Starting phenix.real_space_refine on Sat Aug 23 14:30:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pnu_17785/08_2025/8pnu_17785.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pnu_17785/08_2025/8pnu_17785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pnu_17785/08_2025/8pnu_17785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pnu_17785/08_2025/8pnu_17785.map" model { file = "/net/cci-nas-00/data/ceres_data/8pnu_17785/08_2025/8pnu_17785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pnu_17785/08_2025/8pnu_17785.cif" } resolution = 2.12 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 8244 2.51 5 N 2112 2.21 5 O 2466 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 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: 12888 Number of models: 1 Model: "" Number of chains: 19 Chain: "G" 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: "H" 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: "I" 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: "J" 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: "G" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'ABN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 94 Unusual residues: {'ABN': 1, 'HEM': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 51 Unusual residues: {'ABN': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "H" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "J" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "K" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "L" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "E" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "F" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Restraints were copied for chains: A, B, C, K, L, D, E, F Time building chain proxies: 2.70, per 1000 atoms: 0.21 Number of scatterers: 12888 At special positions: 0 Unit cell: (79.2, 81.84, 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 2466 8.00 N 2112 7.00 C 8244 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 97 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 97 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 97 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 97 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 97 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 97 " distance=2.04 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: 0.95 Conformation dependent library (CDL) restraints added in 644.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.44 Creating SS restraints... Processing helix chain 'G' and resid 3 through 33 removed outlier: 3.524A 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: 3.918A 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: 3.883A 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: 3.659A pdb=" N LEU G 141 " --> pdb=" O LEU G 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 33 removed outlier: 3.524A 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: 3.918A 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: 3.883A 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: 3.660A pdb=" N LEU H 141 " --> pdb=" O LEU H 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 33 removed outlier: 3.524A 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: 3.918A 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: 3.884A 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: 3.660A 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 helix chain 'A' and resid 3 through 33 removed outlier: 3.524A 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: 3.918A 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: 3.884A 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: 3.659A pdb=" N LEU A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 33 removed outlier: 3.524A 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: 3.918A 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: 3.884A 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: 3.659A pdb=" N LEU B 141 " --> pdb=" O LEU B 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 33 removed outlier: 3.524A 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: 3.918A 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: 3.884A 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: 3.660A 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 sheet with id=AA1, first strand: chain 'G' and resid 34 through 38 removed outlier: 7.165A pdb=" N TYR G 41 " --> pdb=" O ILE G 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 34 through 38 removed outlier: 7.165A pdb=" N TYR H 41 " --> pdb=" O ILE H 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 34 through 38 removed outlier: 7.165A pdb=" N TYR I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 6 through 8 Processing sheet with id=AA5, first strand: chain 'J' and resid 12 through 14 removed outlier: 6.778A pdb=" N VAL J 35 " --> pdb=" O THR J 51 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N THR J 51 " --> pdb=" O VAL J 35 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TRP J 37 " --> pdb=" O VAL J 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 12 through 14 Processing sheet with id=AA7, first strand: chain 'K' and resid 6 through 8 Processing sheet with id=AA8, first strand: chain 'K' and resid 12 through 14 removed outlier: 6.778A pdb=" N VAL K 35 " --> pdb=" O THR K 51 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N THR K 51 " --> pdb=" O VAL K 35 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TRP K 37 " --> pdb=" O VAL K 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 12 through 14 Processing sheet with id=AB1, first strand: chain 'L' and resid 6 through 8 Processing sheet with id=AB2, first strand: chain 'L' and resid 12 through 14 removed outlier: 6.778A pdb=" N VAL L 35 " --> pdb=" O THR L 51 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N THR L 51 " --> pdb=" O VAL L 35 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TRP L 37 " --> pdb=" O VAL L 49 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 12 through 14 Processing sheet with id=AB4, first strand: chain 'A' and resid 34 through 38 removed outlier: 7.165A pdb=" N TYR A 41 " --> pdb=" O ILE A 37 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 34 through 38 removed outlier: 7.165A pdb=" N TYR B 41 " --> pdb=" O ILE B 37 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 34 through 38 removed outlier: 7.165A pdb=" N TYR C 41 " --> pdb=" O ILE C 37 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 6 through 8 Processing sheet with id=AB8, first strand: chain 'D' and resid 12 through 14 removed outlier: 6.779A pdb=" N VAL D 35 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N THR D 51 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TRP D 37 " --> pdb=" O VAL D 49 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 12 through 14 Processing sheet with id=AC1, first strand: chain 'E' and resid 6 through 8 Processing sheet with id=AC2, first strand: chain 'E' and resid 12 through 14 removed outlier: 6.778A pdb=" N VAL E 35 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N THR E 51 " --> pdb=" O VAL E 35 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TRP E 37 " --> pdb=" O VAL E 49 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 12 through 14 Processing sheet with id=AC4, first strand: chain 'F' and resid 6 through 8 Processing sheet with id=AC5, first strand: chain 'F' and resid 12 through 14 removed outlier: 6.778A pdb=" N VAL F 35 " --> pdb=" O THR F 51 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N THR F 51 " --> pdb=" O VAL F 35 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TRP F 37 " --> pdb=" O VAL F 49 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 12 through 14 822 hydrogen bonds defined for protein. 2250 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: 1.98 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.39: 5472 1.39 - 1.55: 7416 1.55 - 1.72: 0 1.72 - 1.88: 102 1.88 - 2.05: 24 Bond restraints: 13014 Sorted by residual: bond pdb=" C TYR C 136 " pdb=" O TYR C 136 " ideal model delta sigma weight residual 1.236 1.251 -0.014 1.15e-02 7.56e+03 1.54e+00 bond pdb=" C TYR I 136 " pdb=" O TYR I 136 " ideal model delta sigma weight residual 1.236 1.251 -0.014 1.15e-02 7.56e+03 1.53e+00 bond pdb=" C TYR A 136 " pdb=" O TYR A 136 " ideal model delta sigma weight residual 1.236 1.251 -0.014 1.15e-02 7.56e+03 1.51e+00 bond pdb=" C TYR B 136 " pdb=" O TYR B 136 " ideal model delta sigma weight residual 1.236 1.250 -0.014 1.15e-02 7.56e+03 1.47e+00 bond pdb=" C TYR G 136 " pdb=" O TYR G 136 " ideal model delta sigma weight residual 1.236 1.250 -0.014 1.15e-02 7.56e+03 1.41e+00 ... (remaining 13009 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 16941 1.33 - 2.66: 603 2.66 - 3.99: 114 3.99 - 5.32: 54 5.32 - 6.66: 12 Bond angle restraints: 17724 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 121.06 127.72 -6.66 1.88e+00 2.83e-01 1.25e+01 angle pdb=" C ILE F 52 " pdb=" N ASN F 53 " pdb=" CA ASN F 53 " ideal model delta sigma weight residual 121.06 127.69 -6.63 1.88e+00 2.83e-01 1.24e+01 angle pdb=" C ILE D 52 " pdb=" N ASN D 53 " pdb=" CA ASN D 53 " ideal model delta sigma weight residual 121.06 127.68 -6.62 1.88e+00 2.83e-01 1.24e+01 angle pdb=" C ILE L 52 " pdb=" N ASN L 53 " pdb=" CA ASN L 53 " ideal model delta sigma weight residual 121.06 127.68 -6.62 1.88e+00 2.83e-01 1.24e+01 angle pdb=" C ILE E 52 " pdb=" N ASN E 53 " pdb=" CA ASN E 53 " ideal model delta sigma weight residual 121.06 127.66 -6.60 1.88e+00 2.83e-01 1.23e+01 ... (remaining 17719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 6270 17.80 - 35.60: 708 35.60 - 53.41: 144 53.41 - 71.21: 96 71.21 - 89.01: 30 Dihedral angle restraints: 7248 sinusoidal: 2778 harmonic: 4470 Sorted by residual: dihedral pdb=" CB CYS K 23 " pdb=" SG CYS K 23 " pdb=" SG CYS K 97 " pdb=" CB CYS K 97 " ideal model delta sinusoidal sigma weight residual 93.00 59.91 33.09 1 1.00e+01 1.00e-02 1.56e+01 dihedral pdb=" CB CYS E 23 " pdb=" SG CYS E 23 " pdb=" SG CYS E 97 " pdb=" CB CYS E 97 " ideal model delta sinusoidal sigma weight residual 93.00 59.93 33.07 1 1.00e+01 1.00e-02 1.55e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 97 " pdb=" CB CYS L 97 " ideal model delta sinusoidal sigma weight residual 93.00 59.95 33.05 1 1.00e+01 1.00e-02 1.55e+01 ... (remaining 7245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1032 0.026 - 0.051: 474 0.051 - 0.077: 168 0.077 - 0.102: 85 0.102 - 0.128: 65 Chirality restraints: 1824 Sorted by residual: chirality pdb=" CA ILE B 38 " pdb=" N ILE B 38 " pdb=" C ILE B 38 " pdb=" CB ILE B 38 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CA ILE H 38 " pdb=" N ILE H 38 " pdb=" C ILE H 38 " pdb=" CB ILE H 38 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.07e-01 chirality pdb=" CA ILE I 38 " pdb=" N ILE I 38 " pdb=" C ILE I 38 " pdb=" CB ILE I 38 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 1821 not shown) Planarity restraints: 2250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP L 63 " 0.049 5.00e-02 4.00e+02 7.41e-02 8.78e+00 pdb=" N PRO L 64 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO L 64 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO L 64 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP J 63 " -0.049 5.00e-02 4.00e+02 7.40e-02 8.77e+00 pdb=" N PRO J 64 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO J 64 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO J 64 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP F 63 " -0.049 5.00e-02 4.00e+02 7.40e-02 8.77e+00 pdb=" N PRO F 64 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO F 64 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO F 64 " -0.041 5.00e-02 4.00e+02 ... (remaining 2247 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3216 2.80 - 3.32: 12151 3.32 - 3.85: 22760 3.85 - 4.37: 26836 4.37 - 4.90: 45825 Nonbonded interactions: 110788 Sorted by model distance: nonbonded pdb=" N ABN G 201 " pdb="FE HEM I 202 " model vdw 2.271 3.080 nonbonded pdb=" N ABN A 201 " pdb="FE HEM C 202 " model vdw 2.272 3.080 nonbonded pdb="FE HEM B 201 " pdb=" N ABN B 202 " model vdw 2.272 3.080 nonbonded pdb="FE HEM H 203 " pdb=" N ABN I 201 " model vdw 2.272 3.080 nonbonded pdb="FE HEM B 203 " pdb=" N ABN C 201 " model vdw 2.273 3.080 ... (remaining 110783 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 'G' selection = chain 'A' } ncs_group { reference = chain 'H' selection = chain 'B' } ncs_group { reference = chain 'I' selection = chain 'C' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 5.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.330 Find NCS groups from input model: 0.120 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:6.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 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 0.042 13026 Z= 0.174 Angle : 0.644 6.655 17736 Z= 0.346 Chirality : 0.041 0.128 1824 Planarity : 0.006 0.074 2250 Dihedral : 17.635 89.011 4434 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % 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: 3.29 (0.19), residues: 678 sheet: 0.89 (0.31), residues: 228 loop : 0.42 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 112 TYR 0.008 0.002 TYR I 103 PHE 0.012 0.002 PHE K 48 TRP 0.007 0.001 TRP A 28 HIS 0.002 0.001 HIS H 12 Details of bonding type rmsd covalent geometry : bond 0.00354 (13014) covalent geometry : angle 0.64371 (17724) SS BOND : bond 0.00789 ( 6) SS BOND : angle 0.84058 ( 12) hydrogen bonds : bond 0.11761 ( 786) hydrogen bonds : angle 5.39210 ( 2250) Misc. bond : bond 0.00616 ( 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 332 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 296 time to evaluate : 0.408 Fit side-chains REVERT: I 6 GLU cc_start: 0.7852 (mp0) cc_final: 0.7517 (mp0) REVERT: J 12 LEU cc_start: 0.7975 (tp) cc_final: 0.7735 (tm) REVERT: J 53 ASN cc_start: 0.7279 (t0) cc_final: 0.7028 (t0) REVERT: L 12 LEU cc_start: 0.8032 (tp) cc_final: 0.7715 (tm) REVERT: C 6 GLU cc_start: 0.7887 (mp0) cc_final: 0.7527 (mp0) REVERT: F 12 LEU cc_start: 0.7996 (tp) cc_final: 0.7640 (tm) outliers start: 36 outliers final: 10 residues processed: 332 average time/residue: 0.6081 time to fit residues: 218.6662 Evaluate side-chains 249 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 239 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain J residue 118 SER Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain L residue 118 SER Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain E 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: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.0980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 40 GLN K 4 GLN K 40 GLN K 75 ASN L 4 GLN L 40 GLN L 75 ASN D 4 GLN D 40 GLN E 4 GLN E 40 GLN E 75 ASN F 4 GLN F 40 GLN F 75 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.129773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.103725 restraints weight = 11560.405| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.05 r_work: 0.3040 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 13026 Z= 0.209 Angle : 0.700 6.767 17736 Z= 0.361 Chirality : 0.045 0.133 1824 Planarity : 0.005 0.034 2250 Dihedral : 10.284 89.840 1810 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 3.75 % Allowed : 14.35 % Favored : 81.90 % 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: 2.35 (0.20), residues: 1602 helix: 3.25 (0.18), residues: 678 sheet: 0.72 (0.31), residues: 228 loop : 0.16 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 56 TYR 0.015 0.002 TYR L 108 PHE 0.021 0.003 PHE J 48 TRP 0.014 0.002 TRP H 28 HIS 0.005 0.002 HIS H 58 Details of bonding type rmsd covalent geometry : bond 0.00444 (13014) covalent geometry : angle 0.69996 (17724) SS BOND : bond 0.00651 ( 6) SS BOND : angle 0.46576 ( 12) hydrogen bonds : bond 0.08418 ( 786) hydrogen bonds : angle 5.10902 ( 2250) Misc. bond : bond 0.03408 ( 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 291 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 244 time to evaluate : 0.572 Fit side-chains REVERT: G 2 LEU cc_start: 0.6720 (OUTLIER) cc_final: 0.6341 (mp) REVERT: H 2 LEU cc_start: 0.6787 (OUTLIER) cc_final: 0.6455 (mt) REVERT: I 2 LEU cc_start: 0.6800 (OUTLIER) cc_final: 0.6510 (mt) REVERT: I 6 GLU cc_start: 0.8110 (mp0) cc_final: 0.7639 (mp0) REVERT: L 12 LEU cc_start: 0.7991 (tp) cc_final: 0.7623 (tm) REVERT: A 2 LEU cc_start: 0.6663 (OUTLIER) cc_final: 0.6269 (mp) REVERT: B 2 LEU cc_start: 0.6763 (OUTLIER) cc_final: 0.6415 (mt) REVERT: C 2 LEU cc_start: 0.6779 (OUTLIER) cc_final: 0.6491 (mt) REVERT: C 6 GLU cc_start: 0.8106 (mp0) cc_final: 0.7623 (mp0) REVERT: D 4 GLN cc_start: 0.6571 (OUTLIER) cc_final: 0.6322 (mp10) REVERT: F 12 LEU cc_start: 0.7964 (tp) cc_final: 0.7587 (tm) REVERT: F 118 SER cc_start: 0.6987 (OUTLIER) cc_final: 0.6438 (m) outliers start: 47 outliers final: 17 residues processed: 281 average time/residue: 0.5889 time to fit residues: 179.4451 Evaluate side-chains 263 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 238 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 118 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 32 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 152 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 40 GLN K 40 GLN L 40 GLN D 4 GLN D 40 GLN E 40 GLN F 40 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.133019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.107384 restraints weight = 11732.744| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.05 r_work: 0.3078 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13026 Z= 0.160 Angle : 0.615 6.193 17736 Z= 0.315 Chirality : 0.042 0.136 1824 Planarity : 0.004 0.034 2250 Dihedral : 10.006 89.657 1806 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.07 % Allowed : 15.95 % Favored : 81.98 % 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: 2.35 (0.20), residues: 1602 helix: 3.32 (0.18), residues: 678 sheet: 0.73 (0.31), residues: 228 loop : 0.07 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 86 TYR 0.012 0.001 TYR L 108 PHE 0.018 0.002 PHE J 48 TRP 0.007 0.001 TRP G 28 HIS 0.002 0.001 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00336 (13014) covalent geometry : angle 0.61480 (17724) SS BOND : bond 0.00499 ( 6) SS BOND : angle 0.39961 ( 12) hydrogen bonds : bond 0.07046 ( 786) hydrogen bonds : angle 4.76769 ( 2250) Misc. bond : bond 0.03017 ( 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 271 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 245 time to evaluate : 0.503 Fit side-chains REVERT: H 86 ARG cc_start: 0.7727 (ttp-110) cc_final: 0.7462 (mtt90) REVERT: J 40 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8282 (tt0) REVERT: C 6 GLU cc_start: 0.8078 (mp0) cc_final: 0.7621 (mp0) REVERT: D 40 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8276 (tt0) REVERT: D 118 SER cc_start: 0.6917 (OUTLIER) cc_final: 0.6701 (m) REVERT: E 12 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7586 (tp) REVERT: F 118 SER cc_start: 0.6767 (OUTLIER) cc_final: 0.6332 (m) outliers start: 26 outliers final: 12 residues processed: 264 average time/residue: 0.6248 time to fit residues: 179.2905 Evaluate side-chains 254 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 237 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain J residue 40 GLN Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain D residue 40 GLN Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 118 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 16 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 144 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 152 GLN J 40 GLN L 53 ASN B 152 GLN D 40 GLN F 40 GLN F 53 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.130070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.103737 restraints weight = 11434.624| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.06 r_work: 0.3059 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 2.24 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13026 Z= 0.177 Angle : 0.642 6.143 17736 Z= 0.328 Chirality : 0.043 0.135 1824 Planarity : 0.004 0.033 2250 Dihedral : 9.049 88.870 1806 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.87 % Allowed : 15.71 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.22 (0.20), residues: 1602 helix: 3.20 (0.18), residues: 678 sheet: 0.61 (0.31), residues: 228 loop : 0.02 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 86 TYR 0.015 0.002 TYR L 108 PHE 0.018 0.002 PHE J 48 TRP 0.008 0.001 TRP L 37 HIS 0.003 0.001 HIS H 58 Details of bonding type rmsd covalent geometry : bond 0.00370 (13014) covalent geometry : angle 0.64216 (17724) SS BOND : bond 0.00586 ( 6) SS BOND : angle 0.44483 ( 12) hydrogen bonds : bond 0.07615 ( 786) hydrogen bonds : angle 4.90074 ( 2250) Misc. bond : bond 0.02940 ( 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 284 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 248 time to evaluate : 0.453 Fit side-chains REVERT: G 2 LEU cc_start: 0.6708 (OUTLIER) cc_final: 0.6320 (mp) REVERT: H 86 ARG cc_start: 0.7739 (ttp-110) cc_final: 0.7484 (mtt90) REVERT: I 6 GLU cc_start: 0.8044 (mp0) cc_final: 0.7586 (mp0) REVERT: J 40 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8133 (tt0) REVERT: L 12 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7624 (tp) REVERT: C 6 GLU cc_start: 0.8047 (mp0) cc_final: 0.7591 (mp0) REVERT: C 83 LYS cc_start: 0.6967 (OUTLIER) cc_final: 0.6759 (mtmm) REVERT: D 40 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8131 (tt0) REVERT: D 118 SER cc_start: 0.6857 (OUTLIER) cc_final: 0.6623 (m) REVERT: E 12 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7673 (tp) REVERT: F 12 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7640 (tp) REVERT: F 118 SER cc_start: 0.6746 (OUTLIER) cc_final: 0.6254 (m) outliers start: 36 outliers final: 16 residues processed: 279 average time/residue: 0.5951 time to fit residues: 181.2791 Evaluate side-chains 266 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 241 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain J residue 40 GLN Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain D residue 40 GLN Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 118 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 84 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 135 optimal weight: 0.8980 chunk 74 optimal weight: 0.1980 chunk 26 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 152 GLN J 40 GLN L 53 ASN D 40 GLN F 53 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.132266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.106082 restraints weight = 11711.120| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.08 r_work: 0.3093 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13026 Z= 0.152 Angle : 0.601 6.159 17736 Z= 0.306 Chirality : 0.042 0.138 1824 Planarity : 0.004 0.033 2250 Dihedral : 8.353 88.078 1806 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.63 % Allowed : 16.03 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.37 (0.20), residues: 1602 helix: 3.34 (0.18), residues: 678 sheet: 0.57 (0.29), residues: 270 loop : 0.12 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 86 TYR 0.011 0.001 TYR L 108 PHE 0.016 0.001 PHE E 48 TRP 0.005 0.001 TRP F 37 HIS 0.002 0.001 HIS H 58 Details of bonding type rmsd covalent geometry : bond 0.00319 (13014) covalent geometry : angle 0.60098 (17724) SS BOND : bond 0.00430 ( 6) SS BOND : angle 0.36627 ( 12) hydrogen bonds : bond 0.06736 ( 786) hydrogen bonds : angle 4.67148 ( 2250) Misc. bond : bond 0.02896 ( 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 276 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 243 time to evaluate : 0.559 Fit side-chains REVERT: H 86 ARG cc_start: 0.7679 (ttp-110) cc_final: 0.7419 (mtt90) REVERT: J 40 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8149 (tt0) REVERT: D 40 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8160 (tt0) REVERT: E 12 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7642 (tp) REVERT: F 118 SER cc_start: 0.6751 (OUTLIER) cc_final: 0.6337 (m) outliers start: 33 outliers final: 18 residues processed: 268 average time/residue: 0.5705 time to fit residues: 167.3080 Evaluate side-chains 264 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 242 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain J residue 40 GLN Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain L residue 119 SER Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain D residue 40 GLN Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 119 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 95 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 114 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 99 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 152 GLN J 40 GLN L 53 ASN B 152 GLN D 40 GLN F 53 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.131328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.105171 restraints weight = 11485.777| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.06 r_work: 0.3079 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 2.25 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13026 Z= 0.160 Angle : 0.617 6.133 17736 Z= 0.314 Chirality : 0.042 0.136 1824 Planarity : 0.004 0.032 2250 Dihedral : 8.491 88.799 1806 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.39 % Allowed : 16.03 % 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: 2.34 (0.20), residues: 1602 helix: 3.27 (0.18), residues: 678 sheet: 0.57 (0.29), residues: 270 loop : 0.14 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 86 TYR 0.012 0.001 TYR L 108 PHE 0.016 0.002 PHE D 48 TRP 0.006 0.001 TRP F 37 HIS 0.002 0.001 HIS H 58 Details of bonding type rmsd covalent geometry : bond 0.00338 (13014) covalent geometry : angle 0.61742 (17724) SS BOND : bond 0.00483 ( 6) SS BOND : angle 0.41322 ( 12) hydrogen bonds : bond 0.07069 ( 786) hydrogen bonds : angle 4.72459 ( 2250) Misc. bond : bond 0.03017 ( 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 274 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 244 time to evaluate : 0.533 Fit side-chains REVERT: H 86 ARG cc_start: 0.7673 (ttp-110) cc_final: 0.7433 (mtt90) REVERT: I 6 GLU cc_start: 0.8037 (mp0) cc_final: 0.7576 (mp0) REVERT: I 83 LYS cc_start: 0.6856 (OUTLIER) cc_final: 0.6645 (mtmm) REVERT: J 40 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8171 (tt0) REVERT: L 12 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7577 (tp) REVERT: C 6 GLU cc_start: 0.8037 (mp0) cc_final: 0.7579 (mp0) REVERT: D 40 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8183 (tt0) REVERT: E 12 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7673 (tp) REVERT: F 12 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7597 (tp) REVERT: F 118 SER cc_start: 0.6804 (OUTLIER) cc_final: 0.6364 (m) outliers start: 30 outliers final: 19 residues processed: 267 average time/residue: 0.6188 time to fit residues: 180.1450 Evaluate side-chains 266 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 240 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 83 LYS Chi-restraints excluded: chain J residue 40 GLN Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain L residue 119 SER Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain D residue 40 GLN Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 119 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 6 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 152 GLN J 40 GLN L 53 ASN B 152 GLN D 40 GLN F 53 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.129734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.103471 restraints weight = 11504.383| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.06 r_work: 0.3053 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 2.24 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13026 Z= 0.182 Angle : 0.657 6.115 17736 Z= 0.337 Chirality : 0.043 0.136 1824 Planarity : 0.004 0.033 2250 Dihedral : 8.694 87.969 1806 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.47 % Allowed : 15.79 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.21 (0.20), residues: 1602 helix: 3.17 (0.18), residues: 678 sheet: 0.52 (0.29), residues: 270 loop : 0.07 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 86 TYR 0.015 0.002 TYR L 108 PHE 0.018 0.002 PHE D 48 TRP 0.007 0.001 TRP F 37 HIS 0.003 0.001 HIS H 58 Details of bonding type rmsd covalent geometry : bond 0.00385 (13014) covalent geometry : angle 0.65687 (17724) SS BOND : bond 0.00612 ( 6) SS BOND : angle 0.51263 ( 12) hydrogen bonds : bond 0.07706 ( 786) hydrogen bonds : angle 4.88467 ( 2250) Misc. bond : bond 0.02980 ( 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 272 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 241 time to evaluate : 0.520 Fit side-chains REVERT: H 86 ARG cc_start: 0.7735 (ttp-110) cc_final: 0.7493 (mtt90) REVERT: I 6 GLU cc_start: 0.8063 (mp0) cc_final: 0.7605 (mp0) REVERT: I 83 LYS cc_start: 0.6964 (OUTLIER) cc_final: 0.6756 (mtmm) REVERT: J 40 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8147 (tt0) REVERT: L 12 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7589 (tp) REVERT: B 86 ARG cc_start: 0.7745 (ttp-110) cc_final: 0.7450 (mtp85) REVERT: C 6 GLU cc_start: 0.8060 (mp0) cc_final: 0.7604 (mp0) REVERT: C 83 LYS cc_start: 0.6972 (OUTLIER) cc_final: 0.6758 (mtmm) REVERT: D 40 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8154 (tt0) REVERT: F 12 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7599 (tp) REVERT: F 118 SER cc_start: 0.6837 (OUTLIER) cc_final: 0.6379 (m) outliers start: 31 outliers final: 19 residues processed: 264 average time/residue: 0.6226 time to fit residues: 179.0979 Evaluate side-chains 266 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 240 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 83 LYS Chi-restraints excluded: chain J residue 40 GLN Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain L residue 119 SER Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain D residue 40 GLN Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 119 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 100 optimal weight: 4.9990 chunk 17 optimal weight: 0.0870 chunk 52 optimal weight: 0.0870 chunk 93 optimal weight: 5.9990 chunk 72 optimal weight: 0.2980 chunk 20 optimal weight: 5.9990 chunk 25 optimal weight: 0.4980 chunk 89 optimal weight: 0.1980 chunk 73 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 overall best weight: 0.2336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 40 GLN L 53 ASN D 40 GLN F 53 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.137382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.112021 restraints weight = 11673.349| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.07 r_work: 0.3179 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13026 Z= 0.131 Angle : 0.571 6.334 17736 Z= 0.287 Chirality : 0.040 0.139 1824 Planarity : 0.004 0.031 2250 Dihedral : 7.667 81.133 1806 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.20 % Allowed : 16.99 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.54 (0.20), residues: 1602 helix: 3.52 (0.18), residues: 678 sheet: 0.62 (0.29), residues: 276 loop : 0.18 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 86 TYR 0.009 0.001 TYR C 103 PHE 0.013 0.001 PHE K 48 TRP 0.004 0.001 TRP D 54 HIS 0.001 0.000 HIS B 12 Details of bonding type rmsd covalent geometry : bond 0.00295 (13014) covalent geometry : angle 0.57077 (17724) SS BOND : bond 0.00212 ( 6) SS BOND : angle 0.23838 ( 12) hydrogen bonds : bond 0.05344 ( 786) hydrogen bonds : angle 4.30577 ( 2250) Misc. bond : bond 0.02702 ( 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 259 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 244 time to evaluate : 0.556 Fit side-chains REVERT: H 86 ARG cc_start: 0.7614 (ttp-110) cc_final: 0.7386 (mtt90) REVERT: J 40 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8003 (tt0) REVERT: D 40 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.8012 (tt0) REVERT: F 12 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7558 (tp) REVERT: F 118 SER cc_start: 0.6744 (OUTLIER) cc_final: 0.6460 (m) outliers start: 15 outliers final: 8 residues processed: 255 average time/residue: 0.6258 time to fit residues: 174.1588 Evaluate side-chains 251 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 239 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain J residue 40 GLN Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain D residue 40 GLN Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 118 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 13 optimal weight: 0.9990 chunk 152 optimal weight: 0.0670 chunk 114 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 126 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 153 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 152 GLN J 40 GLN J 53 ASN K 53 ASN L 53 ASN B 152 GLN D 40 GLN D 53 ASN E 53 ASN F 53 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.132372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.106458 restraints weight = 11619.964| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.06 r_work: 0.3096 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13026 Z= 0.154 Angle : 0.612 9.952 17736 Z= 0.309 Chirality : 0.042 0.135 1824 Planarity : 0.004 0.048 2250 Dihedral : 8.295 87.763 1806 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.36 % Allowed : 16.83 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.44 (0.20), residues: 1602 helix: 3.38 (0.18), residues: 678 sheet: 0.55 (0.29), residues: 276 loop : 0.19 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 86 TYR 0.011 0.001 TYR L 108 PHE 0.015 0.001 PHE J 48 TRP 0.006 0.001 TRP G 97 HIS 0.002 0.001 HIS H 58 Details of bonding type rmsd covalent geometry : bond 0.00331 (13014) covalent geometry : angle 0.61230 (17724) SS BOND : bond 0.00426 ( 6) SS BOND : angle 0.37942 ( 12) hydrogen bonds : bond 0.06686 ( 786) hydrogen bonds : angle 4.58192 ( 2250) Misc. bond : bond 0.02854 ( 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 261 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 244 time to evaluate : 0.469 Fit side-chains REVERT: H 86 ARG cc_start: 0.7659 (ttp-110) cc_final: 0.7456 (mtt90) REVERT: J 40 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8135 (tt0) REVERT: J 118 SER cc_start: 0.6763 (OUTLIER) cc_final: 0.6542 (m) REVERT: B 86 ARG cc_start: 0.7687 (ttp-110) cc_final: 0.7399 (mtp85) REVERT: D 40 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.8143 (tt0) REVERT: F 12 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7570 (tp) REVERT: F 118 SER cc_start: 0.6822 (OUTLIER) cc_final: 0.6480 (m) outliers start: 17 outliers final: 10 residues processed: 258 average time/residue: 0.6498 time to fit residues: 182.3886 Evaluate side-chains 258 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 243 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain J residue 40 GLN Chi-restraints excluded: chain J residue 118 SER Chi-restraints excluded: chain L residue 119 SER Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain D residue 40 GLN Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 119 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 95 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 127 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 139 optimal weight: 0.3980 chunk 144 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 152 GLN J 40 GLN J 53 ASN K 53 ASN L 53 ASN D 40 GLN E 53 ASN F 53 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.130391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.104093 restraints weight = 11600.485| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.07 r_work: 0.3063 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 2.25 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13026 Z= 0.180 Angle : 0.669 9.883 17736 Z= 0.345 Chirality : 0.043 0.133 1824 Planarity : 0.005 0.053 2250 Dihedral : 8.575 89.326 1806 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.44 % Allowed : 17.38 % 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: 2.25 (0.20), residues: 1602 helix: 3.22 (0.18), residues: 678 sheet: 0.58 (0.29), residues: 270 loop : 0.05 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 86 TYR 0.014 0.002 TYR L 108 PHE 0.017 0.002 PHE E 48 TRP 0.006 0.001 TRP B 97 HIS 0.003 0.001 HIS H 58 Details of bonding type rmsd covalent geometry : bond 0.00384 (13014) covalent geometry : angle 0.66955 (17724) SS BOND : bond 0.00552 ( 6) SS BOND : angle 0.50332 ( 12) hydrogen bonds : bond 0.07469 ( 786) hydrogen bonds : angle 4.78211 ( 2250) Misc. bond : bond 0.03114 ( 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 258 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 240 time to evaluate : 0.446 Fit side-chains REVERT: H 86 ARG cc_start: 0.7690 (ttp-110) cc_final: 0.7445 (mtp85) REVERT: I 6 GLU cc_start: 0.8063 (mp0) cc_final: 0.7574 (mp0) REVERT: J 40 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8170 (tt0) REVERT: J 118 SER cc_start: 0.6794 (OUTLIER) cc_final: 0.6553 (m) REVERT: B 86 ARG cc_start: 0.7710 (ttp-110) cc_final: 0.7424 (mtp85) REVERT: C 6 GLU cc_start: 0.8062 (mp0) cc_final: 0.7566 (mp0) REVERT: C 83 LYS cc_start: 0.6933 (OUTLIER) cc_final: 0.6731 (mtmm) REVERT: D 40 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8170 (tt0) REVERT: F 12 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7569 (tp) REVERT: F 118 SER cc_start: 0.6882 (OUTLIER) cc_final: 0.6512 (m) outliers start: 18 outliers final: 9 residues processed: 253 average time/residue: 0.6296 time to fit residues: 172.9957 Evaluate side-chains 253 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 238 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain J residue 40 GLN Chi-restraints excluded: chain J residue 118 SER Chi-restraints excluded: chain L residue 119 SER Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain D residue 40 GLN Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 119 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 80 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 137 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 152 GLN J 40 GLN J 53 ASN K 53 ASN K 75 ASN L 53 ASN D 40 GLN E 53 ASN F 53 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.129667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.103377 restraints weight = 11565.792| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.07 r_work: 0.3055 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13026 Z= 0.188 Angle : 0.689 9.879 17736 Z= 0.355 Chirality : 0.043 0.133 1824 Planarity : 0.005 0.053 2250 Dihedral : 8.639 88.018 1806 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.91 % Allowed : 16.91 % 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: 2.13 (0.20), residues: 1602 helix: 3.11 (0.18), residues: 678 sheet: 0.52 (0.29), residues: 270 loop : -0.01 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 86 TYR 0.015 0.002 TYR L 108 PHE 0.017 0.002 PHE K 48 TRP 0.007 0.002 TRP F 37 HIS 0.004 0.001 HIS H 58 Details of bonding type rmsd covalent geometry : bond 0.00402 (13014) covalent geometry : angle 0.68884 (17724) SS BOND : bond 0.00617 ( 6) SS BOND : angle 0.56873 ( 12) hydrogen bonds : bond 0.07722 ( 786) hydrogen bonds : angle 4.86631 ( 2250) Misc. bond : bond 0.03168 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6188.31 seconds wall clock time: 105 minutes 58.79 seconds (6358.79 seconds total)