Starting phenix.real_space_refine on Thu May 15 04:28:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pnu_17785/05_2025/8pnu_17785.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pnu_17785/05_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_17785/05_2025/8pnu_17785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pnu_17785/05_2025/8pnu_17785.map" model { file = "/net/cci-nas-00/data/ceres_data/8pnu_17785/05_2025/8pnu_17785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pnu_17785/05_2025/8pnu_17785.cif" } resolution = 2.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 12888 Number of models: 1 Model: "" Number of chains: 19 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: "B" 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: "C" 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: "E" 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: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'ABN': 1} Classifications: {'undetermined': 1} Chain: "B" 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: "C" 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: H, G, D, F, K, J, L, I Time building chain proxies: 7.25, per 1000 atoms: 0.56 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=1, symmetry=0 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 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: 3.19 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.60 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: 4.04 Time building geometry restraints manager: 3.60 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: 698 35.60 - 53.41: 139 53.41 - 71.21: 96 71.21 - 89.01: 30 Dihedral angle restraints: 7233 sinusoidal: 2763 harmonic: 4470 Sorted by residual: dihedral pdb=" CB CYS J 23 " pdb=" SG CYS J 23 " pdb=" SG CYS J 97 " pdb=" CB CYS J 97 " ideal model delta sinusoidal sigma weight residual 93.00 59.96 33.04 1 1.00e+01 1.00e-02 1.55e+01 dihedral pdb=" C1A HEM H 201 " pdb=" C2A HEM H 201 " pdb=" CAA HEM H 201 " pdb=" CBA HEM H 201 " ideal model delta sinusoidal sigma weight residual 180.00 102.16 77.84 2 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" C1A HEM I 202 " pdb=" C2A HEM I 202 " pdb=" CAA HEM I 202 " pdb=" CBA HEM I 202 " ideal model delta sinusoidal sigma weight residual 180.00 102.17 77.83 2 2.00e+01 2.50e-03 1.15e+01 ... (remaining 7230 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: 2.04 - 2.61: 107 2.61 - 3.18: 10878 3.18 - 3.76: 21177 3.76 - 4.33: 29552 4.33 - 4.90: 49089 Nonbonded interactions: 110803 Sorted by model distance: nonbonded pdb=" SG CYS K 23 " pdb=" SG CYS K 97 " model vdw 2.038 3.760 nonbonded pdb=" SG CYS D 23 " pdb=" SG CYS D 97 " model vdw 2.039 3.760 nonbonded pdb=" SG CYS F 23 " pdb=" SG CYS F 97 " model vdw 2.039 3.760 nonbonded pdb=" SG CYS E 23 " pdb=" SG CYS E 97 " model vdw 2.039 3.760 nonbonded pdb=" SG CYS L 23 " pdb=" SG CYS L 97 " model vdw 2.039 3.760 ... (remaining 110798 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: 0.08 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'H' } ncs_group { reference = chain 'A' selection = chain 'G' } ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'F' selection = chain 'K' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'I' } 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: 7.280 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: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 29.500 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.480 ------------------------------------------------------------------------------- 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 13021 Z= 0.173 Angle : 0.644 6.655 17726 Z= 0.346 Chirality : 0.041 0.128 1824 Planarity : 0.006 0.074 2250 Dihedral : 17.635 89.011 4434 Min Nonbonded Distance : 2.038 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.007 0.001 TRP A 28 HIS 0.002 0.001 HIS H 12 PHE 0.012 0.002 PHE K 48 TYR 0.008 0.002 TYR I 103 ARG 0.003 0.000 ARG H 112 Details of bonding type rmsd hydrogen bonds : bond 0.11761 ( 786) hydrogen bonds : angle 5.39210 ( 2250) SS BOND : bond 0.00806 ( 1) SS BOND : angle 0.83336 ( 2) covalent geometry : bond 0.00354 (13014) covalent geometry : angle 0.64371 (17724) 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 : 1.366 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: 1.2703 time to fit residues: 456.6134 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 : 1.378 ------------------------------------------------------------------------------- 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 131 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 47 optimal weight: 0.0970 chunk 74 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 4 GLN 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.130849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.104969 restraints weight = 11556.020| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.05 r_work: 0.3052 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 13021 Z= 0.197 Angle : 0.678 6.380 17726 Z= 0.350 Chirality : 0.044 0.135 1824 Planarity : 0.005 0.034 2250 Dihedral : 10.020 86.185 1810 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 3.83 % Allowed : 14.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.20), residues: 1602 helix: 3.32 (0.19), residues: 678 sheet: 0.70 (0.31), residues: 228 loop : 0.20 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 28 HIS 0.004 0.002 HIS H 58 PHE 0.020 0.002 PHE K 48 TYR 0.015 0.002 TYR L 108 ARG 0.002 0.000 ARG H 56 Details of bonding type rmsd hydrogen bonds : bond 0.08125 ( 786) hydrogen bonds : angle 5.05709 ( 2250) SS BOND : bond 0.00631 ( 1) SS BOND : angle 0.48027 ( 2) covalent geometry : bond 0.00418 (13014) covalent geometry : angle 0.67818 (17724) Misc. bond : bond 0.02694 ( 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 293 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 245 time to evaluate : 1.293 Fit side-chains REVERT: H 2 LEU cc_start: 0.6759 (OUTLIER) cc_final: 0.6429 (mt) REVERT: I 2 LEU cc_start: 0.6791 (OUTLIER) cc_final: 0.6490 (mt) REVERT: I 6 GLU cc_start: 0.8094 (mp0) cc_final: 0.7616 (mp0) REVERT: J 4 GLN cc_start: 0.6552 (OUTLIER) cc_final: 0.6328 (mp10) REVERT: K 4 GLN cc_start: 0.6534 (OUTLIER) cc_final: 0.6210 (mt0) REVERT: L 12 LEU cc_start: 0.7982 (tp) cc_final: 0.7619 (tm) REVERT: A 2 LEU cc_start: 0.6678 (OUTLIER) cc_final: 0.6474 (mp) REVERT: B 2 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6400 (mt) REVERT: C 6 GLU cc_start: 0.8089 (mp0) cc_final: 0.7603 (mp0) REVERT: C 83 LYS cc_start: 0.7014 (OUTLIER) cc_final: 0.6805 (mtmm) REVERT: D 4 GLN cc_start: 0.6561 (OUTLIER) cc_final: 0.6340 (mp10) REVERT: D 118 SER cc_start: 0.7044 (OUTLIER) cc_final: 0.6763 (m) REVERT: F 12 LEU cc_start: 0.7953 (tp) cc_final: 0.7577 (tm) REVERT: F 118 SER cc_start: 0.6967 (OUTLIER) cc_final: 0.6453 (m) outliers start: 48 outliers final: 15 residues processed: 283 average time/residue: 1.2516 time to fit residues: 384.6178 Evaluate side-chains 267 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 242 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 4 GLN Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain K residue 4 GLN 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 20 THR Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 118 SER 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 27 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 3 optimal weight: 0.0470 chunk 35 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 134 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- 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 L 40 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 = 0.3553 r_free = 0.3553 target = 0.133626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.108062 restraints weight = 11774.147| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.06 r_work: 0.3102 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13021 Z= 0.152 Angle : 0.600 6.204 17726 Z= 0.306 Chirality : 0.041 0.137 1824 Planarity : 0.004 0.034 2250 Dihedral : 10.210 89.413 1806 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.75 % Allowed : 16.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.20), residues: 1602 helix: 3.40 (0.18), residues: 678 sheet: 0.72 (0.31), residues: 228 loop : 0.12 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 28 HIS 0.002 0.001 HIS H 58 PHE 0.017 0.002 PHE J 48 TYR 0.011 0.001 TYR L 108 ARG 0.002 0.000 ARG A 86 Details of bonding type rmsd hydrogen bonds : bond 0.06737 ( 786) hydrogen bonds : angle 4.70489 ( 2250) SS BOND : bond 0.00445 ( 1) SS BOND : angle 0.38127 ( 2) covalent geometry : bond 0.00322 (13014) covalent geometry : angle 0.60020 (17724) Misc. bond : bond 0.02811 ( 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 273 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 251 time to evaluate : 1.308 Fit side-chains REVERT: K 118 SER cc_start: 0.6985 (p) cc_final: 0.6624 (m) REVERT: D 40 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8275 (tt0) REVERT: D 118 SER cc_start: 0.6961 (OUTLIER) cc_final: 0.6740 (m) REVERT: E 118 SER cc_start: 0.6861 (p) cc_final: 0.6600 (m) REVERT: F 118 SER cc_start: 0.6846 (OUTLIER) cc_final: 0.6413 (m) outliers start: 22 outliers final: 11 residues processed: 268 average time/residue: 1.1855 time to fit residues: 346.8433 Evaluate side-chains 259 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 245 time to evaluate : 1.257 ------------------------------------------------------------------------------- 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 116 THR Chi-restraints excluded: chain K 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 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 27 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 101 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 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 = 0.3540 r_free = 0.3540 target = 0.132701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.107127 restraints weight = 11609.774| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.05 r_work: 0.3075 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13021 Z= 0.161 Angle : 0.613 6.168 17726 Z= 0.312 Chirality : 0.042 0.134 1824 Planarity : 0.004 0.034 2250 Dihedral : 9.657 89.945 1806 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 3.27 % Allowed : 15.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.20), residues: 1602 helix: 3.32 (0.18), residues: 678 sheet: 0.59 (0.31), residues: 228 loop : 0.11 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 37 HIS 0.002 0.001 HIS B 58 PHE 0.017 0.002 PHE J 48 TYR 0.013 0.002 TYR F 108 ARG 0.003 0.000 ARG G 86 Details of bonding type rmsd hydrogen bonds : bond 0.07130 ( 786) hydrogen bonds : angle 4.78047 ( 2250) SS BOND : bond 0.00515 ( 1) SS BOND : angle 0.40379 ( 2) covalent geometry : bond 0.00339 (13014) covalent geometry : angle 0.61321 (17724) Misc. bond : bond 0.02939 ( 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 295 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 254 time to evaluate : 1.312 Fit side-chains REVERT: I 6 GLU cc_start: 0.8064 (mp0) cc_final: 0.7579 (mp0) REVERT: K 118 SER cc_start: 0.6940 (p) cc_final: 0.6611 (m) REVERT: L 12 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7632 (tp) REVERT: C 6 GLU cc_start: 0.8070 (mp0) cc_final: 0.7600 (mp0) REVERT: D 40 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.8128 (tt0) REVERT: E 118 SER cc_start: 0.6859 (p) cc_final: 0.6592 (m) REVERT: F 118 SER cc_start: 0.6810 (OUTLIER) cc_final: 0.6365 (m) outliers start: 41 outliers final: 16 residues processed: 288 average time/residue: 1.1750 time to fit residues: 370.6363 Evaluate side-chains 266 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 247 time to evaluate : 1.509 ------------------------------------------------------------------------------- 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 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 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 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 35 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 40 optimal weight: 0.1980 chunk 3 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 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 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 = 0.3502 r_free = 0.3502 target = 0.129676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.103387 restraints weight = 11513.341| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.06 r_work: 0.3056 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 2.24 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13021 Z= 0.182 Angle : 0.651 6.151 17726 Z= 0.333 Chirality : 0.043 0.134 1824 Planarity : 0.004 0.033 2250 Dihedral : 8.797 88.000 1806 Min Nonbonded Distance : 2.495 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.20), residues: 1602 helix: 3.21 (0.18), residues: 678 sheet: 0.48 (0.30), residues: 270 loop : 0.11 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP F 37 HIS 0.003 0.001 HIS B 58 PHE 0.018 0.002 PHE J 48 TYR 0.015 0.002 TYR L 108 ARG 0.003 0.000 ARG B 86 Details of bonding type rmsd hydrogen bonds : bond 0.07758 ( 786) hydrogen bonds : angle 4.95180 ( 2250) SS BOND : bond 0.00651 ( 1) SS BOND : angle 0.49924 ( 2) covalent geometry : bond 0.00382 (13014) covalent geometry : angle 0.65059 (17724) Misc. bond : bond 0.02908 ( 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: 31 poor density : 245 time to evaluate : 1.287 Fit side-chains REVERT: H 86 ARG cc_start: 0.7751 (ttp-110) cc_final: 0.7449 (mtp85) REVERT: I 6 GLU cc_start: 0.8057 (mp0) cc_final: 0.7584 (mp0) REVERT: I 83 LYS cc_start: 0.6982 (OUTLIER) cc_final: 0.6775 (mtmm) REVERT: B 86 ARG cc_start: 0.7748 (ttp-110) cc_final: 0.7461 (mtp85) REVERT: C 6 GLU cc_start: 0.8069 (mp0) cc_final: 0.7609 (mp0) REVERT: C 83 LYS cc_start: 0.6969 (OUTLIER) cc_final: 0.6761 (mtmm) REVERT: D 40 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8068 (tt0) REVERT: F 12 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7628 (tp) REVERT: F 118 SER cc_start: 0.6858 (OUTLIER) cc_final: 0.6365 (m) outliers start: 31 outliers final: 18 residues processed: 269 average time/residue: 1.1735 time to fit residues: 344.6559 Evaluate side-chains 266 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 243 time to evaluate : 1.310 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 147 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 37 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3529 r_free = 0.3529 target = 0.132012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.105952 restraints weight = 11692.701| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.07 r_work: 0.3092 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13021 Z= 0.154 Angle : 0.607 6.160 17726 Z= 0.309 Chirality : 0.042 0.137 1824 Planarity : 0.004 0.033 2250 Dihedral : 8.366 88.409 1806 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.07 % Allowed : 17.15 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.20), residues: 1602 helix: 3.33 (0.18), residues: 678 sheet: 0.55 (0.29), residues: 270 loop : 0.13 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 37 HIS 0.002 0.001 HIS B 58 PHE 0.016 0.001 PHE J 48 TYR 0.011 0.001 TYR L 108 ARG 0.004 0.000 ARG C 86 Details of bonding type rmsd hydrogen bonds : bond 0.06811 ( 786) hydrogen bonds : angle 4.70818 ( 2250) SS BOND : bond 0.00475 ( 1) SS BOND : angle 0.36281 ( 2) covalent geometry : bond 0.00325 (13014) covalent geometry : angle 0.60697 (17724) Misc. bond : bond 0.02938 ( 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 276 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 250 time to evaluate : 1.389 Fit side-chains REVERT: I 6 GLU cc_start: 0.8042 (mp0) cc_final: 0.7573 (mp0) REVERT: I 83 LYS cc_start: 0.6874 (OUTLIER) cc_final: 0.6672 (mtmm) REVERT: K 118 SER cc_start: 0.6817 (p) cc_final: 0.6542 (m) REVERT: L 12 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7596 (tp) REVERT: A 66 MET cc_start: 0.8690 (mmt) cc_final: 0.8474 (mmt) REVERT: C 6 GLU cc_start: 0.8016 (mp0) cc_final: 0.7560 (mp0) REVERT: C 83 LYS cc_start: 0.6878 (OUTLIER) cc_final: 0.6674 (mtmm) REVERT: D 40 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8137 (tt0) REVERT: E 118 SER cc_start: 0.6781 (p) cc_final: 0.6518 (m) REVERT: F 12 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7616 (tp) REVERT: F 118 SER cc_start: 0.6813 (OUTLIER) cc_final: 0.6409 (m) outliers start: 26 outliers final: 18 residues processed: 271 average time/residue: 1.1739 time to fit residues: 347.7427 Evaluate side-chains 271 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 247 time to evaluate : 1.297 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 106 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 151 optimal weight: 0.0050 chunk 123 optimal weight: 6.9990 chunk 141 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 chunk 146 optimal weight: 0.8980 chunk 155 optimal weight: 0.2980 overall best weight: 0.5394 ------------------------------------------------------------------------------- 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 = 0.3547 r_free = 0.3547 target = 0.133447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.107497 restraints weight = 11634.953| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.07 r_work: 0.3114 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 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 : 0.003 0.048 13021 Z= 0.145 Angle : 0.592 6.145 17726 Z= 0.299 Chirality : 0.041 0.136 1824 Planarity : 0.004 0.032 2250 Dihedral : 8.153 87.683 1806 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.99 % Allowed : 16.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.20), residues: 1602 helix: 3.39 (0.18), residues: 678 sheet: 0.59 (0.29), residues: 270 loop : 0.15 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 37 HIS 0.001 0.000 HIS B 58 PHE 0.015 0.001 PHE J 48 TYR 0.010 0.001 TYR D 108 ARG 0.005 0.000 ARG B 86 Details of bonding type rmsd hydrogen bonds : bond 0.06378 ( 786) hydrogen bonds : angle 4.58279 ( 2250) SS BOND : bond 0.00384 ( 1) SS BOND : angle 0.29896 ( 2) covalent geometry : bond 0.00311 (13014) covalent geometry : angle 0.59169 (17724) Misc. bond : bond 0.02821 ( 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 267 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 242 time to evaluate : 1.498 Fit side-chains REVERT: K 118 SER cc_start: 0.6702 (p) cc_final: 0.6490 (m) REVERT: L 12 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7576 (tp) REVERT: A 66 MET cc_start: 0.8683 (mmt) cc_final: 0.8472 (mmt) REVERT: D 40 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8138 (tt0) REVERT: E 118 SER cc_start: 0.6689 (p) cc_final: 0.6467 (m) REVERT: F 12 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7598 (tp) REVERT: F 118 SER cc_start: 0.6776 (OUTLIER) cc_final: 0.6435 (m) outliers start: 25 outliers final: 15 residues processed: 262 average time/residue: 1.1423 time to fit residues: 327.5095 Evaluate side-chains 257 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 238 time to evaluate : 1.263 ------------------------------------------------------------------------------- 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 116 THR Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 116 THR 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 116 THR Chi-restraints excluded: chain F residue 12 LEU 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 151 optimal weight: 0.0970 chunk 57 optimal weight: 0.9990 chunk 126 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 143 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 133 optimal weight: 0.2980 chunk 80 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 81 optimal weight: 0.4980 chunk 131 optimal weight: 3.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 = 0.3558 r_free = 0.3558 target = 0.134329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.108600 restraints weight = 11729.722| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.07 r_work: 0.3130 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13021 Z= 0.141 Angle : 0.586 6.389 17726 Z= 0.296 Chirality : 0.041 0.136 1824 Planarity : 0.004 0.032 2250 Dihedral : 8.026 86.180 1806 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.23 % Allowed : 16.83 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.20), residues: 1602 helix: 3.44 (0.18), residues: 678 sheet: 0.60 (0.29), residues: 270 loop : 0.15 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 54 HIS 0.001 0.000 HIS H 58 PHE 0.014 0.001 PHE D 48 TYR 0.009 0.001 TYR L 108 ARG 0.006 0.000 ARG B 86 Details of bonding type rmsd hydrogen bonds : bond 0.06084 ( 786) hydrogen bonds : angle 4.49254 ( 2250) SS BOND : bond 0.00338 ( 1) SS BOND : angle 0.26306 ( 2) covalent geometry : bond 0.00308 (13014) covalent geometry : angle 0.58645 (17724) Misc. bond : bond 0.02736 ( 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 266 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 238 time to evaluate : 1.492 Fit side-chains REVERT: H 86 ARG cc_start: 0.7664 (ttp-110) cc_final: 0.7358 (mtp85) REVERT: L 12 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7582 (tp) REVERT: B 86 ARG cc_start: 0.7654 (ttp-110) cc_final: 0.7359 (mtp85) REVERT: D 40 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8117 (tt0) REVERT: F 12 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7570 (tp) REVERT: F 118 SER cc_start: 0.6768 (OUTLIER) cc_final: 0.6463 (m) outliers start: 28 outliers final: 18 residues processed: 262 average time/residue: 1.1873 time to fit residues: 342.9428 Evaluate side-chains 256 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 234 time to evaluate : 1.365 ------------------------------------------------------------------------------- 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 152 optimal weight: 0.2980 chunk 105 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 40 optimal weight: 0.4980 chunk 76 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3548 r_free = 0.3548 target = 0.133577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.107573 restraints weight = 11583.687| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.07 r_work: 0.3114 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13021 Z= 0.148 Angle : 0.601 10.005 17726 Z= 0.304 Chirality : 0.041 0.134 1824 Planarity : 0.004 0.046 2250 Dihedral : 8.143 87.384 1806 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.23 % Allowed : 16.83 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.20), residues: 1602 helix: 3.37 (0.18), residues: 678 sheet: 0.57 (0.29), residues: 270 loop : 0.13 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 37 HIS 0.002 0.000 HIS B 58 PHE 0.015 0.001 PHE J 48 TYR 0.010 0.001 TYR L 108 ARG 0.012 0.000 ARG C 86 Details of bonding type rmsd hydrogen bonds : bond 0.06390 ( 786) hydrogen bonds : angle 4.54796 ( 2250) SS BOND : bond 0.00396 ( 1) SS BOND : angle 0.32188 ( 2) covalent geometry : bond 0.00320 (13014) covalent geometry : angle 0.60147 (17724) Misc. bond : bond 0.02948 ( 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 268 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 240 time to evaluate : 1.320 Fit side-chains REVERT: H 86 ARG cc_start: 0.7663 (ttp-110) cc_final: 0.7379 (mtp85) REVERT: L 12 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7581 (tp) REVERT: B 86 ARG cc_start: 0.7660 (ttp-110) cc_final: 0.7383 (mtp85) REVERT: D 40 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8173 (tt0) REVERT: F 12 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7571 (tp) REVERT: F 118 SER cc_start: 0.6823 (OUTLIER) cc_final: 0.6524 (m) outliers start: 28 outliers final: 18 residues processed: 263 average time/residue: 1.1505 time to fit residues: 331.0693 Evaluate side-chains 261 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 239 time to evaluate : 1.320 ------------------------------------------------------------------------------- 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 23 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 105 optimal weight: 0.5980 chunk 118 optimal weight: 0.0770 chunk 114 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 40 optimal weight: 0.0870 chunk 53 optimal weight: 2.9990 chunk 128 optimal weight: 0.1980 overall best weight: 0.3916 ------------------------------------------------------------------------------- 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 = 0.3569 r_free = 0.3569 target = 0.135233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.109610 restraints weight = 11682.946| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.07 r_work: 0.3143 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13021 Z= 0.139 Angle : 0.590 9.927 17726 Z= 0.298 Chirality : 0.041 0.136 1824 Planarity : 0.004 0.049 2250 Dihedral : 7.919 84.635 1806 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.23 % Allowed : 16.83 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.20), residues: 1602 helix: 3.43 (0.18), residues: 678 sheet: 0.58 (0.29), residues: 270 loop : 0.16 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 54 HIS 0.001 0.000 HIS B 58 PHE 0.014 0.001 PHE J 48 TYR 0.008 0.001 TYR D 108 ARG 0.012 0.000 ARG I 86 Details of bonding type rmsd hydrogen bonds : bond 0.05862 ( 786) hydrogen bonds : angle 4.42616 ( 2250) SS BOND : bond 0.00300 ( 1) SS BOND : angle 0.25224 ( 2) covalent geometry : bond 0.00309 (13014) covalent geometry : angle 0.59035 (17724) Misc. bond : bond 0.02743 ( 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 272 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 244 time to evaluate : 1.390 Fit side-chains REVERT: H 86 ARG cc_start: 0.7635 (ttp-110) cc_final: 0.7355 (mtp85) REVERT: B 86 ARG cc_start: 0.7629 (ttp-110) cc_final: 0.7357 (mtp85) REVERT: D 40 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8144 (tt0) REVERT: F 118 SER cc_start: 0.6795 (OUTLIER) cc_final: 0.6550 (m) outliers start: 28 outliers final: 19 residues processed: 268 average time/residue: 1.1979 time to fit residues: 350.8666 Evaluate side-chains 262 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 241 time to evaluate : 1.469 ------------------------------------------------------------------------------- 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 93 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 10 optimal weight: 0.2980 chunk 97 optimal weight: 0.0870 chunk 101 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 K 53 ASN L 53 ASN B 152 GLN E 53 ASN F 53 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.134389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.108413 restraints weight = 11642.282| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.07 r_work: 0.3125 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13021 Z= 0.146 Angle : 0.602 9.937 17726 Z= 0.305 Chirality : 0.041 0.135 1824 Planarity : 0.004 0.033 2250 Dihedral : 8.061 86.818 1806 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.07 % Allowed : 17.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.20), residues: 1602 helix: 3.38 (0.18), residues: 678 sheet: 0.60 (0.29), residues: 270 loop : 0.15 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 97 HIS 0.001 0.000 HIS B 58 PHE 0.014 0.001 PHE J 48 TYR 0.010 0.001 TYR D 108 ARG 0.009 0.000 ARG I 86 Details of bonding type rmsd hydrogen bonds : bond 0.06166 ( 786) hydrogen bonds : angle 4.48570 ( 2250) SS BOND : bond 0.00341 ( 1) SS BOND : angle 0.30232 ( 2) covalent geometry : bond 0.00319 (13014) covalent geometry : angle 0.60187 (17724) Misc. bond : bond 0.02912 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11938.78 seconds wall clock time: 205 minutes 45.83 seconds (12345.83 seconds total)