: 0.38 (0.28), residues: 234 loop : -0.08 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 86 TYR 0.011 0.002 TYR J 96 PHE 0.017 0.002 PHE K 48 TRP 0.004 0.001 TRP D 54 HIS 0.001 0.000 HIS B 46 Details of bonding type rmsd covalent geometry : bond 0.00339 (12966) covalent geometry : angle 0.59873 (17670) hydrogen bonds : bond 0.07005 ( 774) hydrogen bonds : angle 4.68613 ( 2196) Misc. bond : bond 0.02105 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 232 time to evaluate : 0.661 Fit side-chains revert: symmetry clash REVERT: A 86 ARG cc_start: 0.7459 (OUTLIER) cc_final: 0.7213 (mtt-85) REVERT: A 156 SER cc_start: 0.4798 (OUTLIER) cc_final: 0.4457 (m) REVERT: C 156 SER cc_start: 0.4759 (OUTLIER) cc_final: 0.4464 (m) REVERT: E 93 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.7163 (p0) REVERT: F 20 ARG cc_start: 0.7978 (ttt-90) cc_final: 0.7357 (ttt180) REVERT: F 93 ASP cc_start: 0.7511 (OUTLIER) cc_final: 0.7175 (p0) REVERT: F 107 GLU cc_start: 0.7014 (tt0) cc_final: 0.6735 (tt0) REVERT: G 156 SER cc_start: 0.4752 (OUTLIER) cc_final: 0.4453 (m) REVERT: H 82 ASP cc_start: 0.5961 (OUTLIER) cc_final: 0.5700 (t70) REVERT: J 20 ARG cc_start: 0.7962 (ttt-90) cc_final: 0.7347 (ttt180) REVERT: J 93 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.7183 (p0) REVERT: L 93 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.7165 (p0) outliers start: 37 outliers final: 19 residues processed: 260 average time/residue: 0.5529 time to fit residues: 156.9588 Evaluate side-chains 256 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 228 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 86 ARG Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 116 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 77 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 86 ASN F 53 ASN J 53 ASN K 86 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.147736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.121646 restraints weight = 10864.317| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 0.91 r_work: 0.3235 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 2.25 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12972 Z= 0.165 Angle : 0.616 9.315 17670 Z= 0.310 Chirality : 0.042 0.135 1824 Planarity : 0.004 0.030 2244 Dihedral : 8.583 79.865 1806 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.63 % Allowed : 16.27 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.17 (0.20), residues: 1602 helix: 3.29 (0.18), residues: 678 sheet: 0.38 (0.28), residues: 234 loop : -0.08 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 86 TYR 0.011 0.002 TYR J 96 PHE 0.017 0.002 PHE K 48 TRP 0.004 0.001 TRP D 54 HIS 0.001 0.000 HIS I 58 Details of bonding type rmsd covalent geometry : bond 0.00355 (12966) covalent geometry : angle 0.61632 (17670) hydrogen bonds : bond 0.07225 ( 774) hydrogen bonds : angle 4.73747 ( 2196) Misc. bond : bond 0.02245 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 234 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 86 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.7233 (mtt-85) REVERT: A 156 SER cc_start: 0.4745 (OUTLIER) cc_final: 0.4412 (m) REVERT: C 156 SER cc_start: 0.4748 (OUTLIER) cc_final: 0.4454 (m) REVERT: D 93 ASP cc_start: 0.7623 (OUTLIER) cc_final: 0.7414 (p0) REVERT: E 93 ASP cc_start: 0.7527 (OUTLIER) cc_final: 0.7166 (p0) REVERT: F 20 ARG cc_start: 0.7977 (ttt-90) cc_final: 0.7351 (ttt180) REVERT: F 93 ASP cc_start: 0.7517 (OUTLIER) cc_final: 0.7179 (p0) REVERT: F 107 GLU cc_start: 0.7038 (tt0) cc_final: 0.6752 (tt0) REVERT: G 156 SER cc_start: 0.4731 (OUTLIER) cc_final: 0.4434 (m) REVERT: H 82 ASP cc_start: 0.5983 (OUTLIER) cc_final: 0.5723 (t70) REVERT: J 20 ARG cc_start: 0.7963 (ttt-90) cc_final: 0.7344 (ttt180) REVERT: J 93 ASP cc_start: 0.7532 (OUTLIER) cc_final: 0.7197 (p0) REVERT: K 93 ASP cc_start: 0.7620 (OUTLIER) cc_final: 0.7400 (p0) REVERT: L 93 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.7170 (p0) outliers start: 33 outliers final: 19 residues processed: 258 average time/residue: 0.5284 time to fit residues: 148.6147 Evaluate side-chains 260 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 230 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 86 ARG Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 72 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 59 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 86 ASN F 53 ASN J 53 ASN K 86 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.147399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.121269 restraints weight = 10881.718| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 0.92 r_work: 0.3236 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12972 Z= 0.168 Angle : 0.622 7.921 17670 Z= 0.314 Chirality : 0.042 0.135 1824 Planarity : 0.004 0.030 2244 Dihedral : 8.603 80.018 1806 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.39 % Allowed : 16.35 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.14 (0.20), residues: 1602 helix: 3.26 (0.18), residues: 678 sheet: 0.41 (0.29), residues: 234 loop : -0.10 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 86 TYR 0.010 0.002 TYR J 96 PHE 0.017 0.002 PHE K 48 TRP 0.004 0.001 TRP D 54 HIS 0.001 0.001 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00362 (12966) covalent geometry : angle 0.62211 (17670) hydrogen bonds : bond 0.07343 ( 774) hydrogen bonds : angle 4.76810 ( 2196) Misc. bond : bond 0.02303 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 232 time to evaluate : 0.423 Fit side-chains REVERT: A 86 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.7232 (mtt-85) REVERT: A 156 SER cc_start: 0.4773 (OUTLIER) cc_final: 0.4462 (m) REVERT: B 83 LYS cc_start: 0.7010 (mmmt) cc_final: 0.6703 (mmtm) REVERT: C 156 SER cc_start: 0.4692 (OUTLIER) cc_final: 0.4390 (m) REVERT: D 93 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.7422 (p0) REVERT: E 93 ASP cc_start: 0.7532 (OUTLIER) cc_final: 0.7170 (p0) REVERT: F 20 ARG cc_start: 0.7976 (ttt-90) cc_final: 0.7347 (ttt180) REVERT: F 93 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.7172 (p0) REVERT: F 107 GLU cc_start: 0.7067 (tt0) cc_final: 0.6777 (tt0) REVERT: G 86 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.6942 (mtm110) REVERT: G 156 SER cc_start: 0.4679 (OUTLIER) cc_final: 0.4381 (m) REVERT: I 83 LYS cc_start: 0.6978 (mmmt) cc_final: 0.6676 (mmtm) REVERT: J 20 ARG cc_start: 0.7967 (ttt-90) cc_final: 0.7343 (ttt180) REVERT: J 93 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.7219 (p0) REVERT: K 93 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.7420 (p0) REVERT: L 93 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.7171 (p0) outliers start: 30 outliers final: 19 residues processed: 254 average time/residue: 0.5502 time to fit residues: 151.9834 Evaluate side-chains 261 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 231 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 86 ARG Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 29 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 102 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 86 ASN F 53 ASN J 53 ASN K 86 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.147131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.120989 restraints weight = 10790.357| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 0.92 r_work: 0.3228 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 2.24 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12972 Z= 0.173 Angle : 0.632 9.866 17670 Z= 0.319 Chirality : 0.042 0.135 1824 Planarity : 0.004 0.032 2244 Dihedral : 8.640 80.312 1806 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.39 % Allowed : 16.75 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.11 (0.20), residues: 1602 helix: 3.22 (0.18), residues: 678 sheet: 0.42 (0.29), residues: 234 loop : -0.11 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 86 TYR 0.012 0.002 TYR J 96 PHE 0.017 0.002 PHE K 48 TRP 0.005 0.001 TRP D 54 HIS 0.002 0.001 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00372 (12966) covalent geometry : angle 0.63241 (17670) hydrogen bonds : bond 0.07499 ( 774) hydrogen bonds : angle 4.80388 ( 2196) Misc. bond : bond 0.02398 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5827.52 seconds wall clock time: 99 minutes 44.89 seconds (5984.89 seconds total)