Starting phenix.real_space_refine on Wed Jul 30 19:39:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pnu_17785/07_2025/8pnu_17785.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pnu_17785/07_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_17785/07_2025/8pnu_17785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pnu_17785/07_2025/8pnu_17785.map" model { file = "/net/cci-nas-00/data/ceres_data/8pnu_17785/07_2025/8pnu_17785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pnu_17785/07_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 7.99, per 1000 atoms: 0.62 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: 3.45 Conformation dependent library (CDL) restraints added in 1.7 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: 1.90 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: 4.20 Time building geometry restraints manager: 4.03 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: 0.09 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: 6.900 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: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 32.470 Find NCS groups from input model: 0.260 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: 0.000 Load rotamer database and sin/cos tables:13.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.370 ------------------------------------------------------------------------------- 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 : 1.347 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: 1.3288 time to fit residues: 478.9005 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 : 1.723 ------------------------------------------------------------------------------- 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 = 59)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.104966 restraints weight = 11556.015| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.05 r_work: 0.3053 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 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 : 1.249 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: 0.8095 (mp0) cc_final: 0.7617 (mp0) REVERT: J 4 GLN cc_start: 0.6550 (OUTLIER) cc_final: 0.6326 (mp10) REVERT: K 4 GLN cc_start: 0.6532 (OUTLIER) cc_final: 0.6208 (mt0) REVERT: L 12 LEU cc_start: 0.7979 (tp) cc_final: 0.7616 (tm) REVERT: A 2 LEU cc_start: 0.6679 (OUTLIER) cc_final: 0.6475 (mp) REVERT: B 2 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6400 (mt) REVERT: C 6 GLU cc_start: 0.8090 (mp0) cc_final: 0.7605 (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: 0.6339 (mp10) REVERT: D 118 SER cc_start: 0.7041 (OUTLIER) cc_final: 0.6760 (m) REVERT: F 12 LEU cc_start: 0.7948 (tp) cc_final: 0.7572 (tm) REVERT: F 118 SER cc_start: 0.6964 (OUTLIER) cc_final: 0.6450 (m) outliers start: 48 outliers final: 15 residues processed: 283 average time/residue: 1.3255 time to fit residues: 407.5814 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 : 1.455 ------------------------------------------------------------------------------- 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: 0.9990 chunk 25 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 134 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 126 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3541 r_free = 0.3541 target = 0.132709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.107164 restraints weight = 11746.349| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.05 r_work: 0.3082 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13021 Z= 0.163 Angle : 0.619 6.191 17726 Z= 0.317 Chirality : 0.042 0.135 1824 Planarity : 0.004 0.034 2250 Dihedral : 10.277 89.952 1806 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.83 % Allowed : 16.51 % Favored : 81.66 % 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: 2.35 (0.20), residues: 1602 helix: 3.32 (0.18), residues: 678 sheet: 0.69 (0.31), residues: 228 loop : 0.08 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 28 HIS 0.002 0.001 HIS H 58 PHE 0.018 0.002 PHE J 48 TYR 0.012 0.001 TYR L 108 ARG 0.003 0.000 ARG A 86 Details of bonding type rmsd hydrogen bonds : bond 0.07124 ( 786) hydrogen bonds : angle 4.80967 ( 2250) SS BOND : bond 0.00518 ( 1) SS BOND : angle 0.45178 ( 2) covalent geometry : bond 0.00342 (13014) covalent geometry : angle 0.61937 (17724) Misc. bond : bond 0.02943 ( 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 270 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 247 time to evaluate : 1.143 Fit side-chains REVERT: I 6 GLU cc_start: 0.8067 (mp0) cc_final: 0.7603 (mp0) REVERT: J 40 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8284 (tt0) REVERT: C 6 GLU cc_start: 0.8080 (mp0) cc_final: 0.7622 (mp0) REVERT: D 40 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8276 (tt0) REVERT: D 118 SER cc_start: 0.6919 (OUTLIER) cc_final: 0.6693 (m) REVERT: E 118 SER cc_start: 0.6897 (p) cc_final: 0.6604 (m) REVERT: F 118 SER cc_start: 0.6812 (OUTLIER) cc_final: 0.6361 (m) outliers start: 23 outliers final: 12 residues processed: 265 average time/residue: 1.2243 time to fit residues: 353.6365 Evaluate side-chains 255 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 239 time to evaluate : 1.377 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 72 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3541 r_free = 0.3541 target = 0.132775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.107252 restraints weight = 11608.977| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.04 r_work: 0.3106 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2397 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= 0.160 Angle : 0.611 6.162 17726 Z= 0.310 Chirality : 0.042 0.134 1824 Planarity : 0.004 0.033 2250 Dihedral : 9.376 89.515 1806 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 3.03 % Allowed : 15.87 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.32 (0.20), residues: 1602 helix: 3.30 (0.18), residues: 678 sheet: 0.58 (0.31), residues: 228 loop : 0.09 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 37 HIS 0.002 0.001 HIS H 58 PHE 0.018 0.002 PHE J 48 TYR 0.013 0.002 TYR L 108 ARG 0.003 0.000 ARG G 86 Details of bonding type rmsd hydrogen bonds : bond 0.07084 ( 786) hydrogen bonds : angle 4.78700 ( 2250) SS BOND : bond 0.00488 ( 1) SS BOND : angle 0.41869 ( 2) covalent geometry : bond 0.00336 (13014) covalent geometry : angle 0.61078 (17724) Misc. bond : bond 0.02993 ( 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 288 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 250 time to evaluate : 1.265 Fit side-chains REVERT: I 6 GLU cc_start: 0.8076 (mp0) cc_final: 0.7600 (mp0) REVERT: J 40 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8192 (tt0) REVERT: K 118 SER cc_start: 0.6933 (p) cc_final: 0.6599 (m) REVERT: L 12 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7609 (tp) REVERT: C 6 GLU cc_start: 0.8072 (mp0) cc_final: 0.7611 (mp0) REVERT: D 40 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.8200 (tt0) REVERT: D 118 SER cc_start: 0.6839 (OUTLIER) cc_final: 0.6630 (m) REVERT: E 118 SER cc_start: 0.6865 (p) cc_final: 0.6584 (m) REVERT: F 118 SER cc_start: 0.6811 (OUTLIER) cc_final: 0.6360 (m) outliers start: 38 outliers final: 16 residues processed: 284 average time/residue: 1.3727 time to fit residues: 426.0680 Evaluate side-chains 267 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 246 time to evaluate : 1.930 ------------------------------------------------------------------------------- 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 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 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=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: 4.9990 chunk 40 optimal weight: 0.2980 chunk 3 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 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: 1.1784 ------------------------------------------------------------------------------- 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 = 0.129513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.103237 restraints weight = 11510.354| |-----------------------------------------------------------------------------| 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: 2.23 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2498 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= 0.184 Angle : 0.653 6.157 17726 Z= 0.335 Chirality : 0.043 0.135 1824 Planarity : 0.004 0.033 2250 Dihedral : 8.783 87.978 1806 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.47 % Allowed : 15.87 % Favored : 81.66 % 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: 2.16 (0.20), residues: 1602 helix: 3.18 (0.18), residues: 678 sheet: 0.57 (0.32), residues: 228 loop : -0.03 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP F 37 HIS 0.003 0.001 HIS H 58 PHE 0.018 0.002 PHE J 48 TYR 0.015 0.002 TYR L 108 ARG 0.004 0.000 ARG B 86 Details of bonding type rmsd hydrogen bonds : bond 0.07776 ( 786) hydrogen bonds : angle 4.96200 ( 2250) SS BOND : bond 0.00647 ( 1) SS BOND : angle 0.48240 ( 2) covalent geometry : bond 0.00385 (13014) covalent geometry : angle 0.65318 (17724) Misc. bond : bond 0.03000 ( 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 275 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 244 time to evaluate : 1.151 Fit side-chains REVERT: I 6 GLU cc_start: 0.8066 (mp0) cc_final: 0.7596 (mp0) REVERT: I 83 LYS cc_start: 0.6990 (OUTLIER) cc_final: 0.6774 (mtmm) REVERT: J 40 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8156 (tt0) REVERT: C 6 GLU cc_start: 0.8069 (mp0) cc_final: 0.7613 (mp0) REVERT: C 83 LYS cc_start: 0.6974 (OUTLIER) cc_final: 0.6764 (mtmm) REVERT: D 40 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8174 (tt0) REVERT: D 118 SER cc_start: 0.6820 (OUTLIER) cc_final: 0.6593 (m) REVERT: F 12 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7611 (tp) REVERT: F 118 SER cc_start: 0.6853 (OUTLIER) cc_final: 0.6353 (m) outliers start: 31 outliers final: 18 residues processed: 268 average time/residue: 1.2767 time to fit residues: 372.8879 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 : 1.400 ------------------------------------------------------------------------------- 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 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 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 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: 2.9990 chunk 150 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 37 optimal weight: 0.0020 chunk 103 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- 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 = 0.3527 r_free = 0.3527 target = 0.131812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.105709 restraints weight = 11694.940| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.08 r_work: 0.3088 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13021 Z= 0.156 Angle : 0.611 6.181 17726 Z= 0.312 Chirality : 0.042 0.136 1824 Planarity : 0.004 0.033 2250 Dihedral : 8.390 88.508 1806 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.15 % Allowed : 16.99 % 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: 2.34 (0.20), residues: 1602 helix: 3.32 (0.18), residues: 678 sheet: 0.49 (0.29), residues: 270 loop : 0.12 (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 H 58 PHE 0.016 0.001 PHE K 48 TYR 0.011 0.001 TYR L 108 ARG 0.004 0.000 ARG H 86 Details of bonding type rmsd hydrogen bonds : bond 0.06868 ( 786) hydrogen bonds : angle 4.73352 ( 2250) SS BOND : bond 0.00486 ( 1) SS BOND : angle 0.38268 ( 2) covalent geometry : bond 0.00328 (13014) covalent geometry : angle 0.61128 (17724) Misc. bond : bond 0.02957 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 248 time to evaluate : 1.314 Fit side-chains REVERT: G 66 MET cc_start: 0.8695 (mmt) cc_final: 0.8464 (mmt) REVERT: I 6 GLU cc_start: 0.8036 (mp0) cc_final: 0.7561 (mp0) REVERT: I 83 LYS cc_start: 0.6877 (OUTLIER) cc_final: 0.6673 (mtmm) REVERT: J 40 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8157 (tt0) REVERT: K 118 SER cc_start: 0.6817 (p) cc_final: 0.6513 (m) REVERT: L 12 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7601 (tp) REVERT: A 66 MET cc_start: 0.8685 (mmt) cc_final: 0.8460 (mmt) REVERT: C 6 GLU cc_start: 0.8027 (mp0) cc_final: 0.7569 (mp0) REVERT: C 83 LYS cc_start: 0.6881 (OUTLIER) cc_final: 0.6675 (mtmm) REVERT: D 40 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.8191 (tt0) REVERT: F 12 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7617 (tp) REVERT: F 118 SER cc_start: 0.6777 (OUTLIER) cc_final: 0.6376 (m) outliers start: 27 outliers final: 18 residues processed: 271 average time/residue: 1.3799 time to fit residues: 408.6747 Evaluate side-chains 269 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 244 time to evaluate : 1.303 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 90 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 151 optimal weight: 0.0170 chunk 123 optimal weight: 6.9990 chunk 141 optimal weight: 0.7980 chunk 116 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 146 optimal weight: 0.5980 chunk 155 optimal weight: 0.4980 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.133222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.107292 restraints weight = 11645.332| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.07 r_work: 0.3111 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2542 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 6.172 17726 Z= 0.299 Chirality : 0.041 0.136 1824 Planarity : 0.004 0.032 2250 Dihedral : 8.168 87.765 1806 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.23 % Allowed : 16.59 % 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 (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: 3.38 (0.18), residues: 678 sheet: 0.57 (0.29), residues: 270 loop : 0.17 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 37 HIS 0.001 0.000 HIS H 58 PHE 0.015 0.001 PHE J 48 TYR 0.010 0.001 TYR L 108 ARG 0.005 0.000 ARG B 86 Details of bonding type rmsd hydrogen bonds : bond 0.06414 ( 786) hydrogen bonds : angle 4.60126 ( 2250) SS BOND : bond 0.00366 ( 1) SS BOND : angle 0.33786 ( 2) covalent geometry : bond 0.00311 (13014) covalent geometry : angle 0.59202 (17724) Misc. bond : bond 0.02818 ( 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 270 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 242 time to evaluate : 1.109 Fit side-chains REVERT: J 40 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8163 (tt0) REVERT: K 118 SER cc_start: 0.6729 (p) cc_final: 0.6492 (m) REVERT: L 12 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7563 (tp) REVERT: A 66 MET cc_start: 0.8695 (mmt) cc_final: 0.8495 (mmt) REVERT: D 40 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8175 (tt0) REVERT: E 118 SER cc_start: 0.6731 (p) cc_final: 0.6502 (m) REVERT: F 12 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7612 (tp) REVERT: F 118 SER cc_start: 0.6812 (OUTLIER) cc_final: 0.6452 (m) outliers start: 28 outliers final: 19 residues processed: 266 average time/residue: 1.5841 time to fit residues: 461.0637 Evaluate side-chains 263 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 239 time to evaluate : 1.279 ------------------------------------------------------------------------------- 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 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 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 151 optimal weight: 0.3980 chunk 57 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 143 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 115 optimal weight: 0.0870 chunk 81 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.3540 r_free = 0.3540 target = 0.132868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.106866 restraints weight = 11660.890| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.07 r_work: 0.3104 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2544 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= 0.151 Angle : 0.604 6.396 17726 Z= 0.307 Chirality : 0.041 0.135 1824 Planarity : 0.004 0.032 2250 Dihedral : 8.206 87.816 1806 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.39 % Allowed : 16.67 % 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: 2.38 (0.20), residues: 1602 helix: 3.36 (0.18), residues: 678 sheet: 0.56 (0.29), residues: 270 loop : 0.11 (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 0.006 0.000 ARG B 86 Details of bonding type rmsd hydrogen bonds : bond 0.06551 ( 786) hydrogen bonds : angle 4.61073 ( 2250) SS BOND : bond 0.00400 ( 1) SS BOND : angle 0.38857 ( 2) covalent geometry : bond 0.00323 (13014) covalent geometry : angle 0.60362 (17724) Misc. bond : bond 0.02967 ( 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 268 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 238 time to evaluate : 1.296 Fit side-chains REVERT: H 86 ARG cc_start: 0.7680 (ttp-110) cc_final: 0.7381 (mtp85) REVERT: J 40 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8175 (tt0) REVERT: K 118 SER cc_start: 0.6710 (p) cc_final: 0.6492 (m) REVERT: L 12 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7581 (tp) REVERT: A 66 MET cc_start: 0.8696 (mmt) cc_final: 0.8478 (mmt) REVERT: B 86 ARG cc_start: 0.7665 (ttp-110) cc_final: 0.7378 (mtp85) REVERT: D 40 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8199 (tt0) REVERT: E 118 SER cc_start: 0.6715 (p) cc_final: 0.6507 (m) REVERT: F 12 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7583 (tp) REVERT: F 118 SER cc_start: 0.6803 (OUTLIER) cc_final: 0.6448 (m) outliers start: 30 outliers final: 19 residues processed: 263 average time/residue: 1.2052 time to fit residues: 349.6602 Evaluate side-chains 260 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 236 time to evaluate : 1.427 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 152 optimal weight: 0.0980 chunk 105 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 71 optimal weight: 0.0020 chunk 19 optimal weight: 0.9990 chunk 4 optimal weight: 0.0270 overall best weight: 0.3046 ------------------------------------------------------------------------------- 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 = 0.3600 r_free = 0.3600 target = 0.137622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.112812 restraints weight = 11760.836| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.04 r_work: 0.3178 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13021 Z= 0.133 Angle : 0.577 9.916 17726 Z= 0.290 Chirality : 0.041 0.137 1824 Planarity : 0.004 0.031 2250 Dihedral : 7.783 82.808 1806 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.83 % Allowed : 17.38 % 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: 2.49 (0.21), residues: 1602 helix: 3.50 (0.18), residues: 678 sheet: 0.49 (0.29), residues: 276 loop : 0.18 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 54 HIS 0.001 0.000 HIS B 12 PHE 0.013 0.001 PHE K 48 TYR 0.007 0.001 TYR D 108 ARG 0.006 0.000 ARG C 86 Details of bonding type rmsd hydrogen bonds : bond 0.05566 ( 786) hydrogen bonds : angle 4.37319 ( 2250) SS BOND : bond 0.00280 ( 1) SS BOND : angle 0.26393 ( 2) covalent geometry : bond 0.00299 (13014) covalent geometry : angle 0.57696 (17724) Misc. bond : bond 0.02713 ( 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 269 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 246 time to evaluate : 1.384 Fit side-chains REVERT: H 86 ARG cc_start: 0.7621 (ttp-110) cc_final: 0.7371 (mtp85) REVERT: J 40 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.8170 (tt0) REVERT: B 86 ARG cc_start: 0.7619 (ttp-110) cc_final: 0.7369 (mtp85) REVERT: D 40 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8185 (tt0) REVERT: F 12 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7564 (tp) REVERT: F 118 SER cc_start: 0.6781 (OUTLIER) cc_final: 0.6506 (m) outliers start: 23 outliers final: 14 residues processed: 265 average time/residue: 1.1613 time to fit residues: 336.4305 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 : 1.434 ------------------------------------------------------------------------------- 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 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 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 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: 0.7980 chunk 105 optimal weight: 0.9980 chunk 118 optimal weight: 0.0770 chunk 114 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 40 optimal weight: 0.0670 chunk 53 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 overall best weight: 0.5676 ------------------------------------------------------------------------------- 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 = 0.3551 r_free = 0.3551 target = 0.133840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.107849 restraints weight = 11590.430| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.07 r_work: 0.3119 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2576 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= 0.147 Angle : 0.604 9.922 17726 Z= 0.304 Chirality : 0.041 0.135 1824 Planarity : 0.004 0.050 2250 Dihedral : 8.125 87.086 1806 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.07 % Allowed : 16.83 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.41 (0.18), residues: 678 sheet: 0.59 (0.29), residues: 270 loop : 0.16 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 97 HIS 0.002 0.000 HIS B 58 PHE 0.014 0.001 PHE J 48 TYR 0.010 0.001 TYR F 96 ARG 0.012 0.000 ARG I 86 Details of bonding type rmsd hydrogen bonds : bond 0.06300 ( 786) hydrogen bonds : angle 4.51746 ( 2250) SS BOND : bond 0.00361 ( 1) SS BOND : angle 0.36760 ( 2) covalent geometry : bond 0.00322 (13014) covalent geometry : angle 0.60424 (17724) Misc. bond : bond 0.02978 ( 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: 26 poor density : 246 time to evaluate : 1.347 Fit side-chains REVERT: H 86 ARG cc_start: 0.7648 (ttp-110) cc_final: 0.7379 (mtp85) REVERT: J 40 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.8146 (tt0) REVERT: B 86 ARG cc_start: 0.7644 (ttp-110) cc_final: 0.7379 (mtp85) REVERT: D 40 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8176 (tt0) REVERT: F 12 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7571 (tp) REVERT: F 118 SER cc_start: 0.6822 (OUTLIER) cc_final: 0.6524 (m) outliers start: 26 outliers final: 17 residues processed: 268 average time/residue: 1.2797 time to fit residues: 374.3205 Evaluate side-chains 267 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 246 time to evaluate : 1.326 ------------------------------------------------------------------------------- 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 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 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 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: 1.9990 chunk 10 optimal weight: 0.0770 chunk 97 optimal weight: 0.0980 chunk 101 optimal weight: 0.5980 chunk 92 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 152 GLN K 53 ASN L 53 ASN E 53 ASN F 53 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.134603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.108652 restraints weight = 11646.683| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.07 r_work: 0.3131 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: 0.8623 moved from start: 0.2580 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= 0.144 Angle : 0.602 9.936 17726 Z= 0.305 Chirality : 0.041 0.135 1824 Planarity : 0.004 0.053 2250 Dihedral : 8.019 86.092 1806 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.83 % Allowed : 17.30 % 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: 2.44 (0.20), residues: 1602 helix: 3.41 (0.18), residues: 678 sheet: 0.60 (0.29), residues: 270 loop : 0.13 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 37 HIS 0.001 0.000 HIS B 58 PHE 0.014 0.001 PHE D 48 TYR 0.010 0.001 TYR F 96 ARG 0.013 0.000 ARG C 86 Details of bonding type rmsd hydrogen bonds : bond 0.06085 ( 786) hydrogen bonds : angle 4.46947 ( 2250) SS BOND : bond 0.00324 ( 1) SS BOND : angle 0.32727 ( 2) covalent geometry : bond 0.00317 (13014) covalent geometry : angle 0.60174 (17724) Misc. bond : bond 0.02910 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13015.24 seconds wall clock time: 231 minutes 19.52 seconds (13879.52 seconds total)