Starting phenix.real_space_refine on Sat Aug 23 16:57:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g5v_29756/08_2025/8g5v_29756.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g5v_29756/08_2025/8g5v_29756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g5v_29756/08_2025/8g5v_29756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g5v_29756/08_2025/8g5v_29756.map" model { file = "/net/cci-nas-00/data/ceres_data/8g5v_29756/08_2025/8g5v_29756.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g5v_29756/08_2025/8g5v_29756.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 8937 2.51 5 N 2246 2.21 5 O 2484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13739 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1129 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 11, 'TRANS': 129} Chain: "A" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1129 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 11, 'TRANS': 129} Chain: "C" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1151 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 12, 'TRANS': 131} Chain: "D" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1151 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 12, 'TRANS': 131} Chain: "G" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1151 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 12, 'TRANS': 131} Chain: "E" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1144 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 11, 'TRANS': 131} Chain: "I" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1136 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 11, 'TRANS': 130} Chain: "K" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1151 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 12, 'TRANS': 131} Chain: "H" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1151 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 12, 'TRANS': 131} Chain: "F" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1144 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 11, 'TRANS': 131} Chain: "J" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1151 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 12, 'TRANS': 131} Chain: "L" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1151 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 12, 'TRANS': 131} Time building chain proxies: 3.32, per 1000 atoms: 0.24 Number of scatterers: 13739 At special positions: 0 Unit cell: (172.78, 177.02, 72.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 2484 8.00 N 2246 7.00 C 8937 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 519.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3292 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 0 sheets defined 76.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'B' and resid 12 through 17 Processing helix chain 'B' and resid 18 through 19 No H-bonds generated for 'chain 'B' and resid 18 through 19' Processing helix chain 'B' and resid 20 through 24 removed outlier: 3.536A pdb=" N PHE B 24 " --> pdb=" O SER B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 43 removed outlier: 7.076A pdb=" N GLU B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ALA B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 78 through 111 removed outlier: 3.831A pdb=" N MET B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY B 94 " --> pdb=" O ASN B 90 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS B 96 " --> pdb=" O ASN B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 128 removed outlier: 3.668A pdb=" N VAL B 120 " --> pdb=" O ILE B 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 24 removed outlier: 3.740A pdb=" N PHE A 24 " --> pdb=" O SER A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 43 removed outlier: 7.179A pdb=" N GLU A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ALA A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 76 Processing helix chain 'A' and resid 78 through 90 removed outlier: 3.787A pdb=" N ASN A 90 " --> pdb=" O VAL A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 111 removed outlier: 4.025A pdb=" N LYS A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE A 97 " --> pdb=" O MET A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 128 Processing helix chain 'A' and resid 129 through 133 Processing helix chain 'C' and resid 12 through 19 removed outlier: 3.698A pdb=" N LEU C 16 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU C 19 " --> pdb=" O LEU C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 44 removed outlier: 6.975A pdb=" N GLU C 40 " --> pdb=" O ALA C 36 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ALA C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 75 Processing helix chain 'C' and resid 78 through 111 removed outlier: 3.891A pdb=" N MET C 93 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLY C 94 " --> pdb=" O ASN C 90 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS C 96 " --> pdb=" O ASN C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 128 Processing helix chain 'C' and resid 129 through 133 Processing helix chain 'D' and resid 12 through 17 Processing helix chain 'D' and resid 26 through 44 removed outlier: 7.168A pdb=" N GLU D 40 " --> pdb=" O ALA D 36 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ALA D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 76 Processing helix chain 'D' and resid 78 through 109 removed outlier: 3.551A pdb=" N GLY D 94 " --> pdb=" O ASN D 90 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU D 95 " --> pdb=" O THR D 91 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS D 96 " --> pdb=" O ASN D 92 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU D 100 " --> pdb=" O LYS D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 128 Processing helix chain 'D' and resid 129 through 133 removed outlier: 3.520A pdb=" N ARG D 133 " --> pdb=" O PRO D 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 19 removed outlier: 3.616A pdb=" N PHE G 18 " --> pdb=" O LEU G 15 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU G 19 " --> pdb=" O LEU G 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 15 through 19' Processing helix chain 'G' and resid 26 through 39 Processing helix chain 'G' and resid 49 through 75 Processing helix chain 'G' and resid 78 through 111 removed outlier: 3.750A pdb=" N GLY G 94 " --> pdb=" O ASN G 90 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU G 100 " --> pdb=" O LYS G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 128 removed outlier: 3.748A pdb=" N VAL G 120 " --> pdb=" O ILE G 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 18 Processing helix chain 'E' and resid 26 through 44 removed outlier: 6.920A pdb=" N GLU E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ALA E 41 " --> pdb=" O LEU E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 75 Processing helix chain 'E' and resid 79 through 109 removed outlier: 4.278A pdb=" N ASP E 83 " --> pdb=" O PRO E 79 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N MET E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY E 94 " --> pdb=" O ASN E 90 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS E 96 " --> pdb=" O ASN E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 128 removed outlier: 3.597A pdb=" N VAL E 120 " --> pdb=" O ILE E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 133 removed outlier: 3.530A pdb=" N ARG E 133 " --> pdb=" O PRO E 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 17 Processing helix chain 'I' and resid 18 through 19 No H-bonds generated for 'chain 'I' and resid 18 through 19' Processing helix chain 'I' and resid 20 through 24 removed outlier: 3.689A pdb=" N PHE I 24 " --> pdb=" O SER I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 43 removed outlier: 7.038A pdb=" N GLU I 40 " --> pdb=" O ALA I 36 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ALA I 41 " --> pdb=" O LEU I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 75 Processing helix chain 'I' and resid 78 through 111 removed outlier: 4.072A pdb=" N MET I 93 " --> pdb=" O VAL I 89 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLY I 94 " --> pdb=" O ASN I 90 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS I 96 " --> pdb=" O ASN I 92 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE I 97 " --> pdb=" O MET I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 128 Processing helix chain 'K' and resid 6 through 10 Processing helix chain 'K' and resid 26 through 44 removed outlier: 7.267A pdb=" N GLU K 40 " --> pdb=" O ALA K 36 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA K 41 " --> pdb=" O LEU K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 76 Processing helix chain 'K' and resid 78 through 110 removed outlier: 3.912A pdb=" N MET K 93 " --> pdb=" O VAL K 89 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLY K 94 " --> pdb=" O ASN K 90 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYS K 96 " --> pdb=" O ASN K 92 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE K 97 " --> pdb=" O MET K 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 128 Processing helix chain 'H' and resid 12 through 18 Processing helix chain 'H' and resid 20 through 24 removed outlier: 3.911A pdb=" N PHE H 24 " --> pdb=" O SER H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 43 removed outlier: 6.767A pdb=" N GLU H 40 " --> pdb=" O ALA H 36 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ALA H 41 " --> pdb=" O LEU H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 76 Processing helix chain 'H' and resid 78 through 111 removed outlier: 3.986A pdb=" N GLY H 94 " --> pdb=" O ASN H 90 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU H 95 " --> pdb=" O THR H 91 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS H 96 " --> pdb=" O ASN H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 128 Processing helix chain 'H' and resid 129 through 133 Processing helix chain 'F' and resid 12 through 17 Processing helix chain 'F' and resid 18 through 19 No H-bonds generated for 'chain 'F' and resid 18 through 19' Processing helix chain 'F' and resid 20 through 24 removed outlier: 4.167A pdb=" N PHE F 24 " --> pdb=" O SER F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 43 removed outlier: 7.237A pdb=" N GLU F 40 " --> pdb=" O ALA F 36 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ALA F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 78 through 111 removed outlier: 4.485A pdb=" N MET F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY F 94 " --> pdb=" O ASN F 90 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS F 96 " --> pdb=" O ASN F 92 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU F 100 " --> pdb=" O LYS F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 128 Processing helix chain 'F' and resid 129 through 133 Processing helix chain 'J' and resid 12 through 17 Processing helix chain 'J' and resid 20 through 24 removed outlier: 3.991A pdb=" N PHE J 24 " --> pdb=" O SER J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 43 removed outlier: 6.987A pdb=" N GLU J 40 " --> pdb=" O ALA J 36 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ALA J 41 " --> pdb=" O LEU J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 76 Processing helix chain 'J' and resid 78 through 111 removed outlier: 4.589A pdb=" N MET J 93 " --> pdb=" O VAL J 89 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY J 94 " --> pdb=" O ASN J 90 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS J 96 " --> pdb=" O ASN J 92 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU J 100 " --> pdb=" O LYS J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 128 Processing helix chain 'L' and resid 12 through 18 Processing helix chain 'L' and resid 20 through 24 removed outlier: 3.934A pdb=" N PHE L 24 " --> pdb=" O SER L 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 44 removed outlier: 6.907A pdb=" N GLU L 40 " --> pdb=" O ALA L 36 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ALA L 41 " --> pdb=" O LEU L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 76 Processing helix chain 'L' and resid 78 through 110 removed outlier: 3.729A pdb=" N GLY L 94 " --> pdb=" O ASN L 90 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS L 96 " --> pdb=" O ASN L 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 128 Processing helix chain 'L' and resid 129 through 133 946 hydrogen bonds defined for protein. 2775 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.12 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4332 1.34 - 1.46: 3410 1.46 - 1.58: 6315 1.58 - 1.70: 1 1.70 - 1.81: 108 Bond restraints: 14166 Sorted by residual: bond pdb=" CB PRO L 45 " pdb=" CG PRO L 45 " ideal model delta sigma weight residual 1.492 1.624 -0.132 5.00e-02 4.00e+02 6.96e+00 bond pdb=" CG1 ILE H 59 " pdb=" CD1 ILE H 59 " ideal model delta sigma weight residual 1.513 1.456 0.057 3.90e-02 6.57e+02 2.14e+00 bond pdb=" CB VAL E 115 " pdb=" CG2 VAL E 115 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.80e+00 bond pdb=" CG PRO L 45 " pdb=" CD PRO L 45 " ideal model delta sigma weight residual 1.503 1.540 -0.037 3.40e-02 8.65e+02 1.20e+00 bond pdb=" CG1 ILE E 126 " pdb=" CD1 ILE E 126 " ideal model delta sigma weight residual 1.513 1.474 0.039 3.90e-02 6.57e+02 1.03e+00 ... (remaining 14161 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 19053 2.02 - 4.03: 307 4.03 - 6.05: 32 6.05 - 8.06: 3 8.06 - 10.08: 4 Bond angle restraints: 19399 Sorted by residual: angle pdb=" CA PRO L 45 " pdb=" N PRO L 45 " pdb=" CD PRO L 45 " ideal model delta sigma weight residual 112.00 101.92 10.08 1.40e+00 5.10e-01 5.18e+01 angle pdb=" C LEU D 60 " pdb=" N CYS D 61 " pdb=" CA CYS D 61 " ideal model delta sigma weight residual 121.14 115.79 5.35 1.75e+00 3.27e-01 9.34e+00 angle pdb=" CB MET B 66 " pdb=" CG MET B 66 " pdb=" SD MET B 66 " ideal model delta sigma weight residual 112.70 103.90 8.80 3.00e+00 1.11e-01 8.61e+00 angle pdb=" C LEU C 60 " pdb=" N CYS C 61 " pdb=" CA CYS C 61 " ideal model delta sigma weight residual 121.14 116.12 5.02 1.75e+00 3.27e-01 8.21e+00 angle pdb=" C ASN B 75 " pdb=" N LEU B 76 " pdb=" CA LEU B 76 " ideal model delta sigma weight residual 122.64 118.29 4.35 1.70e+00 3.46e-01 6.55e+00 ... (remaining 19394 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 7590 17.22 - 34.43: 628 34.43 - 51.65: 107 51.65 - 68.87: 20 68.87 - 86.08: 2 Dihedral angle restraints: 8347 sinusoidal: 3289 harmonic: 5058 Sorted by residual: dihedral pdb=" CA PHE C 24 " pdb=" C PHE C 24 " pdb=" N PRO C 25 " pdb=" CA PRO C 25 " ideal model delta harmonic sigma weight residual -180.00 -160.10 -19.90 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA LEU E 108 " pdb=" C LEU E 108 " pdb=" N THR E 109 " pdb=" CA THR E 109 " ideal model delta harmonic sigma weight residual 180.00 161.26 18.74 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA LEU G 76 " pdb=" C LEU G 76 " pdb=" N GLU G 77 " pdb=" CA GLU G 77 " ideal model delta harmonic sigma weight residual 180.00 162.27 17.73 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 8344 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1199 0.027 - 0.055: 626 0.055 - 0.082: 241 0.082 - 0.109: 107 0.109 - 0.137: 20 Chirality restraints: 2193 Sorted by residual: chirality pdb=" CG LEU D 55 " pdb=" CB LEU D 55 " pdb=" CD1 LEU D 55 " pdb=" CD2 LEU D 55 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 4.67e-01 chirality pdb=" CA PRO L 45 " pdb=" N PRO L 45 " pdb=" C PRO L 45 " pdb=" CB PRO L 45 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" CA LYS L 96 " pdb=" N LYS L 96 " pdb=" C LYS L 96 " pdb=" CB LYS L 96 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.29e-01 ... (remaining 2190 not shown) Planarity restraints: 2457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER L 44 " -0.056 5.00e-02 4.00e+02 7.92e-02 1.00e+01 pdb=" N PRO L 45 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO L 45 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO L 45 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 71 " 0.015 2.00e-02 2.50e+03 1.65e-02 6.82e+00 pdb=" CG TRP B 71 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP B 71 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP B 71 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 71 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 71 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 71 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 71 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 71 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP B 71 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 18 " -0.018 2.00e-02 2.50e+03 1.71e-02 5.10e+00 pdb=" CG PHE E 18 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE E 18 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE E 18 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE E 18 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE E 18 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE E 18 " -0.001 2.00e-02 2.50e+03 ... (remaining 2454 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2385 2.76 - 3.29: 13441 3.29 - 3.83: 24258 3.83 - 4.36: 27985 4.36 - 4.90: 48728 Nonbonded interactions: 116797 Sorted by model distance: nonbonded pdb=" OE1 GLU J 8 " pdb=" NH1 ARG L 56 " model vdw 2.223 3.120 nonbonded pdb=" NH1 ARG H 56 " pdb=" OE1 GLU F 8 " model vdw 2.232 3.120 nonbonded pdb=" NH1 ARG G 56 " pdb=" OE1 GLU E 8 " model vdw 2.256 3.120 nonbonded pdb=" OG SER D 49 " pdb=" ND1 HIS D 52 " model vdw 2.286 3.120 nonbonded pdb=" O GLU D 64 " pdb=" OG1 THR D 67 " model vdw 2.302 3.040 ... (remaining 116792 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' selection = chain 'B' selection = (chain 'C' and resid 1 through 141) selection = (chain 'D' and resid 1 through 141) selection = (chain 'E' and resid 1 through 141) selection = (chain 'F' and resid 1 through 141) selection = (chain 'G' and resid 1 through 141) selection = (chain 'H' and resid 1 through 141) selection = (chain 'I' and resid 1 through 141) selection = (chain 'J' and resid 1 through 141) selection = (chain 'K' and resid 1 through 141) selection = (chain 'L' and resid 1 through 141) } 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: 6.920 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 12.730 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2364 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 0.132 14166 Z= 0.164 Angle : 0.609 10.080 19399 Z= 0.313 Chirality : 0.040 0.137 2193 Planarity : 0.005 0.079 2457 Dihedral : 12.944 86.081 5055 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.14 (0.21), residues: 1694 helix: 1.65 (0.15), residues: 1182 sheet: None (None), residues: 0 loop : 1.12 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 133 TYR 0.017 0.002 TYR A 88 PHE 0.039 0.002 PHE E 18 TRP 0.042 0.002 TRP B 71 HIS 0.006 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00396 (14166) covalent geometry : angle 0.60877 (19399) hydrogen bonds : bond 0.08005 ( 946) hydrogen bonds : angle 4.49239 ( 2775) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 66 MET cc_start: 0.6091 (mmm) cc_final: 0.5363 (mmp) REVERT: D 72 VAL cc_start: 0.4246 (t) cc_final: 0.3981 (p) REVERT: F 93 MET cc_start: 0.1301 (mmt) cc_final: 0.0428 (mtt) outliers start: 0 outliers final: 2 residues processed: 301 average time/residue: 0.3834 time to fit residues: 130.6032 Evaluate side-chains 158 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 156 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 22 ASP Chi-restraints excluded: chain J residue 47 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 7.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 ASN ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 HIS G 47 HIS K 47 HIS K 90 ASN K 104 HIS F 136 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.206372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.194765 restraints weight = 26524.712| |-----------------------------------------------------------------------------| r_work (start): 0.4450 rms_B_bonded: 1.31 r_work: 0.4394 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.4319 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.4319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3245 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14166 Z= 0.173 Angle : 0.735 13.376 19399 Z= 0.361 Chirality : 0.043 0.356 2193 Planarity : 0.006 0.065 2457 Dihedral : 4.463 22.968 1866 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.69 % Allowed : 9.50 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.20), residues: 1694 helix: 0.97 (0.14), residues: 1267 sheet: None (None), residues: 0 loop : 0.84 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 82 TYR 0.027 0.002 TYR E 88 PHE 0.024 0.002 PHE A 122 TRP 0.043 0.002 TRP I 71 HIS 0.015 0.002 HIS E 47 Details of bonding type rmsd covalent geometry : bond 0.00355 (14166) covalent geometry : angle 0.73496 (19399) hydrogen bonds : bond 0.04126 ( 946) hydrogen bonds : angle 4.67743 ( 2775) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 197 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLU cc_start: 0.3270 (tt0) cc_final: 0.2603 (mm-30) REVERT: E 40 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6899 (mp0) REVERT: I 78 ASP cc_start: 0.5038 (m-30) cc_final: 0.4233 (t0) REVERT: K 66 MET cc_start: 0.5991 (mmp) cc_final: 0.5429 (mmp) REVERT: F 93 MET cc_start: 0.1274 (mmt) cc_final: 0.0668 (mtt) outliers start: 41 outliers final: 13 residues processed: 218 average time/residue: 0.4336 time to fit residues: 106.8252 Evaluate side-chains 169 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 155 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain I residue 82 ARG Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 96 LYS Chi-restraints excluded: chain F residue 70 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 42 optimal weight: 10.0000 chunk 84 optimal weight: 0.0170 chunk 70 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 110 optimal weight: 0.3980 chunk 59 optimal weight: 8.9990 chunk 73 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 135 optimal weight: 8.9990 chunk 144 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 104 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.206009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.193557 restraints weight = 26897.550| |-----------------------------------------------------------------------------| r_work (start): 0.4429 rms_B_bonded: 1.52 r_work: 0.4369 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.4287 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.4287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3585 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14166 Z= 0.127 Angle : 0.628 9.330 19399 Z= 0.305 Chirality : 0.041 0.361 2193 Planarity : 0.005 0.064 2457 Dihedral : 4.116 16.398 1862 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.82 % Allowed : 12.19 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.20), residues: 1694 helix: 1.23 (0.14), residues: 1262 sheet: None (None), residues: 0 loop : 0.96 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 82 TYR 0.026 0.001 TYR F 118 PHE 0.029 0.002 PHE F 24 TRP 0.025 0.002 TRP K 62 HIS 0.004 0.001 HIS J 47 Details of bonding type rmsd covalent geometry : bond 0.00279 (14166) covalent geometry : angle 0.62775 (19399) hydrogen bonds : bond 0.03623 ( 946) hydrogen bonds : angle 4.51262 ( 2775) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 170 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLU cc_start: 0.3624 (tt0) cc_final: 0.2687 (mm-30) REVERT: D 75 ASN cc_start: 0.6087 (OUTLIER) cc_final: 0.5471 (t0) REVERT: E 29 ASP cc_start: 0.6690 (m-30) cc_final: 0.6431 (m-30) REVERT: E 40 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: K 32 ASP cc_start: 0.6290 (t0) cc_final: 0.6046 (m-30) REVERT: K 66 MET cc_start: 0.6284 (mmp) cc_final: 0.5853 (mmp) REVERT: H 1 MET cc_start: 0.0625 (tpp) cc_final: -0.0959 (ttp) REVERT: F 70 THR cc_start: 0.2143 (m) cc_final: 0.1782 (t) REVERT: F 93 MET cc_start: 0.1361 (mmt) cc_final: 0.0660 (mtt) outliers start: 43 outliers final: 14 residues processed: 192 average time/residue: 0.3646 time to fit residues: 79.1570 Evaluate side-chains 161 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 75 ASN Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain I residue 66 MET Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain J residue 7 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 3 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 78 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 chunk 45 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 1 optimal weight: 0.7980 chunk 133 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 ASN ** K 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 HIS F 52 HIS L 99 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.203391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.190252 restraints weight = 26457.622| |-----------------------------------------------------------------------------| r_work (start): 0.4405 rms_B_bonded: 1.43 r_work: 0.4343 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4261 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.4261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4919 moved from start: 0.5998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.142 14166 Z= 0.225 Angle : 0.763 10.868 19399 Z= 0.382 Chirality : 0.046 0.461 2193 Planarity : 0.006 0.063 2457 Dihedral : 4.291 20.066 1862 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.30 % Favored : 97.64 % Rotamer: Outliers : 3.41 % Allowed : 13.11 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.20), residues: 1694 helix: 1.01 (0.14), residues: 1255 sheet: None (None), residues: 0 loop : 0.94 (0.32), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 82 TYR 0.025 0.003 TYR F 118 PHE 0.029 0.002 PHE B 18 TRP 0.035 0.002 TRP K 62 HIS 0.007 0.002 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00486 (14166) covalent geometry : angle 0.76280 (19399) hydrogen bonds : bond 0.04203 ( 946) hydrogen bonds : angle 4.68666 ( 2775) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 216 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 8 GLU cc_start: 0.3980 (tt0) cc_final: 0.3089 (mm-30) REVERT: D 42 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7135 (mt) REVERT: D 72 VAL cc_start: 0.4665 (t) cc_final: 0.4375 (p) REVERT: E 29 ASP cc_start: 0.7615 (m-30) cc_final: 0.7224 (m-30) REVERT: E 90 ASN cc_start: 0.7602 (m-40) cc_final: 0.7384 (m-40) REVERT: K 66 MET cc_start: 0.6333 (mmp) cc_final: 0.5977 (mmp) REVERT: F 74 VAL cc_start: 0.4496 (t) cc_final: 0.4289 (p) REVERT: F 93 MET cc_start: 0.1349 (mmt) cc_final: 0.0697 (mtt) REVERT: J 93 MET cc_start: 0.2452 (mpp) cc_final: 0.0740 (mtt) outliers start: 52 outliers final: 18 residues processed: 240 average time/residue: 0.3885 time to fit residues: 104.7857 Evaluate side-chains 176 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain I residue 52 HIS Chi-restraints excluded: chain K residue 14 GLU Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain F residue 72 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 81 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 55 optimal weight: 0.0270 chunk 157 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 47 HIS ** K 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.199628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.183867 restraints weight = 26144.666| |-----------------------------------------------------------------------------| r_work (start): 0.4329 rms_B_bonded: 1.84 r_work: 0.4256 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.4165 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5386 moved from start: 0.7059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 14166 Z= 0.148 Angle : 0.674 14.478 19399 Z= 0.324 Chirality : 0.042 0.401 2193 Planarity : 0.005 0.066 2457 Dihedral : 4.126 17.470 1862 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.65 % Favored : 98.29 % Rotamer: Outliers : 3.60 % Allowed : 16.06 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.21), residues: 1694 helix: 1.21 (0.14), residues: 1262 sheet: None (None), residues: 0 loop : 1.03 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 133 TYR 0.015 0.001 TYR A 118 PHE 0.032 0.002 PHE L 97 TRP 0.040 0.002 TRP H 62 HIS 0.006 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00324 (14166) covalent geometry : angle 0.67404 (19399) hydrogen bonds : bond 0.03724 ( 946) hydrogen bonds : angle 4.58024 ( 2775) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 201 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 8 GLU cc_start: 0.4091 (tt0) cc_final: 0.3302 (mm-30) REVERT: B 18 PHE cc_start: 0.2701 (OUTLIER) cc_final: 0.2333 (t80) REVERT: B 113 GLU cc_start: 0.7006 (tp30) cc_final: 0.6655 (tt0) REVERT: B 122 PHE cc_start: 0.3896 (t80) cc_final: 0.3543 (t80) REVERT: C 14 GLU cc_start: 0.6217 (OUTLIER) cc_final: 0.5769 (tt0) REVERT: D 29 ASP cc_start: 0.6003 (m-30) cc_final: 0.4875 (t70) REVERT: D 42 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7292 (mt) REVERT: G 29 ASP cc_start: 0.7036 (m-30) cc_final: 0.6800 (m-30) REVERT: E 29 ASP cc_start: 0.7806 (m-30) cc_final: 0.7380 (m-30) REVERT: I 55 LEU cc_start: 0.7123 (tp) cc_final: 0.6803 (tp) REVERT: K 62 TRP cc_start: 0.6535 (OUTLIER) cc_final: 0.6305 (t-100) REVERT: K 66 MET cc_start: 0.6846 (mmp) cc_final: 0.6362 (mmp) REVERT: K 142 THR cc_start: 0.6041 (OUTLIER) cc_final: 0.5838 (p) REVERT: H 66 MET cc_start: 0.4582 (mmt) cc_final: 0.3950 (ptp) REVERT: F 74 VAL cc_start: 0.4211 (OUTLIER) cc_final: 0.3998 (p) REVERT: F 93 MET cc_start: 0.1440 (mmt) cc_final: 0.0717 (mtt) REVERT: J 1 MET cc_start: 0.1636 (OUTLIER) cc_final: 0.1245 (tmm) REVERT: J 93 MET cc_start: 0.3013 (mpp) cc_final: 0.1007 (ttt) REVERT: J 132 TYR cc_start: 0.4981 (m-10) cc_final: 0.4390 (m-10) outliers start: 55 outliers final: 19 residues processed: 231 average time/residue: 0.3732 time to fit residues: 97.0957 Evaluate side-chains 192 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain I residue 49 SER Chi-restraints excluded: chain I residue 52 HIS Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 62 TRP Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 139 ILE Chi-restraints excluded: chain L residue 67 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 163 optimal weight: 0.7980 chunk 104 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 158 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 160 optimal weight: 0.9990 chunk 162 optimal weight: 6.9990 chunk 145 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 ASN ** K 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 GLN L 51 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.188351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.168916 restraints weight = 24295.761| |-----------------------------------------------------------------------------| r_work (start): 0.4178 rms_B_bonded: 1.82 r_work: 0.4084 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3987 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 1.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.137 14166 Z= 0.252 Angle : 0.929 18.326 19399 Z= 0.464 Chirality : 0.051 0.459 2193 Planarity : 0.008 0.186 2457 Dihedral : 5.043 26.008 1862 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.48 % Favored : 96.46 % Rotamer: Outliers : 4.39 % Allowed : 16.97 % Favored : 78.64 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.20), residues: 1694 helix: 0.61 (0.14), residues: 1210 sheet: None (None), residues: 0 loop : 0.66 (0.31), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG K 133 TYR 0.039 0.003 TYR C 88 PHE 0.027 0.003 PHE A 23 TRP 0.050 0.003 TRP I 102 HIS 0.010 0.002 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00564 (14166) covalent geometry : angle 0.92855 (19399) hydrogen bonds : bond 0.05285 ( 946) hydrogen bonds : angle 5.15477 ( 2775) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 270 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: B 18 PHE cc_start: 0.6020 (OUTLIER) cc_final: 0.5342 (t80) REVERT: B 93 MET cc_start: 0.5751 (mtm) cc_final: 0.5329 (mmp) REVERT: A 14 GLU cc_start: 0.2239 (OUTLIER) cc_final: 0.1777 (tm-30) REVERT: C 60 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7684 (mt) REVERT: D 12 THR cc_start: 0.8443 (p) cc_final: 0.8203 (t) REVERT: D 14 GLU cc_start: 0.4759 (OUTLIER) cc_final: 0.3936 (mp0) REVERT: D 75 ASN cc_start: 0.6766 (OUTLIER) cc_final: 0.5950 (t0) REVERT: D 114 THR cc_start: 0.7299 (p) cc_final: 0.6928 (p) REVERT: D 117 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7645 (tm-30) REVERT: G 8 GLU cc_start: 0.7974 (tt0) cc_final: 0.7414 (tm-30) REVERT: G 12 THR cc_start: 0.9162 (p) cc_final: 0.8900 (t) REVERT: G 29 ASP cc_start: 0.8100 (m-30) cc_final: 0.7607 (m-30) REVERT: G 124 VAL cc_start: 0.8304 (p) cc_final: 0.8035 (m) REVERT: E 29 ASP cc_start: 0.8163 (m-30) cc_final: 0.7963 (m-30) REVERT: E 40 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7458 (mp0) REVERT: E 66 MET cc_start: 0.8045 (mmm) cc_final: 0.7442 (mmp) REVERT: K 1 MET cc_start: 0.5127 (tmt) cc_final: 0.4722 (tmt) REVERT: H 66 MET cc_start: 0.4472 (mmt) cc_final: 0.3857 (ptp) REVERT: H 93 MET cc_start: 0.5270 (mmp) cc_final: 0.4734 (mpp) REVERT: F 93 MET cc_start: 0.3202 (mmt) cc_final: 0.2664 (ptp) REVERT: F 122 PHE cc_start: 0.4634 (OUTLIER) cc_final: 0.3728 (m-80) REVERT: F 132 TYR cc_start: 0.0238 (OUTLIER) cc_final: -0.3132 (m-10) REVERT: J 113 GLU cc_start: 0.7003 (mm-30) cc_final: 0.6573 (mp0) REVERT: J 132 TYR cc_start: 0.7122 (m-10) cc_final: 0.6898 (m-80) outliers start: 67 outliers final: 8 residues processed: 311 average time/residue: 0.4602 time to fit residues: 157.5383 Evaluate side-chains 229 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 213 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 75 ASN Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 122 PHE Chi-restraints excluded: chain F residue 132 TYR Chi-restraints excluded: chain L residue 67 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 60 optimal weight: 0.4980 chunk 24 optimal weight: 8.9990 chunk 128 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 47 HIS E 90 ASN E 92 ASN ** K 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 47 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.183845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.162643 restraints weight = 24457.095| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 1.73 r_work: 0.4032 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3935 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 1.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14166 Z= 0.139 Angle : 0.689 11.854 19399 Z= 0.336 Chirality : 0.041 0.346 2193 Planarity : 0.005 0.051 2457 Dihedral : 4.380 23.717 1862 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.77 % Favored : 98.17 % Rotamer: Outliers : 2.23 % Allowed : 21.30 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.21), residues: 1694 helix: 1.09 (0.14), residues: 1249 sheet: None (None), residues: 0 loop : 0.77 (0.32), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 133 TYR 0.017 0.001 TYR C 88 PHE 0.021 0.002 PHE G 97 TRP 0.027 0.002 TRP C 71 HIS 0.006 0.001 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00304 (14166) covalent geometry : angle 0.68884 (19399) hydrogen bonds : bond 0.04002 ( 946) hydrogen bonds : angle 4.70726 ( 2775) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 231 time to evaluate : 0.511 Fit side-chains REVERT: B 18 PHE cc_start: 0.6277 (OUTLIER) cc_final: 0.5654 (t80) REVERT: A 99 GLN cc_start: 0.6285 (mt0) cc_final: 0.6024 (pt0) REVERT: C 22 ASP cc_start: 0.8654 (p0) cc_final: 0.8397 (p0) REVERT: C 32 ASP cc_start: 0.8070 (t0) cc_final: 0.7736 (m-30) REVERT: C 117 GLU cc_start: 0.7118 (tt0) cc_final: 0.6855 (tm-30) REVERT: D 12 THR cc_start: 0.8065 (p) cc_final: 0.7823 (t) REVERT: D 29 ASP cc_start: 0.7711 (m-30) cc_final: 0.7493 (m-30) REVERT: D 117 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7400 (tm-30) REVERT: G 8 GLU cc_start: 0.8066 (tt0) cc_final: 0.7484 (tm-30) REVERT: G 12 THR cc_start: 0.9096 (p) cc_final: 0.8802 (t) REVERT: G 29 ASP cc_start: 0.7869 (m-30) cc_final: 0.7534 (m-30) REVERT: G 132 TYR cc_start: 0.8479 (m-80) cc_final: 0.7916 (m-80) REVERT: E 29 ASP cc_start: 0.8239 (m-30) cc_final: 0.8035 (m-30) REVERT: E 93 MET cc_start: 0.7863 (mpm) cc_final: 0.7408 (mtt) REVERT: K 1 MET cc_start: 0.5456 (tmt) cc_final: 0.5084 (tmt) REVERT: H 66 MET cc_start: 0.4620 (mmt) cc_final: 0.3747 (ptp) REVERT: H 114 THR cc_start: 0.8704 (m) cc_final: 0.8473 (m) REVERT: F 93 MET cc_start: 0.3181 (mmt) cc_final: 0.2747 (ptp) REVERT: J 1 MET cc_start: 0.3196 (OUTLIER) cc_final: 0.2903 (tmm) outliers start: 34 outliers final: 9 residues processed: 249 average time/residue: 0.4434 time to fit residues: 121.7214 Evaluate side-chains 204 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 193 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain J residue 1 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 76 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 105 optimal weight: 0.0050 chunk 87 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 46 optimal weight: 0.2980 chunk 127 optimal weight: 0.0970 chunk 146 optimal weight: 8.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 47 HIS K 51 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.183196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.161619 restraints weight = 24273.920| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 1.78 r_work: 0.4016 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3919 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 1.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14166 Z= 0.128 Angle : 0.673 10.522 19399 Z= 0.324 Chirality : 0.040 0.348 2193 Planarity : 0.005 0.048 2457 Dihedral : 4.192 23.891 1862 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.44 % Allowed : 22.80 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.21), residues: 1694 helix: 1.32 (0.15), residues: 1249 sheet: None (None), residues: 0 loop : 0.93 (0.32), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 133 TYR 0.011 0.001 TYR B 38 PHE 0.015 0.001 PHE G 97 TRP 0.028 0.001 TRP C 71 HIS 0.014 0.001 HIS L 52 Details of bonding type rmsd covalent geometry : bond 0.00276 (14166) covalent geometry : angle 0.67302 (19399) hydrogen bonds : bond 0.03705 ( 946) hydrogen bonds : angle 4.54872 ( 2775) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 208 time to evaluate : 0.517 Fit side-chains REVERT: B 18 PHE cc_start: 0.6346 (OUTLIER) cc_final: 0.5451 (t80) REVERT: B 39 ARG cc_start: 0.7589 (ttm-80) cc_final: 0.7322 (ttm-80) REVERT: B 126 ILE cc_start: 0.7611 (mm) cc_final: 0.7304 (mm) REVERT: A 99 GLN cc_start: 0.6298 (mt0) cc_final: 0.5860 (pt0) REVERT: C 32 ASP cc_start: 0.8074 (t0) cc_final: 0.7788 (m-30) REVERT: C 60 LEU cc_start: 0.8220 (mm) cc_final: 0.7778 (mt) REVERT: C 117 GLU cc_start: 0.7108 (tt0) cc_final: 0.6687 (tm-30) REVERT: D 2 ASP cc_start: 0.6617 (p0) cc_final: 0.5983 (p0) REVERT: D 29 ASP cc_start: 0.7768 (m-30) cc_final: 0.7530 (m-30) REVERT: G 8 GLU cc_start: 0.8027 (tt0) cc_final: 0.7471 (tm-30) REVERT: G 12 THR cc_start: 0.9051 (p) cc_final: 0.8768 (t) REVERT: G 29 ASP cc_start: 0.7968 (m-30) cc_final: 0.7639 (m-30) REVERT: G 132 TYR cc_start: 0.8514 (m-80) cc_final: 0.8230 (m-80) REVERT: E 29 ASP cc_start: 0.8226 (m-30) cc_final: 0.7941 (m-30) REVERT: E 93 MET cc_start: 0.7917 (mpm) cc_final: 0.7473 (mtt) REVERT: K 1 MET cc_start: 0.5396 (tmt) cc_final: 0.5123 (tmt) REVERT: K 83 ASP cc_start: 0.7860 (t0) cc_final: 0.7219 (m-30) REVERT: H 66 MET cc_start: 0.4458 (mmt) cc_final: 0.3490 (ptp) REVERT: H 93 MET cc_start: 0.5548 (mmp) cc_final: 0.4755 (mpp) REVERT: H 114 THR cc_start: 0.8724 (m) cc_final: 0.8505 (m) REVERT: F 93 MET cc_start: 0.3207 (mmt) cc_final: 0.2806 (ptp) REVERT: F 103 PHE cc_start: 0.5403 (t80) cc_final: 0.4862 (t80) REVERT: F 122 PHE cc_start: 0.4475 (OUTLIER) cc_final: 0.3710 (m-80) REVERT: J 1 MET cc_start: 0.3019 (OUTLIER) cc_final: 0.2676 (tmm) REVERT: J 93 MET cc_start: 0.5030 (mpm) cc_final: 0.4394 (mpp) outliers start: 22 outliers final: 10 residues processed: 222 average time/residue: 0.4796 time to fit residues: 117.1445 Evaluate side-chains 204 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 191 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 107 CYS Chi-restraints excluded: chain F residue 122 PHE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 19 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 38 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 161 optimal weight: 6.9990 chunk 163 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 43 optimal weight: 9.9990 chunk 112 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN C 104 HIS K 104 HIS H 47 HIS ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 ASN ** L 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.167692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.143991 restraints weight = 23119.564| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 1.73 r_work: 0.3795 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3686 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 1.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.132 14166 Z= 0.208 Angle : 0.891 22.663 19399 Z= 0.437 Chirality : 0.047 0.345 2193 Planarity : 0.006 0.059 2457 Dihedral : 4.815 39.799 1862 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.42 % Favored : 97.52 % Rotamer: Outliers : 2.16 % Allowed : 22.08 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.20), residues: 1694 helix: 0.90 (0.14), residues: 1255 sheet: None (None), residues: 0 loop : 0.68 (0.32), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 28 TYR 0.026 0.003 TYR J 118 PHE 0.047 0.003 PHE J 122 TRP 0.030 0.003 TRP C 71 HIS 0.023 0.002 HIS F 51 Details of bonding type rmsd covalent geometry : bond 0.00474 (14166) covalent geometry : angle 0.89105 (19399) hydrogen bonds : bond 0.04875 ( 946) hydrogen bonds : angle 5.04487 ( 2775) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 260 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: B 39 ARG cc_start: 0.7953 (ttm-80) cc_final: 0.7719 (ttm-80) REVERT: B 89 VAL cc_start: 0.7726 (t) cc_final: 0.7438 (m) REVERT: B 90 ASN cc_start: 0.7130 (t0) cc_final: 0.6847 (t0) REVERT: A 132 TYR cc_start: 0.4393 (m-10) cc_final: 0.3023 (t80) REVERT: D 2 ASP cc_start: 0.7157 (p0) cc_final: 0.6956 (t70) REVERT: D 26 SER cc_start: 0.7985 (m) cc_final: 0.7616 (p) REVERT: D 40 GLU cc_start: 0.8164 (pt0) cc_final: 0.7706 (pm20) REVERT: D 117 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7791 (tm-30) REVERT: G 8 GLU cc_start: 0.8111 (tt0) cc_final: 0.7500 (tm-30) REVERT: G 12 THR cc_start: 0.9230 (p) cc_final: 0.8989 (t) REVERT: E 29 ASP cc_start: 0.8427 (m-30) cc_final: 0.8083 (m-30) REVERT: E 40 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7745 (mp0) REVERT: E 93 MET cc_start: 0.7833 (mpm) cc_final: 0.7545 (mtt) REVERT: K 40 GLU cc_start: 0.7935 (mp0) cc_final: 0.7723 (pm20) REVERT: K 83 ASP cc_start: 0.8110 (t0) cc_final: 0.7403 (m-30) REVERT: K 91 THR cc_start: 0.8445 (m) cc_final: 0.8198 (p) REVERT: H 27 VAL cc_start: 0.3683 (t) cc_final: 0.3332 (m) REVERT: H 66 MET cc_start: 0.5295 (mmt) cc_final: 0.4214 (ptp) REVERT: H 93 MET cc_start: 0.6657 (mmp) cc_final: 0.6235 (mpt) REVERT: F 93 MET cc_start: 0.3738 (mmt) cc_final: 0.3479 (ptp) REVERT: F 122 PHE cc_start: 0.6068 (OUTLIER) cc_final: 0.4607 (m-80) REVERT: J 93 MET cc_start: 0.5739 (mpm) cc_final: 0.5144 (mpp) REVERT: J 117 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7342 (mt-10) outliers start: 33 outliers final: 13 residues processed: 282 average time/residue: 0.4312 time to fit residues: 134.0533 Evaluate side-chains 223 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 208 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 122 PHE Chi-restraints excluded: chain J residue 136 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 75 optimal weight: 6.9990 chunk 143 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 41 optimal weight: 0.0870 chunk 77 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 147 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 158 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 overall best weight: 5.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN A 52 HIS A 92 ASN H 57 GLN ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 47 HIS ** L 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.150065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.127665 restraints weight = 21919.591| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 1.61 r_work: 0.3573 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 1.5879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.161 14166 Z= 0.319 Angle : 1.009 15.085 19399 Z= 0.511 Chirality : 0.054 0.399 2193 Planarity : 0.008 0.062 2457 Dihedral : 5.462 25.763 1862 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.19 % Favored : 96.75 % Rotamer: Outliers : 1.57 % Allowed : 24.44 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.20), residues: 1694 helix: 0.30 (0.14), residues: 1213 sheet: None (None), residues: 0 loop : 0.48 (0.31), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 98 TYR 0.041 0.003 TYR B 88 PHE 0.051 0.004 PHE F 9 TRP 0.071 0.004 TRP I 62 HIS 0.023 0.003 HIS F 51 Details of bonding type rmsd covalent geometry : bond 0.00752 (14166) covalent geometry : angle 1.00933 (19399) hydrogen bonds : bond 0.05748 ( 946) hydrogen bonds : angle 5.50526 ( 2775) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 299 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: A 39 ARG cc_start: 0.8540 (tpp80) cc_final: 0.8339 (ttm-80) REVERT: A 117 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7916 (pp20) REVERT: A 132 TYR cc_start: 0.5572 (m-10) cc_final: 0.3508 (t80) REVERT: C 60 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8164 (mp) REVERT: C 90 ASN cc_start: 0.8014 (OUTLIER) cc_final: 0.7707 (m-40) REVERT: C 124 VAL cc_start: 0.8928 (t) cc_final: 0.8696 (t) REVERT: D 14 GLU cc_start: 0.5057 (OUTLIER) cc_final: 0.4483 (mp0) REVERT: D 117 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7944 (tm-30) REVERT: G 8 GLU cc_start: 0.8108 (tt0) cc_final: 0.7469 (tm-30) REVERT: G 12 THR cc_start: 0.9292 (p) cc_final: 0.9014 (t) REVERT: G 124 VAL cc_start: 0.8534 (p) cc_final: 0.8296 (p) REVERT: E 7 LYS cc_start: 0.8434 (tppt) cc_final: 0.8226 (mmtm) REVERT: E 29 ASP cc_start: 0.8558 (m-30) cc_final: 0.8304 (m-30) REVERT: E 93 MET cc_start: 0.7918 (mpm) cc_final: 0.7687 (mtt) REVERT: I 39 ARG cc_start: 0.8331 (tpp80) cc_final: 0.7838 (ttt180) REVERT: K 40 GLU cc_start: 0.7850 (mp0) cc_final: 0.7593 (pm20) REVERT: K 83 ASP cc_start: 0.8192 (t0) cc_final: 0.7605 (m-30) REVERT: K 85 VAL cc_start: 0.8411 (t) cc_final: 0.8110 (p) REVERT: F 7 LYS cc_start: 0.6166 (pttt) cc_final: 0.5704 (tppt) REVERT: F 29 ASP cc_start: 0.7716 (m-30) cc_final: 0.7498 (m-30) REVERT: F 64 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6732 (mt-10) REVERT: F 117 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8053 (tm-30) REVERT: J 101 LEU cc_start: 0.8786 (mm) cc_final: 0.8570 (mt) outliers start: 24 outliers final: 11 residues processed: 316 average time/residue: 0.5202 time to fit residues: 179.2827 Evaluate side-chains 250 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 236 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain L residue 70 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 22 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN D 57 GLN I 90 ASN J 104 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.149199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.125565 restraints weight = 22328.116| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 1.70 r_work: 0.3560 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 1.6017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14166 Z= 0.161 Angle : 0.753 11.246 19399 Z= 0.370 Chirality : 0.043 0.346 2193 Planarity : 0.006 0.055 2457 Dihedral : 4.736 31.168 1862 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.01 % Favored : 97.93 % Rotamer: Outliers : 1.57 % Allowed : 27.52 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.21), residues: 1694 helix: 0.74 (0.14), residues: 1246 sheet: None (None), residues: 0 loop : 0.83 (0.33), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 39 TYR 0.017 0.002 TYR A 38 PHE 0.021 0.002 PHE L 24 TRP 0.033 0.002 TRP I 62 HIS 0.006 0.001 HIS F 104 Details of bonding type rmsd covalent geometry : bond 0.00364 (14166) covalent geometry : angle 0.75256 (19399) hydrogen bonds : bond 0.04276 ( 946) hydrogen bonds : angle 4.95438 ( 2775) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4547.66 seconds wall clock time: 78 minutes 14.38 seconds (4694.38 seconds total)