Starting phenix.real_space_refine on Thu Jul 31 12:36:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g5v_29756/07_2025/8g5v_29756.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g5v_29756/07_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_29756/07_2025/8g5v_29756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g5v_29756/07_2025/8g5v_29756.map" model { file = "/net/cci-nas-00/data/ceres_data/8g5v_29756/07_2025/8g5v_29756.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g5v_29756/07_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-5711/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: 10.51, per 1000 atoms: 0.76 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: 3.46 Conformation dependent library (CDL) restraints added in 1.6 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: 1.00 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: 3.89 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: 11.390 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: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 33.490 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.200 ------------------------------------------------------------------------------- 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 : 1.305 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: 0.8193 time to fit residues: 280.1359 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 : 1.408 ------------------------------------------------------------------------------- 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 = 55)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.194632 restraints weight = 26442.701| |-----------------------------------------------------------------------------| r_work (start): 0.4446 rms_B_bonded: 1.30 r_work: 0.4391 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.4315 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.4315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3195 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 : 1.420 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: 0.3206 (tt0) cc_final: 0.2576 (mm-30) REVERT: G 66 MET cc_start: 0.7331 (OUTLIER) cc_final: 0.7071 (mpp) REVERT: E 40 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.6895 (mp0) REVERT: I 78 ASP cc_start: 0.4879 (m-30) cc_final: 0.3965 (t0) REVERT: K 66 MET cc_start: 0.6032 (mmp) cc_final: 0.5425 (mmp) REVERT: H 1 MET cc_start: 0.0639 (tpp) cc_final: 0.0096 (ttp) REVERT: H 93 MET cc_start: 0.4796 (mmp) cc_final: 0.4555 (mmp) REVERT: F 1 MET cc_start: 0.0252 (ttm) cc_final: -0.0081 (pmm) REVERT: F 93 MET cc_start: 0.1286 (mmt) cc_final: 0.0664 (mtt) outliers start: 40 outliers final: 13 residues processed: 208 average time/residue: 0.8458 time to fit residues: 200.3636 Evaluate side-chains 167 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 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: 6.9990 chunk 39 optimal weight: 4.9990 chunk 54 optimal weight: 0.3980 chunk 121 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 92 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 47 HIS I 52 HIS K 51 HIS H 47 HIS J 104 HIS L 99 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.203367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.189255 restraints weight = 26376.866| |-----------------------------------------------------------------------------| r_work (start): 0.4396 rms_B_bonded: 1.47 r_work: 0.4332 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.4248 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.4248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5427 moved from start: 0.6961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.118 14166 Z= 0.259 Angle : 0.930 16.428 19399 Z= 0.468 Chirality : 0.051 0.466 2193 Planarity : 0.007 0.069 2457 Dihedral : 4.956 33.977 1862 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.46 % Allowed : 12.19 % Favored : 83.36 % 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: 0.49 (0.20), residues: 1694 helix: 0.39 (0.14), residues: 1247 sheet: None (None), residues: 0 loop : 0.59 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP K 62 HIS 0.012 0.003 HIS J 104 PHE 0.063 0.004 PHE F 24 TYR 0.055 0.004 TYR F 118 ARG 0.021 0.001 ARG G 82 Details of bonding type rmsd hydrogen bonds : bond 0.05249 ( 946) hydrogen bonds : angle 5.06399 ( 2775) covalent geometry : bond 0.00580 (14166) covalent geometry : angle 0.93043 (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 305 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 237 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 8 GLU cc_start: 0.4369 (tt0) cc_final: 0.3404 (mm-30) REVERT: B 83 ASP cc_start: 0.5403 (OUTLIER) cc_final: 0.5192 (p0) REVERT: B 113 GLU cc_start: 0.6910 (tp30) cc_final: 0.6677 (tt0) REVERT: D 29 ASP cc_start: 0.5967 (m-30) cc_final: 0.4979 (t70) REVERT: D 42 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7397 (mt) REVERT: G 12 THR cc_start: 0.8634 (p) cc_final: 0.8084 (t) REVERT: G 29 ASP cc_start: 0.7151 (m-30) cc_final: 0.6788 (m-30) REVERT: E 29 ASP cc_start: 0.7918 (m-30) cc_final: 0.7648 (m-30) REVERT: I 66 MET cc_start: 0.5069 (OUTLIER) cc_final: 0.4460 (mpt) REVERT: K 66 MET cc_start: 0.6898 (mmp) cc_final: 0.6495 (mmp) REVERT: H 72 VAL cc_start: 0.1822 (t) cc_final: 0.1483 (p) REVERT: F 1 MET cc_start: 0.1312 (ttm) cc_final: 0.0817 (pmm) REVERT: F 74 VAL cc_start: 0.4757 (OUTLIER) cc_final: 0.4491 (p) REVERT: F 93 MET cc_start: 0.1780 (mmt) cc_final: 0.1052 (mtt) outliers start: 68 outliers final: 17 residues processed: 276 average time/residue: 0.9150 time to fit residues: 284.3986 Evaluate side-chains 186 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 89 VAL 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 D residue 109 THR 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 I residue 66 MET Chi-restraints excluded: chain K residue 22 ASP 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: 7.9990 chunk 77 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 152 optimal weight: 0.5980 chunk 126 optimal weight: 0.0370 chunk 6 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 ASN I 52 HIS F 52 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.200912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.184900 restraints weight = 25630.935| |-----------------------------------------------------------------------------| r_work (start): 0.4335 rms_B_bonded: 1.81 r_work: 0.4258 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work (final): 0.4258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5492 moved from start: 0.7491 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= 0.135 Angle : 0.661 13.220 19399 Z= 0.323 Chirality : 0.041 0.344 2193 Planarity : 0.005 0.054 2457 Dihedral : 4.316 19.598 1862 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.71 % Favored : 98.23 % Rotamer: Outliers : 3.60 % Allowed : 17.17 % Favored : 79.23 % 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: 1.43 (0.20), residues: 1694 helix: 1.09 (0.14), residues: 1255 sheet: None (None), residues: 0 loop : 0.89 (0.32), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 71 HIS 0.005 0.001 HIS B 47 PHE 0.026 0.002 PHE A 24 TYR 0.012 0.001 TYR B 38 ARG 0.010 0.001 ARG K 133 Details of bonding type rmsd hydrogen bonds : bond 0.03786 ( 946) hydrogen bonds : angle 4.59898 ( 2775) covalent geometry : bond 0.00289 (14166) covalent geometry : angle 0.66110 (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 252 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 197 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 8 GLU cc_start: 0.3829 (tt0) cc_final: 0.3224 (mm-30) REVERT: D 14 GLU cc_start: 0.4248 (OUTLIER) cc_final: 0.3097 (mp0) REVERT: D 29 ASP cc_start: 0.6055 (m-30) cc_final: 0.5012 (t70) REVERT: D 42 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7507 (mt) REVERT: G 12 THR cc_start: 0.8772 (p) cc_final: 0.8497 (t) REVERT: G 28 ARG cc_start: 0.7102 (tpm170) cc_final: 0.6832 (tpp-160) REVERT: G 29 ASP cc_start: 0.7363 (m-30) cc_final: 0.7099 (m-30) REVERT: E 29 ASP cc_start: 0.7967 (m-30) cc_final: 0.7724 (m-30) REVERT: K 66 MET cc_start: 0.6984 (mmp) cc_final: 0.6714 (mmp) REVERT: H 72 VAL cc_start: 0.2077 (t) cc_final: 0.1783 (p) REVERT: F 74 VAL cc_start: 0.4243 (t) cc_final: 0.3998 (p) REVERT: F 93 MET cc_start: 0.1641 (mmt) cc_final: 0.0847 (mtt) REVERT: J 93 MET cc_start: 0.2659 (mpp) cc_final: 0.0851 (ttm) REVERT: J 132 TYR cc_start: 0.4937 (m-10) cc_final: 0.4734 (m-10) REVERT: L 1 MET cc_start: 0.0538 (OUTLIER) cc_final: -0.1097 (ppp) outliers start: 55 outliers final: 19 residues processed: 224 average time/residue: 0.9357 time to fit residues: 236.2817 Evaluate side-chains 186 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 84 LEU 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 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 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: 1.9990 chunk 140 optimal weight: 0.0030 chunk 162 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 chunk 120 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 overall best weight: 1.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 90 ASN ** H 57 GLN ** 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 = 0.4424 r_free = 0.4424 target = 0.192461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.174344 restraints weight = 25055.743| |-----------------------------------------------------------------------------| r_work (start): 0.4232 rms_B_bonded: 1.54 r_work: 0.4159 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.4068 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6223 moved from start: 0.9112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 14166 Z= 0.198 Angle : 0.736 14.545 19399 Z= 0.368 Chirality : 0.043 0.307 2193 Planarity : 0.006 0.066 2457 Dihedral : 4.388 22.868 1862 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.36 % Favored : 97.58 % Rotamer: Outliers : 4.00 % Allowed : 17.04 % Favored : 78.96 % 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: 1.44 (0.20), residues: 1694 helix: 1.11 (0.14), residues: 1242 sheet: None (None), residues: 0 loop : 0.85 (0.32), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 62 HIS 0.059 0.002 HIS I 52 PHE 0.046 0.002 PHE A 24 TYR 0.017 0.002 TYR L 118 ARG 0.010 0.001 ARG K 133 Details of bonding type rmsd hydrogen bonds : bond 0.04291 ( 946) hydrogen bonds : angle 4.74137 ( 2775) covalent geometry : bond 0.00430 (14166) covalent geometry : angle 0.73643 (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 275 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 214 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLU cc_start: 0.4782 (tt0) cc_final: 0.4077 (mm-30) REVERT: B 122 PHE cc_start: 0.6377 (t80) cc_final: 0.6171 (t80) REVERT: D 14 GLU cc_start: 0.4726 (OUTLIER) cc_final: 0.3616 (mp0) REVERT: D 42 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7842 (mt) REVERT: G 12 THR cc_start: 0.8996 (p) cc_final: 0.8675 (t) REVERT: G 29 ASP cc_start: 0.7871 (m-30) cc_final: 0.7661 (m-30) REVERT: E 29 ASP cc_start: 0.8170 (m-30) cc_final: 0.7920 (m-30) REVERT: E 40 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7385 (mp0) REVERT: I 8 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7697 (pt0) REVERT: H 66 MET cc_start: 0.4527 (mmt) cc_final: 0.3637 (ptp) REVERT: H 127 ARG cc_start: 0.6880 (OUTLIER) cc_final: 0.5769 (mtt180) REVERT: F 74 VAL cc_start: 0.5039 (OUTLIER) cc_final: 0.4819 (p) REVERT: F 93 MET cc_start: 0.2309 (mmt) cc_final: 0.1812 (ptp) REVERT: J 116 ILE cc_start: 0.7509 (OUTLIER) cc_final: 0.7187 (tt) REVERT: J 136 ASN cc_start: 0.5452 (p0) cc_final: 0.5244 (p0) REVERT: L 1 MET cc_start: 0.1235 (OUTLIER) cc_final: -0.0126 (ppp) outliers start: 61 outliers final: 19 residues processed: 248 average time/residue: 1.2040 time to fit residues: 330.6180 Evaluate side-chains 209 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 182 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain I residue 8 GLU Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain H residue 127 ARG Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 116 ILE Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 67 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 128 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 148 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 HIS I 47 HIS F 52 HIS L 52 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.174348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.151811 restraints weight = 23616.155| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 1.58 r_work: 0.3893 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3791 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 1.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 14166 Z= 0.269 Angle : 0.960 16.753 19399 Z= 0.484 Chirality : 0.053 0.352 2193 Planarity : 0.008 0.097 2457 Dihedral : 5.456 32.759 1862 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.19 % Favored : 96.75 % Rotamer: Outliers : 4.98 % Allowed : 16.97 % Favored : 78.05 % 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: 0.69 (0.20), residues: 1694 helix: 0.56 (0.14), residues: 1214 sheet: None (None), residues: 0 loop : 0.59 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP L 62 HIS 0.034 0.003 HIS L 52 PHE 0.032 0.003 PHE L 97 TYR 0.053 0.003 TYR J 132 ARG 0.017 0.001 ARG D 82 Details of bonding type rmsd hydrogen bonds : bond 0.05720 ( 946) hydrogen bonds : angle 5.26464 ( 2775) covalent geometry : bond 0.00590 (14166) covalent geometry : angle 0.95988 (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 357 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 281 time to evaluate : 2.195 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.2200 (OUTLIER) cc_final: 0.1776 (pp20) REVERT: A 132 TYR cc_start: 0.4627 (m-10) cc_final: 0.3089 (t80) REVERT: D 14 GLU cc_start: 0.5048 (OUTLIER) cc_final: 0.4407 (mp0) REVERT: D 40 GLU cc_start: 0.8139 (tt0) cc_final: 0.7805 (pm20) REVERT: D 117 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7952 (tm-30) REVERT: G 7 LYS cc_start: 0.8479 (ttmt) cc_final: 0.8169 (ttmt) REVERT: G 29 ASP cc_start: 0.7898 (m-30) cc_final: 0.7528 (m-30) REVERT: G 78 ASP cc_start: 0.6062 (OUTLIER) cc_final: 0.5304 (m-30) REVERT: G 117 GLU cc_start: 0.7936 (pt0) cc_final: 0.7734 (pt0) REVERT: E 29 ASP cc_start: 0.8331 (m-30) cc_final: 0.8120 (m-30) REVERT: I 66 MET cc_start: 0.5515 (OUTLIER) cc_final: 0.5254 (mmt) REVERT: K 1 MET cc_start: 0.5425 (OUTLIER) cc_final: 0.4795 (ttt) REVERT: K 83 ASP cc_start: 0.8364 (t0) cc_final: 0.7515 (m-30) REVERT: K 127 ARG cc_start: 0.6295 (tpt170) cc_final: 0.6072 (tpt-90) REVERT: H 66 MET cc_start: 0.4251 (mmt) cc_final: 0.3606 (ptp) REVERT: F 132 TYR cc_start: 0.0809 (OUTLIER) cc_final: -0.2483 (m-10) REVERT: J 93 MET cc_start: 0.3588 (OUTLIER) cc_final: 0.3024 (tpt) outliers start: 76 outliers final: 20 residues processed: 331 average time/residue: 1.6558 time to fit residues: 605.1475 Evaluate side-chains 233 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 206 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain D residue 14 GLU 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 72 VAL Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain I residue 66 MET Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain F residue 52 HIS 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 93 MET 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: 0.9980 chunk 33 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 67 optimal weight: 0.0770 chunk 163 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 60 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN H 47 HIS ** H 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.172583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.150331 restraints weight = 23560.593| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 1.66 r_work: 0.3854 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3749 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 1.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 14166 Z= 0.145 Angle : 0.692 11.719 19399 Z= 0.346 Chirality : 0.042 0.334 2193 Planarity : 0.006 0.148 2457 Dihedral : 4.671 23.810 1862 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.23 % Allowed : 23.46 % Favored : 74.31 % 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: 1.15 (0.21), residues: 1694 helix: 0.91 (0.14), residues: 1246 sheet: None (None), residues: 0 loop : 0.70 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 71 HIS 0.035 0.002 HIS F 52 PHE 0.017 0.001 PHE G 97 TYR 0.018 0.001 TYR J 118 ARG 0.019 0.001 ARG G 82 Details of bonding type rmsd hydrogen bonds : bond 0.04328 ( 946) hydrogen bonds : angle 4.83976 ( 2775) covalent geometry : bond 0.00313 (14166) covalent geometry : angle 0.69164 (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 269 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 235 time to evaluate : 4.571 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.2321 (OUTLIER) cc_final: 0.2088 (pp20) REVERT: A 132 TYR cc_start: 0.4442 (m-10) cc_final: 0.2871 (t80) REVERT: D 14 GLU cc_start: 0.4783 (OUTLIER) cc_final: 0.4371 (mp0) REVERT: D 40 GLU cc_start: 0.8144 (tt0) cc_final: 0.7906 (pm20) REVERT: D 117 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7776 (tm-30) REVERT: G 117 GLU cc_start: 0.7996 (pt0) cc_final: 0.7789 (pt0) REVERT: G 132 TYR cc_start: 0.8635 (m-80) cc_final: 0.8403 (m-80) REVERT: E 29 ASP cc_start: 0.8401 (m-30) cc_final: 0.8180 (m-30) REVERT: I 39 ARG cc_start: 0.8225 (tpp80) cc_final: 0.7767 (tpp80) REVERT: I 66 MET cc_start: 0.5759 (OUTLIER) cc_final: 0.5520 (mmt) REVERT: K 1 MET cc_start: 0.5614 (OUTLIER) cc_final: 0.5151 (ttt) REVERT: K 83 ASP cc_start: 0.8276 (t0) cc_final: 0.7533 (m-30) REVERT: K 127 ARG cc_start: 0.6116 (tpt170) cc_final: 0.5913 (tpt-90) REVERT: H 66 MET cc_start: 0.4870 (mmt) cc_final: 0.3638 (ptp) REVERT: F 9 PHE cc_start: 0.6234 (m-80) cc_final: 0.5625 (m-80) REVERT: F 68 LEU cc_start: 0.6443 (OUTLIER) cc_final: 0.6241 (tp) REVERT: J 1 MET cc_start: 0.4114 (OUTLIER) cc_final: 0.3049 (ttt) REVERT: J 4 ASP cc_start: 0.6777 (OUTLIER) cc_final: 0.6118 (t0) REVERT: J 93 MET cc_start: 0.4270 (mmm) cc_final: 0.3070 (ttt) REVERT: L 18 PHE cc_start: -0.0127 (OUTLIER) cc_final: -0.2374 (m-10) outliers start: 34 outliers final: 11 residues processed: 260 average time/residue: 1.6933 time to fit residues: 486.2161 Evaluate side-chains 221 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 202 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 16 LEU 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 66 MET Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 4 ASP Chi-restraints excluded: chain L residue 18 PHE Chi-restraints excluded: chain L residue 67 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 104 optimal weight: 8.9990 chunk 83 optimal weight: 0.0470 chunk 154 optimal weight: 0.6980 chunk 151 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 HIS J 47 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.167725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.144359 restraints weight = 22944.115| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 1.63 r_work: 0.3804 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3700 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 1.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14166 Z= 0.147 Angle : 0.680 9.319 19399 Z= 0.338 Chirality : 0.042 0.307 2193 Planarity : 0.005 0.047 2457 Dihedral : 4.334 22.507 1862 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.42 % Allowed : 23.26 % Favored : 74.31 % 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: 1.35 (0.21), residues: 1694 helix: 1.06 (0.15), residues: 1257 sheet: None (None), residues: 0 loop : 0.77 (0.32), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 71 HIS 0.004 0.001 HIS H 47 PHE 0.017 0.002 PHE G 97 TYR 0.017 0.001 TYR D 88 ARG 0.013 0.001 ARG G 82 Details of bonding type rmsd hydrogen bonds : bond 0.04013 ( 946) hydrogen bonds : angle 4.75160 ( 2775) covalent geometry : bond 0.00325 (14166) covalent geometry : angle 0.67979 (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 281 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 244 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 14 GLU cc_start: 0.7366 (pm20) cc_final: 0.7117 (pm20) REVERT: B 99 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7489 (tt0) REVERT: A 132 TYR cc_start: 0.4240 (m-10) cc_final: 0.2675 (t80) REVERT: D 14 GLU cc_start: 0.4859 (OUTLIER) cc_final: 0.4409 (mp0) REVERT: D 117 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7775 (tm-30) REVERT: G 7 LYS cc_start: 0.8465 (ttmt) cc_final: 0.7946 (tppt) REVERT: G 78 ASP cc_start: 0.5189 (OUTLIER) cc_final: 0.4761 (m-30) REVERT: G 86 VAL cc_start: 0.6577 (t) cc_final: 0.6336 (p) REVERT: G 117 GLU cc_start: 0.7977 (pt0) cc_final: 0.7746 (pt0) REVERT: E 29 ASP cc_start: 0.8315 (m-30) cc_final: 0.8090 (m-30) REVERT: I 39 ARG cc_start: 0.8329 (tpp80) cc_final: 0.7665 (ttt180) REVERT: K 1 MET cc_start: 0.5662 (OUTLIER) cc_final: 0.5410 (ttt) REVERT: K 83 ASP cc_start: 0.8293 (t0) cc_final: 0.7583 (m-30) REVERT: K 87 SER cc_start: 0.8448 (t) cc_final: 0.8210 (p) REVERT: H 27 VAL cc_start: 0.3776 (t) cc_final: 0.3388 (m) REVERT: H 66 MET cc_start: 0.4798 (mmt) cc_final: 0.3820 (ptp) REVERT: F 9 PHE cc_start: 0.6346 (m-80) cc_final: 0.6097 (m-80) REVERT: F 29 ASP cc_start: 0.6563 (m-30) cc_final: 0.6341 (m-30) REVERT: J 1 MET cc_start: 0.4526 (OUTLIER) cc_final: 0.3472 (ttt) REVERT: J 93 MET cc_start: 0.5217 (mmm) cc_final: 0.3722 (ttt) REVERT: L 9 PHE cc_start: 0.4838 (m-10) cc_final: 0.4079 (m-80) outliers start: 37 outliers final: 14 residues processed: 268 average time/residue: 1.1689 time to fit residues: 343.6985 Evaluate side-chains 224 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 205 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain L residue 40 GLU Chi-restraints excluded: chain L residue 67 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 34 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 27 optimal weight: 0.0970 chunk 75 optimal weight: 3.9990 chunk 146 optimal weight: 7.9990 chunk 123 optimal weight: 8.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 92 ASN F 104 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.159790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.135584 restraints weight = 22640.848| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 1.78 r_work: 0.3684 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3574 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 1.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14166 Z= 0.158 Angle : 0.710 13.000 19399 Z= 0.348 Chirality : 0.043 0.257 2193 Planarity : 0.005 0.044 2457 Dihedral : 4.387 22.728 1862 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.83 % Allowed : 24.44 % Favored : 73.72 % 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: 1.43 (0.21), residues: 1694 helix: 1.12 (0.15), residues: 1258 sheet: None (None), residues: 0 loop : 0.78 (0.33), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 71 HIS 0.006 0.001 HIS F 51 PHE 0.026 0.002 PHE L 103 TYR 0.022 0.002 TYR D 88 ARG 0.013 0.001 ARG B 39 Details of bonding type rmsd hydrogen bonds : bond 0.04117 ( 946) hydrogen bonds : angle 4.75931 ( 2775) covalent geometry : bond 0.00357 (14166) covalent geometry : angle 0.70996 (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 266 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 238 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.3014 (OUTLIER) cc_final: 0.1353 (pp20) REVERT: A 46 GLU cc_start: 0.7877 (mp0) cc_final: 0.7605 (mp0) REVERT: A 132 TYR cc_start: 0.4713 (m-10) cc_final: 0.3019 (t80) REVERT: C 14 GLU cc_start: 0.8231 (tt0) cc_final: 0.8027 (tt0) REVERT: D 14 GLU cc_start: 0.4666 (OUTLIER) cc_final: 0.4134 (mp0) REVERT: D 117 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7544 (tm-30) REVERT: G 7 LYS cc_start: 0.8384 (ttmt) cc_final: 0.8132 (ttmm) REVERT: G 96 LYS cc_start: 0.8856 (ptpp) cc_final: 0.8640 (ptpp) REVERT: G 117 GLU cc_start: 0.8043 (pt0) cc_final: 0.7823 (pt0) REVERT: E 29 ASP cc_start: 0.8251 (m-30) cc_final: 0.7891 (m-30) REVERT: E 40 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7487 (mp0) REVERT: I 39 ARG cc_start: 0.8435 (tpp80) cc_final: 0.7793 (ttt180) REVERT: I 66 MET cc_start: 0.6245 (mmt) cc_final: 0.5596 (mmt) REVERT: K 1 MET cc_start: 0.5906 (OUTLIER) cc_final: 0.5633 (ttt) REVERT: K 67 THR cc_start: 0.8483 (m) cc_final: 0.7910 (p) REVERT: K 83 ASP cc_start: 0.8166 (t0) cc_final: 0.7398 (m-30) REVERT: K 87 SER cc_start: 0.8439 (t) cc_final: 0.8112 (p) REVERT: H 30 LEU cc_start: 0.5223 (pp) cc_final: 0.4944 (tp) REVERT: H 66 MET cc_start: 0.4884 (mmt) cc_final: 0.3821 (ptp) REVERT: H 93 MET cc_start: 0.6756 (mpm) cc_final: 0.6358 (mmt) REVERT: F 28 ARG cc_start: 0.7721 (tpp-160) cc_final: 0.7491 (tpm170) REVERT: F 95 LEU cc_start: 0.6197 (OUTLIER) cc_final: 0.5858 (tm) REVERT: J 1 MET cc_start: 0.4708 (OUTLIER) cc_final: 0.3871 (ttt) REVERT: J 93 MET cc_start: 0.5838 (mmm) cc_final: 0.5150 (mpp) REVERT: L 9 PHE cc_start: 0.4788 (m-10) cc_final: 0.3777 (m-80) REVERT: L 18 PHE cc_start: -0.0366 (OUTLIER) cc_final: -0.2272 (m-10) REVERT: L 40 GLU cc_start: 0.6868 (tp30) cc_final: 0.6566 (pm20) REVERT: L 66 MET cc_start: 0.6262 (ppp) cc_final: 0.5733 (mmt) REVERT: L 99 GLN cc_start: 0.6242 (mt0) cc_final: 0.5776 (mm-40) outliers start: 28 outliers final: 13 residues processed: 255 average time/residue: 1.1715 time to fit residues: 327.7789 Evaluate side-chains 232 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 212 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain L residue 18 PHE Chi-restraints excluded: chain L residue 67 THR 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: 1.9990 chunk 49 optimal weight: 5.9990 chunk 139 optimal weight: 0.0000 chunk 31 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 136 optimal weight: 0.6980 chunk 121 optimal weight: 8.9990 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.158296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.134304 restraints weight = 22445.130| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 1.77 r_work: 0.3672 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3563 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 1.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14166 Z= 0.137 Angle : 0.690 12.495 19399 Z= 0.336 Chirality : 0.042 0.302 2193 Planarity : 0.005 0.050 2457 Dihedral : 4.277 23.939 1862 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.18 % Allowed : 26.34 % Favored : 72.48 % 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: 1.55 (0.21), residues: 1694 helix: 1.20 (0.15), residues: 1257 sheet: None (None), residues: 0 loop : 0.86 (0.32), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 71 HIS 0.005 0.001 HIS F 51 PHE 0.015 0.001 PHE L 97 TYR 0.016 0.001 TYR D 88 ARG 0.008 0.001 ARG K 28 Details of bonding type rmsd hydrogen bonds : bond 0.03891 ( 946) hydrogen bonds : angle 4.67508 ( 2775) covalent geometry : bond 0.00313 (14166) covalent geometry : angle 0.69040 (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: 18 poor density : 243 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 96 LYS cc_start: 0.8166 (mttp) cc_final: 0.7672 (tppt) REVERT: A 46 GLU cc_start: 0.7919 (mp0) cc_final: 0.7585 (mp0) REVERT: A 132 TYR cc_start: 0.4827 (m-10) cc_final: 0.3032 (t80) REVERT: C 14 GLU cc_start: 0.8280 (tt0) cc_final: 0.8061 (tt0) REVERT: C 60 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8206 (mt) REVERT: C 124 VAL cc_start: 0.8900 (t) cc_final: 0.8653 (t) REVERT: D 14 GLU cc_start: 0.4620 (OUTLIER) cc_final: 0.4189 (mp0) REVERT: D 28 ARG cc_start: 0.7542 (tpm170) cc_final: 0.7266 (tpm170) REVERT: D 117 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7473 (tm-30) REVERT: G 7 LYS cc_start: 0.8370 (ttmt) cc_final: 0.8105 (ttmm) REVERT: G 39 ARG cc_start: 0.8196 (ttm-80) cc_final: 0.7899 (ttp80) REVERT: G 117 GLU cc_start: 0.8025 (pt0) cc_final: 0.7802 (pt0) REVERT: E 29 ASP cc_start: 0.8255 (m-30) cc_final: 0.8031 (m-30) REVERT: I 39 ARG cc_start: 0.8449 (tpp80) cc_final: 0.7833 (ttt180) REVERT: I 66 MET cc_start: 0.6222 (mmt) cc_final: 0.5523 (mmt) REVERT: K 83 ASP cc_start: 0.8130 (t0) cc_final: 0.7404 (m-30) REVERT: K 87 SER cc_start: 0.8354 (t) cc_final: 0.8079 (p) REVERT: K 96 LYS cc_start: 0.7370 (pttt) cc_final: 0.7077 (ptpp) REVERT: H 30 LEU cc_start: 0.5283 (pp) cc_final: 0.4644 (mt) REVERT: H 66 MET cc_start: 0.5032 (mmt) cc_final: 0.3962 (ptp) REVERT: F 7 LYS cc_start: 0.5673 (pttt) cc_final: 0.5042 (tppt) REVERT: F 28 ARG cc_start: 0.7782 (tpp-160) cc_final: 0.7456 (tpp-160) REVERT: J 1 MET cc_start: 0.4812 (OUTLIER) cc_final: 0.4022 (ttt) REVERT: J 93 MET cc_start: 0.5925 (mmm) cc_final: 0.5289 (mpp) REVERT: L 9 PHE cc_start: 0.5082 (m-10) cc_final: 0.4052 (m-80) REVERT: L 18 PHE cc_start: -0.0480 (OUTLIER) cc_final: -0.2328 (m-10) REVERT: L 39 ARG cc_start: 0.7905 (tpp80) cc_final: 0.7532 (tmm-80) REVERT: L 40 GLU cc_start: 0.7114 (tp30) cc_final: 0.6813 (pm20) REVERT: L 66 MET cc_start: 0.6423 (ppp) cc_final: 0.6202 (mmp) REVERT: L 99 GLN cc_start: 0.6382 (mt0) cc_final: 0.5896 (mt0) outliers start: 18 outliers final: 8 residues processed: 253 average time/residue: 1.2911 time to fit residues: 356.7011 Evaluate side-chains 225 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 213 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain L residue 18 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 19 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 136 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 157 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 51 HIS F 99 GLN ** L 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.155583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.131920 restraints weight = 22720.154| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 1.76 r_work: 0.3643 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3534 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 1.5226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14166 Z= 0.139 Angle : 0.691 10.825 19399 Z= 0.339 Chirality : 0.042 0.271 2193 Planarity : 0.005 0.053 2457 Dihedral : 4.207 22.108 1862 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.44 % Allowed : 26.93 % 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: 1.65 (0.21), residues: 1694 helix: 1.26 (0.15), residues: 1253 sheet: None (None), residues: 0 loop : 0.91 (0.33), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 71 HIS 0.006 0.001 HIS F 51 PHE 0.033 0.002 PHE J 97 TYR 0.015 0.001 TYR D 88 ARG 0.009 0.001 ARG C 39 Details of bonding type rmsd hydrogen bonds : bond 0.03795 ( 946) hydrogen bonds : angle 4.67179 ( 2775) covalent geometry : bond 0.00317 (14166) covalent geometry : angle 0.69089 (19399) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11613.59 seconds wall clock time: 210 minutes 8.60 seconds (12608.60 seconds total)