Starting phenix.real_space_refine on Thu May 15 18:35:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g5v_29756/05_2025/8g5v_29756.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g5v_29756/05_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_29756/05_2025/8g5v_29756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g5v_29756/05_2025/8g5v_29756.map" model { file = "/net/cci-nas-00/data/ceres_data/8g5v_29756/05_2025/8g5v_29756.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g5v_29756/05_2025/8g5v_29756.cif" } resolution = 3.0 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= 0.005 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.70, per 1000 atoms: 0.71 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: 3.20 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.17 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: 3.73 Time building geometry restraints manager: 3.76 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: 12.460 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 32.410 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.540 ------------------------------------------------------------------------------- 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 (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: 2.14 (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 TRP 0.042 0.002 TRP B 71 HIS 0.006 0.001 HIS A 104 PHE 0.039 0.002 PHE E 18 TYR 0.017 0.002 TYR A 88 ARG 0.003 0.000 ARG D 133 Details of bonding type rmsd hydrogen bonds : bond 0.08005 ( 946) hydrogen bonds : angle 4.49239 ( 2775) covalent geometry : bond 0.00396 (14166) covalent geometry : angle 0.60877 (19399) *********************** 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 : 1.374 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: 0.5362 (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: 0.8392 time to fit residues: 286.2391 Evaluate side-chains 157 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 155 time to evaluate : 1.445 ------------------------------------------------------------------------------- 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 141 optimal weight: 1.9990 chunk 127 optimal weight: 0.0970 chunk 70 optimal weight: 7.9990 chunk 43 optimal weight: 0.2980 chunk 85 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 131 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 = 0.4564 r_free = 0.4564 target = 0.206223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.194630 restraints weight = 26442.702| |-----------------------------------------------------------------------------| r_work (start): 0.4446 rms_B_bonded: 1.30 r_work: 0.4390 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.4315 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.4315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3200 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 14166 Z= 0.169 Angle : 0.692 11.805 19399 Z= 0.342 Chirality : 0.041 0.329 2193 Planarity : 0.006 0.066 2457 Dihedral : 4.324 21.603 1866 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.62 % Allowed : 9.31 % Favored : 88.07 % 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: 1.45 (0.20), residues: 1694 helix: 1.12 (0.14), residues: 1267 sheet: None (None), residues: 0 loop : 0.83 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP I 71 HIS 0.010 0.002 HIS K 51 PHE 0.021 0.002 PHE A 122 TYR 0.022 0.002 TYR E 88 ARG 0.010 0.001 ARG I 82 Details of bonding type rmsd hydrogen bonds : bond 0.03985 ( 946) hydrogen bonds : angle 4.58322 ( 2775) covalent geometry : bond 0.00365 (14166) covalent geometry : angle 0.69196 (19399) *********************** 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 229 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 189 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLU cc_start: 0.3203 (tt0) cc_final: 0.2580 (mm-30) REVERT: G 66 MET cc_start: 0.7345 (OUTLIER) cc_final: 0.7086 (mpp) REVERT: E 40 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.6905 (mp0) REVERT: I 78 ASP cc_start: 0.4962 (m-30) cc_final: 0.4018 (t0) REVERT: K 66 MET cc_start: 0.6041 (mmp) cc_final: 0.5431 (mmp) REVERT: H 1 MET cc_start: 0.0636 (tpp) cc_final: 0.0102 (ttp) REVERT: H 93 MET cc_start: 0.4804 (mmp) cc_final: 0.4557 (mmp) REVERT: F 1 MET cc_start: 0.0231 (ttm) cc_final: -0.0110 (pmm) REVERT: F 93 MET cc_start: 0.1309 (mmt) cc_final: 0.0679 (mtt) REVERT: L 82 ARG cc_start: 0.4726 (ttp80) cc_final: 0.4496 (ttp-170) outliers start: 40 outliers final: 13 residues processed: 208 average time/residue: 0.8541 time to fit residues: 201.6226 Evaluate side-chains 168 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 TYR 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 66 MET 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 101 LEU Chi-restraints excluded: chain I residue 82 ARG Chi-restraints excluded: chain K residue 89 VAL 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 4 optimal weight: 6.9990 chunk 137 optimal weight: 0.9990 chunk 158 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 121 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 92 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 51 HIS H 47 HIS J 104 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 = 0.4531 r_free = 0.4531 target = 0.203235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.189967 restraints weight = 26450.960| |-----------------------------------------------------------------------------| r_work (start): 0.4401 rms_B_bonded: 1.61 r_work: 0.4330 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.4246 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.4246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5155 moved from start: 0.6294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.138 14166 Z= 0.252 Angle : 0.860 16.076 19399 Z= 0.434 Chirality : 0.049 0.384 2193 Planarity : 0.007 0.069 2457 Dihedral : 4.694 23.645 1862 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.00 % Allowed : 12.52 % 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 (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: 0.77 (0.20), residues: 1694 helix: 0.61 (0.14), residues: 1254 sheet: None (None), residues: 0 loop : 0.65 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP K 62 HIS 0.011 0.002 HIS J 104 PHE 0.050 0.003 PHE F 24 TYR 0.061 0.003 TYR F 118 ARG 0.019 0.001 ARG G 82 Details of bonding type rmsd hydrogen bonds : bond 0.04901 ( 946) hydrogen bonds : angle 4.91689 ( 2775) covalent geometry : bond 0.00554 (14166) covalent geometry : angle 0.86011 (19399) *********************** 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 275 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 214 time to evaluate : 1.507 Fit side-chains revert: symmetry clash REVERT: B 8 GLU cc_start: 0.4368 (tt0) cc_final: 0.3264 (mm-30) REVERT: B 83 ASP cc_start: 0.5247 (OUTLIER) cc_final: 0.5024 (p0) REVERT: D 29 ASP cc_start: 0.5691 (m-30) cc_final: 0.4793 (t70) REVERT: D 42 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7180 (mt) REVERT: G 66 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7791 (mmm) REVERT: E 29 ASP cc_start: 0.7774 (m-30) cc_final: 0.7468 (m-30) REVERT: E 90 ASN cc_start: 0.7632 (m-40) cc_final: 0.7431 (m-40) REVERT: E 112 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.6209 (tpp80) REVERT: K 66 MET cc_start: 0.6599 (mmp) cc_final: 0.6194 (mmp) REVERT: H 72 VAL cc_start: 0.1760 (t) cc_final: 0.1437 (p) REVERT: F 1 MET cc_start: 0.1391 (ttm) cc_final: 0.0693 (pmm) REVERT: F 74 VAL cc_start: 0.4668 (OUTLIER) cc_final: 0.4422 (p) REVERT: F 93 MET cc_start: 0.1728 (mmt) cc_final: 0.1005 (mtt) REVERT: L 82 ARG cc_start: 0.5255 (ttp80) cc_final: 0.4339 (ttp80) outliers start: 61 outliers final: 13 residues processed: 249 average time/residue: 0.9329 time to fit residues: 260.8987 Evaluate side-chains 178 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain G residue 66 MET Chi-restraints excluded: chain G residue 85 VAL 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 19 LEU Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain J residue 1 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 154 optimal weight: 3.9990 chunk 143 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 152 optimal weight: 0.4980 chunk 126 optimal weight: 0.3980 chunk 6 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 90 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 52 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.201883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.187002 restraints weight = 25895.319| |-----------------------------------------------------------------------------| r_work (start): 0.4356 rms_B_bonded: 1.75 r_work: 0.4283 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.4193 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5306 moved from start: 0.6792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14166 Z= 0.128 Angle : 0.643 13.252 19399 Z= 0.313 Chirality : 0.041 0.351 2193 Planarity : 0.005 0.055 2457 Dihedral : 4.219 19.387 1862 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.77 % Favored : 98.17 % Rotamer: Outliers : 3.67 % Allowed : 16.51 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.58 (0.20), residues: 1694 helix: 1.19 (0.14), residues: 1255 sheet: None (None), residues: 0 loop : 0.98 (0.32), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 71 HIS 0.005 0.001 HIS B 47 PHE 0.028 0.002 PHE A 24 TYR 0.019 0.001 TYR J 132 ARG 0.007 0.001 ARG A 39 Details of bonding type rmsd hydrogen bonds : bond 0.03661 ( 946) hydrogen bonds : angle 4.55945 ( 2775) covalent geometry : bond 0.00275 (14166) covalent geometry : angle 0.64252 (19399) *********************** 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 247 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 191 time to evaluate : 1.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLU cc_start: 0.3827 (tt0) cc_final: 0.2940 (mm-30) REVERT: B 122 PHE cc_start: 0.4025 (t80) cc_final: 0.3502 (t80) REVERT: C 14 GLU cc_start: 0.6035 (OUTLIER) cc_final: 0.5802 (tt0) REVERT: D 29 ASP cc_start: 0.5985 (m-30) cc_final: 0.4904 (t70) REVERT: D 42 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7201 (mt) REVERT: G 29 ASP cc_start: 0.7120 (m-30) cc_final: 0.6850 (m-30) REVERT: E 29 ASP cc_start: 0.7940 (m-30) cc_final: 0.7574 (m-30) REVERT: E 90 ASN cc_start: 0.7801 (m-40) cc_final: 0.7570 (m-40) REVERT: K 66 MET cc_start: 0.7008 (mmp) cc_final: 0.6706 (mmp) REVERT: H 72 VAL cc_start: 0.1892 (t) cc_final: 0.1586 (p) REVERT: F 1 MET cc_start: 0.1440 (ttm) cc_final: 0.0984 (pmm) REVERT: F 74 VAL cc_start: 0.4372 (t) cc_final: 0.4166 (p) REVERT: F 93 MET cc_start: 0.1575 (mmt) cc_final: 0.0882 (mtt) REVERT: J 93 MET cc_start: 0.2489 (mpp) cc_final: 0.0669 (ttm) REVERT: L 1 MET cc_start: 0.1278 (OUTLIER) cc_final: -0.0597 (ppp) REVERT: L 82 ARG cc_start: 0.5356 (ttp80) cc_final: 0.4674 (ttp-170) outliers start: 56 outliers final: 19 residues processed: 225 average time/residue: 0.8524 time to fit residues: 217.7789 Evaluate side-chains 178 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 71 TRP Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 109 THR 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 I residue 52 HIS Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 93 MET Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 139 ILE Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 67 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 45 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 140 optimal weight: 4.9990 chunk 162 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 156 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 136 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 ASN ** E 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.191140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.172592 restraints weight = 24689.982| |-----------------------------------------------------------------------------| r_work (start): 0.4214 rms_B_bonded: 1.78 r_work: 0.4127 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.4031 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6533 moved from start: 0.9964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 14166 Z= 0.242 Angle : 0.845 17.080 19399 Z= 0.423 Chirality : 0.049 0.469 2193 Planarity : 0.007 0.101 2457 Dihedral : 4.736 23.437 1862 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.25 % Favored : 96.69 % Rotamer: Outliers : 4.91 % Allowed : 16.78 % Favored : 78.31 % 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: 1.10 (0.20), residues: 1694 helix: 0.83 (0.14), residues: 1212 sheet: None (None), residues: 0 loop : 0.85 (0.31), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.003 TRP H 62 HIS 0.007 0.002 HIS G 104 PHE 0.023 0.003 PHE F 122 TYR 0.025 0.003 TYR C 88 ARG 0.020 0.001 ARG D 82 Details of bonding type rmsd hydrogen bonds : bond 0.04902 ( 946) hydrogen bonds : angle 5.03196 ( 2775) covalent geometry : bond 0.00544 (14166) covalent geometry : angle 0.84495 (19399) *********************** 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 327 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 252 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.2452 (OUTLIER) cc_final: 0.1903 (tm-30) REVERT: A 97 PHE cc_start: 0.2230 (m-80) cc_final: 0.1774 (m-10) REVERT: C 95 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7906 (tt) REVERT: D 14 GLU cc_start: 0.4640 (OUTLIER) cc_final: 0.3814 (mp0) REVERT: G 29 ASP cc_start: 0.8027 (m-30) cc_final: 0.7800 (m-30) REVERT: G 78 ASP cc_start: 0.5154 (OUTLIER) cc_final: 0.4938 (m-30) REVERT: E 29 ASP cc_start: 0.8187 (m-30) cc_final: 0.7913 (m-30) REVERT: E 40 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7172 (mp0) REVERT: I 78 ASP cc_start: 0.5351 (m-30) cc_final: 0.4610 (t0) REVERT: K 1 MET cc_start: 0.5381 (tmt) cc_final: 0.5004 (tmt) REVERT: K 119 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8591 (mt) REVERT: K 136 ASN cc_start: 0.7484 (OUTLIER) cc_final: 0.7234 (m110) REVERT: H 66 MET cc_start: 0.4667 (mmt) cc_final: 0.4006 (ptp) REVERT: F 74 VAL cc_start: 0.5241 (OUTLIER) cc_final: 0.5033 (p) REVERT: F 93 MET cc_start: 0.2950 (mmt) cc_final: 0.2273 (ptp) REVERT: F 132 TYR cc_start: -0.0840 (OUTLIER) cc_final: -0.3562 (m-10) REVERT: J 1 MET cc_start: 0.3364 (OUTLIER) cc_final: 0.3098 (tmm) REVERT: L 1 MET cc_start: 0.1098 (OUTLIER) cc_final: -0.0878 (ppp) REVERT: L 82 ARG cc_start: 0.5488 (ttp80) cc_final: 0.4722 (ttp80) outliers start: 75 outliers final: 18 residues processed: 294 average time/residue: 1.1228 time to fit residues: 365.0795 Evaluate side-chains 220 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain G residue 78 ASP 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 101 LEU Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 93 MET Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 136 ASN Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 132 TYR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 68 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 128 optimal weight: 0.9980 chunk 118 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 102 optimal weight: 0.0770 chunk 3 optimal weight: 0.0870 chunk 134 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 148 optimal weight: 4.9990 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS G 75 ASN K 99 GLN ** H 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.187487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.166340 restraints weight = 24956.402| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 1.85 r_work: 0.4072 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3973 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6524 moved from start: 1.0340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14166 Z= 0.132 Angle : 0.651 9.744 19399 Z= 0.321 Chirality : 0.041 0.317 2193 Planarity : 0.005 0.048 2457 Dihedral : 4.317 22.076 1862 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.65 % Favored : 98.29 % Rotamer: Outliers : 3.15 % Allowed : 19.72 % Favored : 77.13 % 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: 1.65 (0.21), residues: 1694 helix: 1.27 (0.15), residues: 1244 sheet: None (None), residues: 0 loop : 0.93 (0.32), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 71 HIS 0.012 0.001 HIS L 52 PHE 0.040 0.002 PHE A 24 TYR 0.023 0.001 TYR J 132 ARG 0.012 0.001 ARG H 39 Details of bonding type rmsd hydrogen bonds : bond 0.03831 ( 946) hydrogen bonds : angle 4.61397 ( 2775) covalent geometry : bond 0.00284 (14166) covalent geometry : angle 0.65142 (19399) *********************** 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 266 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 218 time to evaluate : 1.437 Fit side-chains revert: symmetry clash REVERT: C 32 ASP cc_start: 0.8196 (t0) cc_final: 0.7820 (m-30) REVERT: C 95 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7510 (tt) REVERT: C 117 GLU cc_start: 0.7160 (tt0) cc_final: 0.6782 (tm-30) REVERT: D 12 THR cc_start: 0.7893 (p) cc_final: 0.7667 (t) REVERT: D 14 GLU cc_start: 0.4330 (OUTLIER) cc_final: 0.3685 (mp0) REVERT: G 29 ASP cc_start: 0.7853 (m-30) cc_final: 0.7433 (m-30) REVERT: G 86 VAL cc_start: 0.6085 (t) cc_final: 0.5860 (p) REVERT: E 2 ASP cc_start: 0.7030 (t0) cc_final: 0.6744 (t0) REVERT: E 29 ASP cc_start: 0.8296 (m-30) cc_final: 0.8043 (m-30) REVERT: K 119 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8674 (mt) REVERT: H 66 MET cc_start: 0.4729 (mmt) cc_final: 0.4093 (ptp) REVERT: H 72 VAL cc_start: 0.2620 (t) cc_final: 0.2240 (p) REVERT: F 1 MET cc_start: 0.2094 (ttt) cc_final: 0.1716 (pmm) REVERT: F 60 LEU cc_start: 0.4771 (OUTLIER) cc_final: 0.4560 (mm) REVERT: F 93 MET cc_start: 0.2907 (mmt) cc_final: 0.2313 (ptp) REVERT: J 1 MET cc_start: 0.3012 (OUTLIER) cc_final: 0.2605 (tmm) REVERT: J 118 TYR cc_start: 0.5447 (t80) cc_final: 0.5123 (t80) REVERT: J 132 TYR cc_start: 0.6885 (m-10) cc_final: 0.6646 (m-80) REVERT: J 136 ASN cc_start: 0.6352 (p0) cc_final: 0.6130 (p0) REVERT: L 82 ARG cc_start: 0.5546 (ttp80) cc_final: 0.4962 (ttp-170) outliers start: 48 outliers final: 14 residues processed: 251 average time/residue: 1.0627 time to fit residues: 294.9894 Evaluate side-chains 209 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 190 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 116 ILE 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 53 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 121 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 163 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 overall best weight: 4.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 HIS ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 GLN D 99 GLN ** G 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 HIS ** L 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.161385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.138214 restraints weight = 22934.564| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 1.75 r_work: 0.3726 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 1.5074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.134 14166 Z= 0.353 Angle : 1.115 17.585 19399 Z= 0.575 Chirality : 0.058 0.362 2193 Planarity : 0.009 0.172 2457 Dihedral : 6.098 39.658 1862 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.66 % Favored : 96.22 % Rotamer: Outliers : 4.46 % Allowed : 19.13 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.22 (0.20), residues: 1694 helix: -0.06 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : 0.08 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP I 62 HIS 0.016 0.003 HIS D 47 PHE 0.033 0.004 PHE F 103 TYR 0.034 0.004 TYR J 38 ARG 0.023 0.002 ARG A 39 Details of bonding type rmsd hydrogen bonds : bond 0.07168 ( 946) hydrogen bonds : angle 5.86496 ( 2775) covalent geometry : bond 0.00804 (14166) covalent geometry : angle 1.11466 (19399) *********************** 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 353 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 285 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 GLU cc_start: 0.7827 (pm20) cc_final: 0.7520 (pm20) REVERT: B 114 THR cc_start: 0.8607 (m) cc_final: 0.8389 (m) REVERT: A 14 GLU cc_start: 0.4108 (OUTLIER) cc_final: 0.3829 (pp20) REVERT: A 132 TYR cc_start: 0.4745 (m-80) cc_final: 0.3488 (t80) REVERT: C 1 MET cc_start: 0.7599 (OUTLIER) cc_final: 0.7376 (ttp) REVERT: C 12 THR cc_start: 0.9077 (p) cc_final: 0.8835 (m) REVERT: C 29 ASP cc_start: 0.8458 (t0) cc_final: 0.8036 (t0) REVERT: D 12 THR cc_start: 0.8843 (p) cc_final: 0.8609 (t) REVERT: D 14 GLU cc_start: 0.5080 (OUTLIER) cc_final: 0.4650 (mp0) REVERT: G 117 GLU cc_start: 0.8219 (pt0) cc_final: 0.7984 (pt0) REVERT: G 127 ARG cc_start: 0.6854 (OUTLIER) cc_final: 0.6283 (mtm-85) REVERT: I 65 LEU cc_start: 0.6796 (OUTLIER) cc_final: 0.6495 (mt) REVERT: K 1 MET cc_start: 0.5740 (OUTLIER) cc_final: 0.5306 (ttt) REVERT: K 40 GLU cc_start: 0.8060 (mp0) cc_final: 0.7805 (pm20) REVERT: K 83 ASP cc_start: 0.8164 (t0) cc_final: 0.7463 (m-30) REVERT: K 87 SER cc_start: 0.8557 (t) cc_final: 0.8341 (p) REVERT: H 30 LEU cc_start: 0.4817 (pp) cc_final: 0.4446 (tp) REVERT: H 66 MET cc_start: 0.5305 (mmt) cc_final: 0.4208 (ptp) REVERT: F 1 MET cc_start: 0.2013 (ttt) cc_final: 0.1571 (mpp) REVERT: F 93 MET cc_start: 0.4296 (mmt) cc_final: 0.3696 (mmm) REVERT: F 122 PHE cc_start: 0.6552 (OUTLIER) cc_final: 0.4660 (m-80) REVERT: F 132 TYR cc_start: 0.1925 (OUTLIER) cc_final: -0.1158 (m-10) REVERT: J 117 GLU cc_start: 0.7747 (mp0) cc_final: 0.7372 (mm-30) REVERT: L 9 PHE cc_start: 0.5495 (m-10) cc_final: 0.4822 (m-80) REVERT: L 18 PHE cc_start: 0.0586 (OUTLIER) cc_final: -0.2078 (m-10) outliers start: 68 outliers final: 14 residues processed: 329 average time/residue: 1.1678 time to fit residues: 422.5814 Evaluate side-chains 231 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 208 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 ASP Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 127 ARG Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 122 PHE Chi-restraints excluded: chain F residue 132 TYR Chi-restraints excluded: chain L residue 18 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 104 optimal weight: 6.9990 chunk 83 optimal weight: 0.0070 chunk 154 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 overall best weight: 0.9800 ------------------------------------------------------------------------------- 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 57 GLN E 47 HIS J 47 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.162118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.139654 restraints weight = 22525.181| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 1.61 r_work: 0.3734 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3627 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 1.5087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 14166 Z= 0.152 Angle : 0.724 12.232 19399 Z= 0.365 Chirality : 0.042 0.320 2193 Planarity : 0.006 0.050 2457 Dihedral : 4.821 30.808 1862 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.13 % Favored : 97.82 % Rotamer: Outliers : 2.29 % Allowed : 24.77 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.91 (0.20), residues: 1694 helix: 0.77 (0.14), residues: 1246 sheet: None (None), residues: 0 loop : 0.50 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 71 HIS 0.006 0.001 HIS F 104 PHE 0.024 0.002 PHE A 24 TYR 0.012 0.001 TYR F 38 ARG 0.017 0.001 ARG B 39 Details of bonding type rmsd hydrogen bonds : bond 0.04624 ( 946) hydrogen bonds : angle 5.07655 ( 2775) covalent geometry : bond 0.00340 (14166) covalent geometry : angle 0.72354 (19399) *********************** 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 290 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 255 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 GLU cc_start: 0.7922 (pm20) cc_final: 0.7595 (pm20) REVERT: B 39 ARG cc_start: 0.8373 (ttm-80) cc_final: 0.8117 (ttm-80) REVERT: A 100 LEU cc_start: 0.8845 (tt) cc_final: 0.8630 (tp) REVERT: A 132 TYR cc_start: 0.4729 (m-80) cc_final: 0.3089 (t80) REVERT: D 12 THR cc_start: 0.8574 (p) cc_final: 0.8330 (t) REVERT: G 39 ARG cc_start: 0.8131 (ttm-80) cc_final: 0.7864 (ttp80) REVERT: G 117 GLU cc_start: 0.8166 (pt0) cc_final: 0.7934 (pt0) REVERT: G 127 ARG cc_start: 0.6782 (OUTLIER) cc_final: 0.5783 (mtt90) REVERT: E 88 TYR cc_start: 0.8046 (t80) cc_final: 0.7834 (t80) REVERT: I 39 ARG cc_start: 0.8269 (tpp80) cc_final: 0.7619 (ttt180) REVERT: I 78 ASP cc_start: 0.5692 (m-30) cc_final: 0.4383 (t0) REVERT: K 46 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7433 (pm20) REVERT: K 83 ASP cc_start: 0.8137 (t0) cc_final: 0.7523 (m-30) REVERT: H 30 LEU cc_start: 0.5079 (pp) cc_final: 0.4836 (tp) REVERT: H 66 MET cc_start: 0.5341 (mmt) cc_final: 0.4195 (ptp) REVERT: J 1 MET cc_start: 0.4999 (OUTLIER) cc_final: 0.4118 (ttt) REVERT: J 93 MET cc_start: 0.5677 (mmm) cc_final: 0.4927 (mpp) REVERT: J 117 GLU cc_start: 0.7561 (mp0) cc_final: 0.7293 (mm-30) REVERT: L 9 PHE cc_start: 0.5261 (m-10) cc_final: 0.4801 (m-80) REVERT: L 40 GLU cc_start: 0.6359 (OUTLIER) cc_final: 0.6108 (pm20) outliers start: 35 outliers final: 11 residues processed: 280 average time/residue: 1.2315 time to fit residues: 375.9378 Evaluate side-chains 233 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 218 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 127 ARG Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain H residue 136 ASN Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain L residue 40 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 34 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 16 optimal weight: 0.0980 chunk 38 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 27 optimal weight: 0.0170 chunk 75 optimal weight: 6.9990 chunk 146 optimal weight: 8.9990 chunk 123 optimal weight: 1.9990 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 HIS A 52 HIS D 99 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.160178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.136569 restraints weight = 22734.255| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 1.83 r_work: 0.3688 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 1.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14166 Z= 0.137 Angle : 0.705 11.285 19399 Z= 0.348 Chirality : 0.042 0.334 2193 Planarity : 0.005 0.045 2457 Dihedral : 4.498 28.271 1862 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.77 % Allowed : 26.61 % Favored : 71.63 % 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: 1.27 (0.21), residues: 1694 helix: 1.03 (0.15), residues: 1248 sheet: None (None), residues: 0 loop : 0.62 (0.32), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 125 HIS 0.005 0.001 HIS F 104 PHE 0.023 0.002 PHE L 103 TYR 0.017 0.001 TYR E 88 ARG 0.010 0.001 ARG B 39 Details of bonding type rmsd hydrogen bonds : bond 0.04075 ( 946) hydrogen bonds : angle 4.87929 ( 2775) covalent geometry : bond 0.00301 (14166) covalent geometry : angle 0.70458 (19399) *********************** 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 260 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 233 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 GLU cc_start: 0.8035 (pm20) cc_final: 0.7689 (pm20) REVERT: A 132 TYR cc_start: 0.4943 (m-80) cc_final: 0.3158 (t80) REVERT: C 39 ARG cc_start: 0.7795 (ttm-80) cc_final: 0.7555 (ttm-80) REVERT: D 12 THR cc_start: 0.8371 (p) cc_final: 0.8094 (t) REVERT: G 39 ARG cc_start: 0.8121 (ttm-80) cc_final: 0.7866 (ttm110) REVERT: G 86 VAL cc_start: 0.6769 (t) cc_final: 0.6521 (p) REVERT: G 117 GLU cc_start: 0.8183 (pt0) cc_final: 0.7919 (pt0) REVERT: I 39 ARG cc_start: 0.8237 (tpp80) cc_final: 0.7996 (tpp80) REVERT: I 96 LYS cc_start: 0.8458 (mtpt) cc_final: 0.7687 (tppt) REVERT: K 46 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7484 (pm20) REVERT: K 83 ASP cc_start: 0.8021 (t0) cc_final: 0.7427 (m-30) REVERT: K 96 LYS cc_start: 0.7338 (ptmt) cc_final: 0.6709 (ptpp) REVERT: K 133 ARG cc_start: 0.8817 (ttm-80) cc_final: 0.8592 (ttp-170) REVERT: H 30 LEU cc_start: 0.5137 (pp) cc_final: 0.4577 (mt) REVERT: H 66 MET cc_start: 0.5414 (mmt) cc_final: 0.4156 (ptp) REVERT: H 93 MET cc_start: 0.7078 (mpm) cc_final: 0.6771 (mpm) REVERT: F 7 LYS cc_start: 0.5596 (pttt) cc_final: 0.4709 (tppt) REVERT: J 1 MET cc_start: 0.4921 (OUTLIER) cc_final: 0.4111 (ttt) REVERT: L 9 PHE cc_start: 0.4981 (m-10) cc_final: 0.4619 (m-10) REVERT: L 31 LEU cc_start: 0.6043 (tt) cc_final: 0.5789 (tp) REVERT: L 40 GLU cc_start: 0.6422 (OUTLIER) cc_final: 0.6087 (pm20) REVERT: L 82 ARG cc_start: 0.5862 (ttp80) cc_final: 0.5477 (ttm110) outliers start: 27 outliers final: 8 residues processed: 248 average time/residue: 1.2741 time to fit residues: 343.2347 Evaluate side-chains 223 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 212 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain H residue 136 ASN Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain L residue 40 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 56 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 139 optimal weight: 0.0770 chunk 31 optimal weight: 0.7980 chunk 157 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 121 optimal weight: 9.9990 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS ** H 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 47 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.159183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.134871 restraints weight = 22553.196| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 1.76 r_work: 0.3681 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3571 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 1.5308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14166 Z= 0.133 Angle : 0.689 10.572 19399 Z= 0.337 Chirality : 0.042 0.344 2193 Planarity : 0.005 0.053 2457 Dihedral : 4.322 27.704 1862 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.05 % Allowed : 27.65 % Favored : 71.30 % 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: 1.45 (0.21), residues: 1694 helix: 1.14 (0.15), residues: 1248 sheet: None (None), residues: 0 loop : 0.76 (0.32), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 125 HIS 0.006 0.001 HIS F 104 PHE 0.027 0.001 PHE A 24 TYR 0.014 0.001 TYR L 38 ARG 0.013 0.001 ARG B 39 Details of bonding type rmsd hydrogen bonds : bond 0.03865 ( 946) hydrogen bonds : angle 4.74339 ( 2775) covalent geometry : bond 0.00290 (14166) covalent geometry : angle 0.68870 (19399) ********************** 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 261 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 245 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 GLU cc_start: 0.7942 (pm20) cc_final: 0.7607 (pm20) REVERT: A 132 TYR cc_start: 0.5314 (m-80) cc_final: 0.3296 (t80) REVERT: D 12 THR cc_start: 0.8347 (p) cc_final: 0.8045 (t) REVERT: G 28 ARG cc_start: 0.7867 (tpm170) cc_final: 0.7576 (tpm170) REVERT: G 39 ARG cc_start: 0.8150 (ttm-80) cc_final: 0.7925 (ttm110) REVERT: G 67 THR cc_start: 0.9003 (m) cc_final: 0.8511 (p) REVERT: G 86 VAL cc_start: 0.6685 (t) cc_final: 0.6411 (p) REVERT: G 117 GLU cc_start: 0.8137 (pt0) cc_final: 0.7892 (pt0) REVERT: E 7 LYS cc_start: 0.8408 (tppt) cc_final: 0.8177 (mmtm) REVERT: I 39 ARG cc_start: 0.8301 (tpp80) cc_final: 0.7792 (ttt180) REVERT: I 92 ASN cc_start: 0.6719 (t0) cc_final: 0.6417 (m110) REVERT: I 96 LYS cc_start: 0.8359 (mtpt) cc_final: 0.8154 (mtmm) REVERT: K 46 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7428 (pm20) REVERT: K 83 ASP cc_start: 0.8092 (t0) cc_final: 0.7491 (m-30) REVERT: K 96 LYS cc_start: 0.7263 (ptmt) cc_final: 0.6708 (ptpp) REVERT: H 30 LEU cc_start: 0.5534 (pp) cc_final: 0.5023 (mt) REVERT: H 93 MET cc_start: 0.7155 (mpm) cc_final: 0.6737 (mmt) REVERT: F 7 LYS cc_start: 0.5778 (pttt) cc_final: 0.4943 (tppt) REVERT: F 120 VAL cc_start: 0.8106 (t) cc_final: 0.7888 (t) REVERT: J 1 MET cc_start: 0.4953 (OUTLIER) cc_final: 0.4252 (ttt) REVERT: J 60 LEU cc_start: 0.7095 (mt) cc_final: 0.6893 (tp) REVERT: J 93 MET cc_start: 0.5764 (mmm) cc_final: 0.5104 (mpp) REVERT: L 9 PHE cc_start: 0.5400 (m-10) cc_final: 0.4979 (m-80) REVERT: L 40 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.6321 (pm20) REVERT: L 66 MET cc_start: 0.6370 (ppp) cc_final: 0.6074 (mmp) REVERT: L 82 ARG cc_start: 0.6049 (ttp80) cc_final: 0.5642 (ttp-110) outliers start: 16 outliers final: 7 residues processed: 253 average time/residue: 1.3379 time to fit residues: 367.4053 Evaluate side-chains 234 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 224 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain L residue 40 GLU Chi-restraints excluded: chain L residue 68 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 19 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 110 optimal weight: 0.0370 chunk 123 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 157 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.158671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.135012 restraints weight = 22742.684| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 1.88 r_work: 0.3676 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3567 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 1.5416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14166 Z= 0.126 Angle : 0.684 15.839 19399 Z= 0.334 Chirality : 0.041 0.401 2193 Planarity : 0.005 0.059 2457 Dihedral : 4.230 25.144 1862 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.31 % Allowed : 27.79 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.52 (0.21), residues: 1694 helix: 1.17 (0.15), residues: 1260 sheet: None (None), residues: 0 loop : 0.88 (0.33), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP I 62 HIS 0.005 0.001 HIS L 104 PHE 0.022 0.001 PHE A 24 TYR 0.013 0.001 TYR L 38 ARG 0.013 0.001 ARG B 39 Details of bonding type rmsd hydrogen bonds : bond 0.03716 ( 946) hydrogen bonds : angle 4.66683 ( 2775) covalent geometry : bond 0.00278 (14166) covalent geometry : angle 0.68404 (19399) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10734.21 seconds wall clock time: 185 minutes 30.05 seconds (11130.05 seconds total)