Starting phenix.real_space_refine on Mon Dec 30 08:49:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pnu_17785/12_2024/8pnu_17785.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pnu_17785/12_2024/8pnu_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_17785/12_2024/8pnu_17785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pnu_17785/12_2024/8pnu_17785.map" model { file = "/net/cci-nas-00/data/ceres_data/8pnu_17785/12_2024/8pnu_17785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pnu_17785/12_2024/8pnu_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-5532/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: 8.32, per 1000 atoms: 0.65 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: 3.67 Conformation dependent library (CDL) restraints added in 1.8 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: 1.94 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: 4.61 Time building geometry restraints manager: 4.00 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 2 through 156) selection = (chain 'B' and resid 2 through 156) selection = (chain 'C' and resid 2 through 156) selection = (chain 'G' and resid 2 through 156) selection = (chain 'H' and resid 2 through 156) selection = (chain 'I' and resid 2 through 156) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 33.550 Find NCS groups from input model: 0.600 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:14.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.040 ------------------------------------------------------------------------------- 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 13014 Z= 0.237 Angle : 0.644 6.655 17724 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 *********************** 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 : 1.662 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: 1.3435 time to fit residues: 483.2165 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 : 1.701 ------------------------------------------------------------------------------- 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: 0.3980 chunk 74 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 13014 Z= 0.285 Angle : 0.682 6.530 17724 Z= 0.352 Chirality : 0.044 0.133 1824 Planarity : 0.005 0.034 2250 Dihedral : 10.069 86.337 1810 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.04 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: 2.41 (0.20), residues: 1602 helix: 3.31 (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 0.001 HIS C 58 PHE 0.021 0.002 PHE J 48 TYR 0.015 0.002 TYR L 108 ARG 0.002 0.000 ARG H 56 *********************** 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 292 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 244 time to evaluate : 1.509 Fit side-chains REVERT: G 2 LEU cc_start: 0.6837 (OUTLIER) cc_final: 0.6471 (mp) REVERT: H 2 LEU cc_start: 0.6867 (OUTLIER) cc_final: 0.6569 (mt) REVERT: I 2 LEU cc_start: 0.6872 (OUTLIER) cc_final: 0.6614 (mt) REVERT: I 6 GLU cc_start: 0.7959 (mp0) cc_final: 0.7606 (mp0) REVERT: L 12 LEU cc_start: 0.8133 (tp) cc_final: 0.7872 (tm) REVERT: B 2 LEU cc_start: 0.6851 (OUTLIER) cc_final: 0.6542 (mt) REVERT: C 6 GLU cc_start: 0.7955 (mp0) cc_final: 0.7593 (mp0) REVERT: D 118 SER cc_start: 0.7259 (OUTLIER) cc_final: 0.7039 (m) REVERT: F 12 LEU cc_start: 0.8102 (tp) cc_final: 0.7828 (tm) REVERT: F 118 SER cc_start: 0.7222 (OUTLIER) cc_final: 0.6764 (m) outliers start: 48 outliers final: 15 residues processed: 282 average time/residue: 1.3584 time to fit residues: 416.1937 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 : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain A residue 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 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 78 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 153 optimal weight: 6.9990 chunk 126 optimal weight: 0.9990 chunk 140 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 40 GLN K 40 GLN L 40 GLN D 40 GLN E 40 GLN F 40 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13014 Z= 0.234 Angle : 0.622 6.203 17724 Z= 0.319 Chirality : 0.042 0.134 1824 Planarity : 0.004 0.034 2250 Dihedral : 10.174 89.824 1806 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.99 % Allowed : 16.35 % 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 0.007 0.001 TRP H 28 HIS 0.002 0.001 HIS H 58 PHE 0.018 0.002 PHE J 48 TYR 0.012 0.002 TYR F 108 ARG 0.003 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 246 time to evaluate : 1.696 Fit side-chains REVERT: I 6 GLU cc_start: 0.7929 (mp0) cc_final: 0.7568 (mp0) REVERT: J 40 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8203 (tt0) REVERT: L 53 ASN cc_start: 0.7143 (t0) cc_final: 0.6867 (t0) REVERT: C 6 GLU cc_start: 0.7933 (mp0) cc_final: 0.7596 (mp0) REVERT: D 40 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.8201 (tt0) REVERT: F 53 ASN cc_start: 0.7166 (t0) cc_final: 0.6868 (t0) REVERT: F 118 SER cc_start: 0.7063 (OUTLIER) cc_final: 0.6672 (m) outliers start: 25 outliers final: 12 residues processed: 266 average time/residue: 1.3125 time to fit residues: 380.1832 Evaluate side-chains 250 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 235 time to evaluate : 1.700 ------------------------------------------------------------------------------- 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 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 140 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 134 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 B 152 GLN D 40 GLN F 40 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 13014 Z= 0.275 Angle : 0.672 6.127 17724 Z= 0.344 Chirality : 0.044 0.133 1824 Planarity : 0.005 0.034 2250 Dihedral : 9.158 86.845 1806 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.95 % Allowed : 16.19 % 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: 2.12 (0.20), residues: 1602 helix: 3.13 (0.18), residues: 678 sheet: 0.53 (0.32), residues: 228 loop : -0.02 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP L 37 HIS 0.004 0.001 HIS B 58 PHE 0.019 0.002 PHE J 48 TYR 0.017 0.002 TYR D 108 ARG 0.003 0.000 ARG G 86 *********************** 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 280 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 243 time to evaluate : 1.535 Fit side-chains REVERT: G 2 LEU cc_start: 0.6876 (OUTLIER) cc_final: 0.6495 (mp) REVERT: I 6 GLU cc_start: 0.7990 (mp0) cc_final: 0.7641 (mp0) REVERT: J 40 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8042 (tt0) REVERT: L 12 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7842 (tp) REVERT: L 53 ASN cc_start: 0.7247 (t0) cc_final: 0.6913 (t0) REVERT: C 6 GLU cc_start: 0.7983 (mp0) cc_final: 0.7632 (mp0) REVERT: D 40 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8049 (tt0) REVERT: E 12 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7929 (tp) REVERT: F 12 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7827 (tp) REVERT: F 53 ASN cc_start: 0.7270 (t0) cc_final: 0.6903 (t0) REVERT: F 118 SER cc_start: 0.7061 (OUTLIER) cc_final: 0.6589 (m) outliers start: 37 outliers final: 16 residues processed: 275 average time/residue: 1.2523 time to fit residues: 376.5417 Evaluate side-chains 257 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 234 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain J residue 40 GLN Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain D residue 40 GLN Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 118 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 2 optimal weight: 0.0980 chunk 112 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 chunk 104 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 76 optimal weight: 0.2980 chunk 135 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 D 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13014 Z= 0.207 Angle : 0.586 6.137 17724 Z= 0.299 Chirality : 0.041 0.137 1824 Planarity : 0.004 0.034 2250 Dihedral : 8.199 87.043 1806 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.55 % Allowed : 16.35 % 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: 2.39 (0.20), residues: 1602 helix: 3.39 (0.18), residues: 678 sheet: 0.53 (0.30), residues: 270 loop : 0.11 (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 K 48 TYR 0.009 0.001 TYR F 108 ARG 0.004 0.000 ARG C 86 *********************** 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 278 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 246 time to evaluate : 1.574 Fit side-chains REVERT: J 40 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8037 (tt0) REVERT: L 53 ASN cc_start: 0.7053 (t0) cc_final: 0.6784 (t0) REVERT: D 40 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8043 (tt0) REVERT: E 12 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7893 (tp) REVERT: F 53 ASN cc_start: 0.7079 (t0) cc_final: 0.6792 (t0) REVERT: F 118 SER cc_start: 0.7010 (OUTLIER) cc_final: 0.6666 (m) outliers start: 32 outliers final: 16 residues processed: 269 average time/residue: 1.2497 time to fit residues: 368.8148 Evaluate side-chains 262 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 242 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain J residue 40 GLN Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain 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 E residue 12 LEU Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 119 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.6980 chunk 135 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 88 optimal weight: 0.0970 chunk 37 optimal weight: 0.0470 chunk 150 optimal weight: 1.9990 chunk 125 optimal weight: 0.0570 chunk 69 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 40 GLN D 40 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13014 Z= 0.195 Angle : 0.563 6.111 17724 Z= 0.282 Chirality : 0.041 0.137 1824 Planarity : 0.004 0.032 2250 Dihedral : 7.790 82.457 1806 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.07 % Allowed : 16.67 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.56 (0.20), residues: 1602 helix: 3.54 (0.18), residues: 678 sheet: 0.54 (0.29), residues: 276 loop : 0.24 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 54 HIS 0.001 0.000 HIS H 12 PHE 0.013 0.001 PHE E 48 TYR 0.008 0.001 TYR L 96 ARG 0.005 0.000 ARG C 86 *********************** 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 270 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 244 time to evaluate : 1.419 Fit side-chains REVERT: J 40 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.8009 (tt0) REVERT: J 53 ASN cc_start: 0.6982 (t0) cc_final: 0.6772 (t0) REVERT: K 53 ASN cc_start: 0.6896 (t0) cc_final: 0.6655 (t0) REVERT: L 12 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7757 (tp) REVERT: L 53 ASN cc_start: 0.6940 (t0) cc_final: 0.6687 (t0) REVERT: D 40 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.8033 (tt0) REVERT: D 53 ASN cc_start: 0.6983 (t0) cc_final: 0.6767 (t0) REVERT: E 12 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7835 (tp) REVERT: E 53 ASN cc_start: 0.6899 (t0) cc_final: 0.6659 (t0) REVERT: F 12 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7780 (tp) REVERT: F 53 ASN cc_start: 0.6948 (t0) cc_final: 0.6707 (t0) REVERT: F 118 SER cc_start: 0.7029 (OUTLIER) cc_final: 0.6731 (m) outliers start: 26 outliers final: 15 residues processed: 262 average time/residue: 1.1838 time to fit residues: 340.4250 Evaluate side-chains 258 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 237 time to evaluate : 1.428 ------------------------------------------------------------------------------- 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 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 12 LEU Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 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 145 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 85 optimal weight: 0.0970 chunk 110 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 150 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 B 152 GLN D 40 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13014 Z= 0.228 Angle : 0.614 9.030 17724 Z= 0.313 Chirality : 0.042 0.135 1824 Planarity : 0.004 0.032 2250 Dihedral : 8.399 88.384 1806 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.39 % Allowed : 16.35 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.41 (0.20), residues: 1602 helix: 3.36 (0.18), residues: 678 sheet: 0.61 (0.29), residues: 270 loop : 0.14 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 37 HIS 0.003 0.001 HIS B 58 PHE 0.015 0.002 PHE K 48 TYR 0.013 0.002 TYR L 108 ARG 0.005 0.000 ARG C 86 *********************** 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 276 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 246 time to evaluate : 1.747 Fit side-chains REVERT: I 6 GLU cc_start: 0.7940 (mp0) cc_final: 0.7565 (mp0) REVERT: J 40 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8082 (tt0) REVERT: L 12 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7752 (tp) REVERT: L 53 ASN cc_start: 0.7139 (t0) cc_final: 0.6835 (t0) REVERT: C 6 GLU cc_start: 0.7944 (mp0) cc_final: 0.7571 (mp0) REVERT: D 40 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8093 (tt0) REVERT: F 12 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7774 (tp) REVERT: F 53 ASN cc_start: 0.7151 (t0) cc_final: 0.6831 (t0) REVERT: F 118 SER cc_start: 0.7095 (OUTLIER) cc_final: 0.6760 (m) outliers start: 30 outliers final: 19 residues processed: 268 average time/residue: 1.2963 time to fit residues: 380.3044 Evaluate side-chains 268 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 244 time to evaluate : 1.486 ------------------------------------------------------------------------------- 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 60 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 B 152 GLN D 40 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13014 Z= 0.234 Angle : 0.627 6.141 17724 Z= 0.321 Chirality : 0.042 0.134 1824 Planarity : 0.004 0.032 2250 Dihedral : 8.458 88.987 1806 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.31 % Allowed : 16.43 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.30 (0.20), residues: 1602 helix: 3.28 (0.18), residues: 678 sheet: 0.57 (0.29), residues: 270 loop : 0.06 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 37 HIS 0.003 0.001 HIS B 58 PHE 0.016 0.002 PHE J 48 TYR 0.013 0.002 TYR L 108 ARG 0.005 0.000 ARG C 86 *********************** 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 271 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 242 time to evaluate : 1.504 Fit side-chains REVERT: I 6 GLU cc_start: 0.7972 (mp0) cc_final: 0.7587 (mp0) REVERT: J 40 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8092 (tt0) REVERT: L 12 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7760 (tp) REVERT: L 53 ASN cc_start: 0.7157 (t0) cc_final: 0.6843 (t0) REVERT: C 6 GLU cc_start: 0.7969 (mp0) cc_final: 0.7581 (mp0) REVERT: D 40 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8110 (tt0) REVERT: F 12 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7747 (tp) REVERT: F 53 ASN cc_start: 0.7182 (t0) cc_final: 0.6849 (t0) REVERT: F 118 SER cc_start: 0.7094 (OUTLIER) cc_final: 0.6767 (m) outliers start: 29 outliers final: 18 residues processed: 263 average time/residue: 1.2674 time to fit residues: 364.3054 Evaluate side-chains 265 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 242 time to evaluate : 1.572 ------------------------------------------------------------------------------- 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 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 131 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 126 optimal weight: 0.5980 chunk 132 optimal weight: 0.6980 chunk 139 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 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 B 152 GLN D 40 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13014 Z= 0.222 Angle : 0.610 6.169 17724 Z= 0.312 Chirality : 0.042 0.134 1824 Planarity : 0.004 0.033 2250 Dihedral : 8.284 88.090 1806 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.23 % Allowed : 16.91 % 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: 0.57 (0.29), residues: 270 loop : 0.08 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 37 HIS 0.002 0.001 HIS B 58 PHE 0.015 0.001 PHE J 48 TYR 0.011 0.001 TYR L 108 ARG 0.006 0.000 ARG I 86 *********************** 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 272 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 244 time to evaluate : 1.419 Fit side-chains REVERT: I 6 GLU cc_start: 0.7959 (mp0) cc_final: 0.7570 (mp0) REVERT: J 40 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8102 (tt0) REVERT: L 12 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7749 (tp) REVERT: L 53 ASN cc_start: 0.7112 (t0) cc_final: 0.6814 (t0) REVERT: C 6 GLU cc_start: 0.7958 (mp0) cc_final: 0.7567 (mp0) REVERT: D 40 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8109 (tt0) REVERT: F 12 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7752 (tp) REVERT: F 53 ASN cc_start: 0.7134 (t0) cc_final: 0.6826 (t0) REVERT: F 118 SER cc_start: 0.7072 (OUTLIER) cc_final: 0.6790 (m) outliers start: 28 outliers final: 19 residues processed: 266 average time/residue: 1.3284 time to fit residues: 385.2799 Evaluate side-chains 265 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 241 time to evaluate : 1.478 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 0.6980 chunk 90 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 chunk 155 optimal weight: 5.9990 chunk 143 optimal weight: 7.9990 chunk 123 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 B 152 GLN D 40 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13014 Z= 0.245 Angle : 0.646 6.498 17724 Z= 0.333 Chirality : 0.042 0.133 1824 Planarity : 0.004 0.051 2250 Dihedral : 8.559 89.940 1806 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.23 % Allowed : 16.91 % 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: 2.21 (0.20), residues: 1602 helix: 3.21 (0.18), residues: 678 sheet: 0.51 (0.29), residues: 270 loop : 0.02 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 37 HIS 0.003 0.001 HIS B 58 PHE 0.016 0.002 PHE E 48 TYR 0.014 0.002 TYR L 108 ARG 0.013 0.001 ARG I 86 ********************** 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 268 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 240 time to evaluate : 1.500 Fit side-chains REVERT: I 6 GLU cc_start: 0.7975 (mp0) cc_final: 0.7577 (mp0) REVERT: J 40 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8103 (tt0) REVERT: L 12 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7762 (tp) REVERT: L 53 ASN cc_start: 0.7177 (t0) cc_final: 0.6853 (t0) REVERT: C 6 GLU cc_start: 0.7965 (mp0) cc_final: 0.7566 (mp0) REVERT: D 40 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8123 (tt0) REVERT: F 12 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7771 (tp) REVERT: F 53 ASN cc_start: 0.7200 (t0) cc_final: 0.6857 (t0) REVERT: F 118 SER cc_start: 0.7118 (OUTLIER) cc_final: 0.6817 (m) outliers start: 28 outliers final: 19 residues processed: 262 average time/residue: 1.3172 time to fit residues: 376.4179 Evaluate side-chains 262 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 238 time to evaluate : 1.372 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 B 152 GLN D 40 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.129630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.103489 restraints weight = 11492.831| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.06 r_work: 0.3056 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 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 : 0.004 0.063 13014 Z= 0.262 Angle : 0.671 6.684 17724 Z= 0.348 Chirality : 0.043 0.133 1824 Planarity : 0.005 0.052 2250 Dihedral : 8.636 88.183 1806 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.99 % Allowed : 17.30 % Favored : 80.70 % 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: 2.11 (0.20), residues: 1602 helix: 3.12 (0.18), residues: 678 sheet: 0.50 (0.29), residues: 270 loop : -0.05 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 37 HIS 0.004 0.001 HIS H 58 PHE 0.017 0.002 PHE K 48 TYR 0.015 0.002 TYR L 108 ARG 0.013 0.001 ARG C 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6042.72 seconds wall clock time: 109 minutes 56.05 seconds (6596.05 seconds total)