Starting phenix.real_space_refine on Sun Apr 5 07:23:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m72_63667/04_2026/9m72_63667.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m72_63667/04_2026/9m72_63667.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9m72_63667/04_2026/9m72_63667.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m72_63667/04_2026/9m72_63667.map" model { file = "/net/cci-nas-00/data/ceres_data/9m72_63667/04_2026/9m72_63667.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m72_63667/04_2026/9m72_63667.cif" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.113 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 39 5.16 5 C 5562 2.51 5 N 1464 2.21 5 O 1707 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8772 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1184 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 12, 'TRANS': 136} Chain: "A" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 913 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "B" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 827 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain: "H" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1184 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 12, 'TRANS': 136} Chain: "D" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 913 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "F" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 827 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain: "I" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1184 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 12, 'TRANS': 136} Chain: "E" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 913 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "G" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 827 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 3, 'TRANS': 103} Time building chain proxies: 1.72, per 1000 atoms: 0.20 Number of scatterers: 8772 At special positions: 0 Unit cell: (130.54, 138.03, 77.04, 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 39 16.00 O 1707 8.00 N 1464 7.00 C 5562 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 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: 0.60 Conformation dependent library (CDL) restraints added in 334.4 milliseconds 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2076 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 21 sheets defined 14.9% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'C' and resid 10 through 19 removed outlier: 3.717A pdb=" N TRP C 14 " --> pdb=" O LYS C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 29 removed outlier: 3.545A pdb=" N LEU C 23 " --> pdb=" O ASP C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 36 Processing helix chain 'C' and resid 51 through 63 removed outlier: 3.964A pdb=" N ARG C 55 " --> pdb=" O GLN C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 77 Processing helix chain 'C' and resid 85 through 89 Processing helix chain 'H' and resid 10 through 19 removed outlier: 3.754A pdb=" N TRP H 14 " --> pdb=" O LYS H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 29 removed outlier: 3.534A pdb=" N LEU H 23 " --> pdb=" O ASP H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 36 Processing helix chain 'H' and resid 51 through 63 removed outlier: 3.937A pdb=" N ARG H 55 " --> pdb=" O GLN H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 77 Processing helix chain 'H' and resid 85 through 89 Processing helix chain 'I' and resid 10 through 19 removed outlier: 3.722A pdb=" N TRP I 14 " --> pdb=" O LYS I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 29 removed outlier: 3.553A pdb=" N LEU I 23 " --> pdb=" O ASP I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 31 through 36 Processing helix chain 'I' and resid 51 through 63 removed outlier: 3.939A pdb=" N ARG I 55 " --> pdb=" O GLN I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 77 Processing helix chain 'I' and resid 85 through 89 Processing sheet with id=AA1, first strand: chain 'C' and resid 78 through 79 removed outlier: 6.400A pdb=" N VAL C 44 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N TRP C 137 " --> pdb=" O VAL C 44 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N PHE C 46 " --> pdb=" O TRP C 137 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N MET C 139 " --> pdb=" O PHE C 46 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N TYR C 48 " --> pdb=" O MET C 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 103 through 106 removed outlier: 7.332A pdb=" N ILE C 112 " --> pdb=" O GLU C 104 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 9 through 12 removed outlier: 3.769A pdb=" N VAL A 10 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A 117 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY A 49 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LYS A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N TRP A 47 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN A 59 " --> pdb=" O GLU A 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 19 through 23 Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.520A pdb=" N GLU B 105 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 19 through 24 removed outlier: 3.811A pdb=" N VAL B 19 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE B 75 " --> pdb=" O VAL B 19 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 44 through 48 removed outlier: 6.539A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR B 36 " --> pdb=" O PHE B 87 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 78 through 79 removed outlier: 6.379A pdb=" N VAL H 44 " --> pdb=" O ALA H 135 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N TRP H 137 " --> pdb=" O VAL H 44 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N PHE H 46 " --> pdb=" O TRP H 137 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N MET H 139 " --> pdb=" O PHE H 46 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N TYR H 48 " --> pdb=" O MET H 139 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 103 through 106 removed outlier: 7.349A pdb=" N ILE H 112 " --> pdb=" O GLU H 104 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 9 through 12 removed outlier: 3.780A pdb=" N VAL D 10 " --> pdb=" O SER D 115 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR D 117 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LYS D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N TRP D 47 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN D 59 " --> pdb=" O GLU D 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 19 through 23 Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 13 Processing sheet with id=AB4, first strand: chain 'F' and resid 19 through 24 removed outlier: 3.814A pdb=" N VAL F 19 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE F 75 " --> pdb=" O VAL F 19 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 44 through 48 removed outlier: 6.547A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR F 36 " --> pdb=" O PHE F 87 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE F 87 " --> pdb=" O TYR F 36 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 78 through 79 removed outlier: 6.434A pdb=" N VAL I 44 " --> pdb=" O ALA I 135 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N TRP I 137 " --> pdb=" O VAL I 44 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N PHE I 46 " --> pdb=" O TRP I 137 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N MET I 139 " --> pdb=" O PHE I 46 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TYR I 48 " --> pdb=" O MET I 139 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 103 through 106 removed outlier: 7.326A pdb=" N ILE I 112 " --> pdb=" O GLU I 104 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 9 through 12 removed outlier: 3.728A pdb=" N VAL E 10 " --> pdb=" O SER E 115 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR E 117 " --> pdb=" O VAL E 10 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LYS E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N TRP E 47 " --> pdb=" O LYS E 38 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN E 59 " --> pdb=" O GLU E 50 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 19 through 23 Processing sheet with id=AC1, first strand: chain 'G' and resid 10 through 13 Processing sheet with id=AC2, first strand: chain 'G' and resid 19 through 24 removed outlier: 3.834A pdb=" N VAL G 19 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE G 75 " --> pdb=" O VAL G 19 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP G 70 " --> pdb=" O SER G 67 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 44 through 48 removed outlier: 6.550A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) 233 hydrogen bonds defined for protein. 627 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: 1.05 Time building geometry restraints manager: 0.80 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: 2787 1.34 - 1.46: 2126 1.46 - 1.58: 4009 1.58 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 8982 Sorted by residual: bond pdb=" CA PHE H 89 " pdb=" CB PHE H 89 " ideal model delta sigma weight residual 1.522 1.533 -0.011 1.32e-02 5.74e+03 6.39e-01 bond pdb=" CA PHE C 89 " pdb=" CB PHE C 89 " ideal model delta sigma weight residual 1.522 1.533 -0.011 1.32e-02 5.74e+03 6.37e-01 bond pdb=" CA PHE I 89 " pdb=" CB PHE I 89 " ideal model delta sigma weight residual 1.522 1.532 -0.010 1.32e-02 5.74e+03 5.90e-01 bond pdb=" CA VAL F 58 " pdb=" CB VAL F 58 " ideal model delta sigma weight residual 1.526 1.537 -0.011 1.55e-02 4.16e+03 5.09e-01 bond pdb=" CA VAL G 58 " pdb=" CB VAL G 58 " ideal model delta sigma weight residual 1.526 1.537 -0.011 1.55e-02 4.16e+03 5.07e-01 ... (remaining 8977 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.93: 11684 0.93 - 1.86: 363 1.86 - 2.79: 95 2.79 - 3.72: 30 3.72 - 4.65: 8 Bond angle restraints: 12180 Sorted by residual: angle pdb=" CA GLN H 16 " pdb=" CB GLN H 16 " pdb=" CG GLN H 16 " ideal model delta sigma weight residual 114.10 117.93 -3.83 2.00e+00 2.50e-01 3.66e+00 angle pdb=" N ASP E 108 " pdb=" CA ASP E 108 " pdb=" C ASP E 108 " ideal model delta sigma weight residual 107.67 111.50 -3.83 2.09e+00 2.29e-01 3.36e+00 angle pdb=" CB GLN H 16 " pdb=" CG GLN H 16 " pdb=" CD GLN H 16 " ideal model delta sigma weight residual 112.60 115.70 -3.10 1.70e+00 3.46e-01 3.32e+00 angle pdb=" CA PHE H 89 " pdb=" C PHE H 89 " pdb=" N THR H 90 " ideal model delta sigma weight residual 114.76 116.79 -2.03 1.14e+00 7.69e-01 3.16e+00 angle pdb=" CA GLY H 142 " pdb=" C GLY H 142 " pdb=" N SER H 143 " ideal model delta sigma weight residual 114.85 116.53 -1.68 9.50e-01 1.11e+00 3.14e+00 ... (remaining 12175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 4872 17.87 - 35.74: 386 35.74 - 53.61: 76 53.61 - 71.49: 9 71.49 - 89.36: 12 Dihedral angle restraints: 5355 sinusoidal: 2100 harmonic: 3255 Sorted by residual: dihedral pdb=" CB CYS G 23 " pdb=" SG CYS G 23 " pdb=" SG CYS G 88 " pdb=" CB CYS G 88 " ideal model delta sinusoidal sigma weight residual 93.00 168.23 -75.23 1 1.00e+01 1.00e-02 7.15e+01 dihedral pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " pdb=" SG CYS F 88 " pdb=" CB CYS F 88 " ideal model delta sinusoidal sigma weight residual 93.00 167.20 -74.20 1 1.00e+01 1.00e-02 6.99e+01 dihedral pdb=" CB CYS B 23 " pdb=" SG CYS B 23 " pdb=" SG CYS B 88 " pdb=" CB CYS B 88 " ideal model delta sinusoidal sigma weight residual 93.00 165.99 -72.99 1 1.00e+01 1.00e-02 6.79e+01 ... (remaining 5352 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 752 0.025 - 0.049: 350 0.049 - 0.073: 114 0.073 - 0.098: 48 0.098 - 0.122: 71 Chirality restraints: 1335 Sorted by residual: chirality pdb=" CA PRO G 40 " pdb=" N PRO G 40 " pdb=" C PRO G 40 " pdb=" CB PRO G 40 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CB ILE B 75 " pdb=" CA ILE B 75 " pdb=" CG1 ILE B 75 " pdb=" CG2 ILE B 75 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.12 2.00e-01 2.50e+01 3.66e-01 chirality pdb=" CA PRO F 40 " pdb=" N PRO F 40 " pdb=" C PRO F 40 " pdb=" CB PRO F 40 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.55e-01 ... (remaining 1332 not shown) Planarity restraints: 1551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 83 " -0.035 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO C 84 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 84 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 84 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE I 83 " 0.025 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO I 84 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO I 84 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO I 84 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 119 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.87e+00 pdb=" C VAL H 119 " -0.024 2.00e-02 2.50e+03 pdb=" O VAL H 119 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU H 120 " 0.008 2.00e-02 2.50e+03 ... (remaining 1548 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 521 2.73 - 3.28: 7957 3.28 - 3.82: 12852 3.82 - 4.36: 14955 4.36 - 4.90: 27446 Nonbonded interactions: 63731 Sorted by model distance: nonbonded pdb=" OH TYR F 36 " pdb=" OE1 GLN F 89 " model vdw 2.193 3.040 nonbonded pdb=" OH TYR B 36 " pdb=" OE1 GLN B 89 " model vdw 2.230 3.040 nonbonded pdb=" OH TYR G 36 " pdb=" OE1 GLN G 89 " model vdw 2.249 3.040 nonbonded pdb=" OG SER A 55 " pdb=" OD1 ASN A 57 " model vdw 2.269 3.040 nonbonded pdb=" OG SER E 55 " pdb=" OD1 ASN E 57 " model vdw 2.273 3.040 ... (remaining 63726 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.060 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 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 : 0.002 0.021 8988 Z= 0.092 Angle : 0.450 4.647 12192 Z= 0.246 Chirality : 0.040 0.122 1335 Planarity : 0.003 0.054 1551 Dihedral : 13.858 89.357 3261 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.31 % Allowed : 0.00 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.26), residues: 1110 helix: 1.34 (0.47), residues: 147 sheet: -1.12 (0.28), residues: 372 loop : -1.61 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 132 TYR 0.010 0.001 TYR H 63 PHE 0.008 0.001 PHE H 89 TRP 0.007 0.001 TRP C 137 HIS 0.002 0.000 HIS F 55 Details of bonding type rmsd covalent geometry : bond 0.00198 ( 8982) covalent geometry : angle 0.45042 (12180) SS BOND : bond 0.00159 ( 6) SS BOND : angle 0.39260 ( 12) hydrogen bonds : bond 0.27143 ( 233) hydrogen bonds : angle 9.15977 ( 627) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 115 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: C 16 GLN cc_start: 0.8001 (tm-30) cc_final: 0.7591 (tm-30) REVERT: I 16 GLN cc_start: 0.8038 (tm-30) cc_final: 0.7707 (tm-30) outliers start: 3 outliers final: 0 residues processed: 115 average time/residue: 0.0942 time to fit residues: 14.9578 Evaluate side-chains 101 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.0570 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** 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 = 0.3902 r_free = 0.3902 target = 0.165485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.144397 restraints weight = 11009.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.144868 restraints weight = 10291.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.145089 restraints weight = 9899.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.145555 restraints weight = 9669.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.145705 restraints weight = 9234.536| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8988 Z= 0.128 Angle : 0.494 4.476 12192 Z= 0.265 Chirality : 0.042 0.141 1335 Planarity : 0.003 0.040 1551 Dihedral : 3.814 19.565 1212 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.62 % Allowed : 6.50 % Favored : 92.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.25), residues: 1110 helix: 1.03 (0.45), residues: 153 sheet: -1.31 (0.26), residues: 393 loop : -1.54 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 132 TYR 0.014 0.001 TYR G 50 PHE 0.006 0.001 PHE G 62 TRP 0.008 0.001 TRP A 47 HIS 0.005 0.001 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 8982) covalent geometry : angle 0.49444 (12180) SS BOND : bond 0.00357 ( 6) SS BOND : angle 0.47399 ( 12) hydrogen bonds : bond 0.04467 ( 233) hydrogen bonds : angle 6.59270 ( 627) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 123 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: C 16 GLN cc_start: 0.7964 (tm-30) cc_final: 0.7635 (tm-30) REVERT: H 16 GLN cc_start: 0.8206 (tm-30) cc_final: 0.7927 (tm-30) REVERT: I 16 GLN cc_start: 0.8107 (tm-30) cc_final: 0.7840 (tm-30) outliers start: 6 outliers final: 3 residues processed: 127 average time/residue: 0.0904 time to fit residues: 16.1206 Evaluate side-chains 116 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 113 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain H residue 95 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 55 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 49 optimal weight: 0.2980 chunk 77 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN H 65 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** 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 = 0.3889 r_free = 0.3889 target = 0.164396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.143247 restraints weight = 11007.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.144184 restraints weight = 10148.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.144187 restraints weight = 9843.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.144802 restraints weight = 9656.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.144844 restraints weight = 9126.285| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 8988 Z= 0.120 Angle : 0.497 8.501 12192 Z= 0.261 Chirality : 0.042 0.133 1335 Planarity : 0.003 0.029 1551 Dihedral : 3.841 20.419 1212 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 1.24 % Allowed : 9.29 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.25), residues: 1110 helix: 1.03 (0.45), residues: 153 sheet: -1.12 (0.26), residues: 393 loop : -1.52 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 132 TYR 0.016 0.001 TYR F 50 PHE 0.005 0.001 PHE G 62 TRP 0.006 0.001 TRP H 137 HIS 0.004 0.001 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8982) covalent geometry : angle 0.49717 (12180) SS BOND : bond 0.00230 ( 6) SS BOND : angle 0.36438 ( 12) hydrogen bonds : bond 0.03840 ( 233) hydrogen bonds : angle 5.77994 ( 627) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: C 16 GLN cc_start: 0.7997 (tm-30) cc_final: 0.7642 (tm-30) REVERT: H 16 GLN cc_start: 0.8211 (tm-30) cc_final: 0.7890 (tm-30) REVERT: I 16 GLN cc_start: 0.8157 (tm-30) cc_final: 0.7834 (tm-30) outliers start: 12 outliers final: 12 residues processed: 114 average time/residue: 0.0842 time to fit residues: 13.4695 Evaluate side-chains 119 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain G residue 19 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 32 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 42 optimal weight: 0.0170 chunk 48 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 4 optimal weight: 0.0770 chunk 13 optimal weight: 0.0980 chunk 2 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** 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 = 0.3620 r_free = 0.3620 target = 0.144988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.121741 restraints weight = 11712.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.119697 restraints weight = 12849.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.120178 restraints weight = 13414.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.120399 restraints weight = 12961.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.120510 restraints weight = 12230.339| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8988 Z= 0.087 Angle : 0.461 7.061 12192 Z= 0.240 Chirality : 0.041 0.130 1335 Planarity : 0.003 0.025 1551 Dihedral : 3.692 19.388 1212 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.83 % Allowed : 10.32 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.25), residues: 1110 helix: 1.19 (0.45), residues: 153 sheet: -0.65 (0.27), residues: 381 loop : -1.54 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 132 TYR 0.010 0.001 TYR C 63 PHE 0.005 0.001 PHE F 83 TRP 0.006 0.001 TRP H 137 HIS 0.003 0.001 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 8982) covalent geometry : angle 0.46068 (12180) SS BOND : bond 0.00249 ( 6) SS BOND : angle 0.41979 ( 12) hydrogen bonds : bond 0.02919 ( 233) hydrogen bonds : angle 5.17783 ( 627) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: C 16 GLN cc_start: 0.7960 (tm-30) cc_final: 0.7615 (tm-30) REVERT: H 16 GLN cc_start: 0.8168 (tm-30) cc_final: 0.7840 (tm-30) REVERT: I 16 GLN cc_start: 0.8105 (tm-30) cc_final: 0.7813 (tm-30) REVERT: I 27 ASN cc_start: 0.8862 (t0) cc_final: 0.8640 (t0) outliers start: 8 outliers final: 7 residues processed: 118 average time/residue: 0.0936 time to fit residues: 15.1624 Evaluate side-chains 116 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 109 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain I residue 95 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 64 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.136521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.112153 restraints weight = 11779.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.110947 restraints weight = 14066.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.111180 restraints weight = 15107.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.111519 restraints weight = 14110.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.111622 restraints weight = 13680.420| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 8988 Z= 0.161 Angle : 0.522 5.024 12192 Z= 0.277 Chirality : 0.043 0.126 1335 Planarity : 0.003 0.025 1551 Dihedral : 3.938 21.386 1212 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 1.65 % Allowed : 10.01 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.25), residues: 1110 helix: 0.99 (0.45), residues: 153 sheet: -0.79 (0.27), residues: 393 loop : -1.63 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 132 TYR 0.022 0.002 TYR F 50 PHE 0.008 0.001 PHE D 64 TRP 0.009 0.002 TRP E 33 HIS 0.005 0.001 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 8982) covalent geometry : angle 0.52245 (12180) SS BOND : bond 0.00213 ( 6) SS BOND : angle 0.38043 ( 12) hydrogen bonds : bond 0.03786 ( 233) hydrogen bonds : angle 5.10638 ( 627) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: C 16 GLN cc_start: 0.8041 (tm-30) cc_final: 0.7668 (tm-30) REVERT: C 119 VAL cc_start: 0.8318 (t) cc_final: 0.8086 (t) REVERT: H 16 GLN cc_start: 0.8315 (tm-30) cc_final: 0.7965 (tm-30) REVERT: D 107 MET cc_start: 0.8983 (ptp) cc_final: 0.8654 (ptp) REVERT: I 16 GLN cc_start: 0.8223 (tm-30) cc_final: 0.7890 (tm-30) REVERT: E 107 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8648 (mtp) outliers start: 16 outliers final: 15 residues processed: 122 average time/residue: 0.0994 time to fit residues: 16.6338 Evaluate side-chains 130 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain G residue 19 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** 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 = 0.3628 r_free = 0.3628 target = 0.144292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.121543 restraints weight = 11534.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.119557 restraints weight = 10966.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.119549 restraints weight = 11804.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.119702 restraints weight = 11949.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.119855 restraints weight = 11240.826| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8988 Z= 0.125 Angle : 0.500 6.644 12192 Z= 0.263 Chirality : 0.042 0.124 1335 Planarity : 0.003 0.025 1551 Dihedral : 3.923 21.229 1212 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 1.75 % Allowed : 11.04 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.25), residues: 1110 helix: 1.03 (0.45), residues: 153 sheet: -0.68 (0.27), residues: 393 loop : -1.59 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 132 TYR 0.017 0.001 TYR B 50 PHE 0.006 0.001 PHE G 87 TRP 0.007 0.001 TRP H 137 HIS 0.003 0.001 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 8982) covalent geometry : angle 0.49895 (12180) SS BOND : bond 0.00313 ( 6) SS BOND : angle 1.03077 ( 12) hydrogen bonds : bond 0.03207 ( 233) hydrogen bonds : angle 4.93727 ( 627) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: C 16 GLN cc_start: 0.8004 (tm-30) cc_final: 0.7587 (tm-30) REVERT: H 16 GLN cc_start: 0.8298 (tm-30) cc_final: 0.7941 (tm-30) REVERT: D 107 MET cc_start: 0.8997 (ptp) cc_final: 0.8680 (ptp) REVERT: I 16 GLN cc_start: 0.8200 (tm-30) cc_final: 0.7882 (tm-30) outliers start: 17 outliers final: 14 residues processed: 118 average time/residue: 0.0884 time to fit residues: 14.4232 Evaluate side-chains 126 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain G residue 43 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 56 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 103 optimal weight: 0.0370 chunk 62 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** 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 = 0.3554 r_free = 0.3554 target = 0.140242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.117266 restraints weight = 11702.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.117266 restraints weight = 11816.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.117266 restraints weight = 11816.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.117266 restraints weight = 11816.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.117266 restraints weight = 11816.582| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8988 Z= 0.114 Angle : 0.490 6.491 12192 Z= 0.256 Chirality : 0.042 0.128 1335 Planarity : 0.003 0.025 1551 Dihedral : 3.858 20.455 1212 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 1.96 % Allowed : 11.04 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.25), residues: 1110 helix: 1.12 (0.45), residues: 153 sheet: -0.60 (0.27), residues: 393 loop : -1.57 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 132 TYR 0.016 0.001 TYR B 50 PHE 0.005 0.001 PHE G 62 TRP 0.007 0.001 TRP H 137 HIS 0.003 0.001 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 8982) covalent geometry : angle 0.48946 (12180) SS BOND : bond 0.00275 ( 6) SS BOND : angle 0.78039 ( 12) hydrogen bonds : bond 0.03026 ( 233) hydrogen bonds : angle 4.74579 ( 627) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: C 16 GLN cc_start: 0.7985 (tm-30) cc_final: 0.7593 (tm-30) REVERT: H 16 GLN cc_start: 0.8265 (tm-30) cc_final: 0.7912 (tm-30) REVERT: D 107 MET cc_start: 0.8961 (ptp) cc_final: 0.8674 (ptp) REVERT: I 16 GLN cc_start: 0.8173 (tm-30) cc_final: 0.7860 (tm-30) REVERT: G 31 ASN cc_start: 0.8516 (t0) cc_final: 0.8223 (t0) outliers start: 19 outliers final: 18 residues processed: 120 average time/residue: 0.0845 time to fit residues: 14.3148 Evaluate side-chains 131 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 43 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 2 optimal weight: 0.7980 chunk 103 optimal weight: 0.0370 chunk 51 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 33 optimal weight: 0.2980 chunk 105 optimal weight: 0.0000 chunk 89 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 6 optimal weight: 0.0040 chunk 13 optimal weight: 0.0670 overall best weight: 0.0812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 HIS I 65 ASN ** E 6 GLN ** 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 = 0.3928 r_free = 0.3928 target = 0.168063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.147139 restraints weight = 10920.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.148274 restraints weight = 9670.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.148811 restraints weight = 8821.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.149591 restraints weight = 8345.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.149591 restraints weight = 7898.030| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8988 Z= 0.079 Angle : 0.451 4.909 12192 Z= 0.234 Chirality : 0.040 0.135 1335 Planarity : 0.003 0.025 1551 Dihedral : 3.588 18.528 1212 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.83 % Allowed : 12.69 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.26), residues: 1110 helix: 1.44 (0.46), residues: 153 sheet: -0.12 (0.28), residues: 381 loop : -1.46 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 132 TYR 0.010 0.001 TYR C 63 PHE 0.005 0.001 PHE F 83 TRP 0.010 0.001 TRP E 36 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00187 ( 8982) covalent geometry : angle 0.45084 (12180) SS BOND : bond 0.00232 ( 6) SS BOND : angle 0.54504 ( 12) hydrogen bonds : bond 0.02202 ( 233) hydrogen bonds : angle 4.38302 ( 627) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: C 16 GLN cc_start: 0.7928 (tm-30) cc_final: 0.7574 (tm-30) REVERT: C 119 VAL cc_start: 0.8254 (OUTLIER) cc_final: 0.7993 (t) REVERT: B 4 MET cc_start: 0.7939 (ttm) cc_final: 0.7645 (ttm) REVERT: B 31 ASN cc_start: 0.8497 (t0) cc_final: 0.8185 (t0) REVERT: H 16 GLN cc_start: 0.8124 (tm-30) cc_final: 0.7759 (tm-30) REVERT: H 133 ARG cc_start: 0.8748 (mtp85) cc_final: 0.8362 (ptp-110) REVERT: D 107 MET cc_start: 0.8847 (ptp) cc_final: 0.8633 (ptp) REVERT: I 16 GLN cc_start: 0.8063 (tm-30) cc_final: 0.7774 (tm-30) REVERT: G 31 ASN cc_start: 0.8545 (t0) cc_final: 0.8293 (t0) outliers start: 8 outliers final: 7 residues processed: 121 average time/residue: 0.0927 time to fit residues: 15.4813 Evaluate side-chains 121 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain G residue 43 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 61 optimal weight: 0.0970 chunk 22 optimal weight: 0.3980 chunk 39 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 88 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** 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 = 0.3846 r_free = 0.3846 target = 0.161089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.138947 restraints weight = 11084.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.139539 restraints weight = 10197.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.140329 restraints weight = 9634.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.141030 restraints weight = 9121.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.141060 restraints weight = 8836.514| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8988 Z= 0.097 Angle : 0.470 6.697 12192 Z= 0.243 Chirality : 0.041 0.127 1335 Planarity : 0.003 0.026 1551 Dihedral : 3.571 18.219 1212 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.93 % Allowed : 12.69 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.26), residues: 1110 helix: 1.54 (0.46), residues: 153 sheet: -0.10 (0.28), residues: 381 loop : -1.50 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 132 TYR 0.024 0.001 TYR G 49 PHE 0.004 0.001 PHE G 62 TRP 0.005 0.001 TRP A 36 HIS 0.004 0.001 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 8982) covalent geometry : angle 0.46970 (12180) SS BOND : bond 0.00225 ( 6) SS BOND : angle 0.54107 ( 12) hydrogen bonds : bond 0.02573 ( 233) hydrogen bonds : angle 4.28226 ( 627) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 16 GLN cc_start: 0.7969 (tm-30) cc_final: 0.7605 (tm-30) REVERT: C 119 VAL cc_start: 0.8280 (t) cc_final: 0.8037 (t) REVERT: B 4 MET cc_start: 0.7915 (ttm) cc_final: 0.7652 (ttm) REVERT: H 16 GLN cc_start: 0.8176 (tm-30) cc_final: 0.7821 (tm-30) REVERT: D 107 MET cc_start: 0.8924 (ptp) cc_final: 0.8681 (ptp) REVERT: I 16 GLN cc_start: 0.8123 (tm-30) cc_final: 0.7829 (tm-30) REVERT: G 31 ASN cc_start: 0.8586 (t0) cc_final: 0.8332 (t0) outliers start: 9 outliers final: 9 residues processed: 115 average time/residue: 0.0962 time to fit residues: 15.2228 Evaluate side-chains 121 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain G residue 43 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 57 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 75 optimal weight: 0.1980 chunk 97 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** 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 = 0.3718 r_free = 0.3718 target = 0.150713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.127353 restraints weight = 11282.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.126545 restraints weight = 14129.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.127220 restraints weight = 15033.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.127545 restraints weight = 12599.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.128361 restraints weight = 11553.639| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8988 Z= 0.128 Angle : 0.495 6.933 12192 Z= 0.259 Chirality : 0.042 0.133 1335 Planarity : 0.003 0.026 1551 Dihedral : 3.718 18.696 1212 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 1.14 % Allowed : 12.49 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.26), residues: 1110 helix: 1.42 (0.46), residues: 153 sheet: -0.36 (0.28), residues: 393 loop : -1.50 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 132 TYR 0.037 0.002 TYR G 49 PHE 0.005 0.001 PHE D 64 TRP 0.006 0.001 TRP H 137 HIS 0.003 0.001 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8982) covalent geometry : angle 0.49529 (12180) SS BOND : bond 0.00244 ( 6) SS BOND : angle 0.61148 ( 12) hydrogen bonds : bond 0.02983 ( 233) hydrogen bonds : angle 4.39188 ( 627) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 16 GLN cc_start: 0.7969 (tm-30) cc_final: 0.7613 (tm-30) REVERT: C 119 VAL cc_start: 0.8270 (OUTLIER) cc_final: 0.8024 (t) REVERT: B 4 MET cc_start: 0.7939 (ttm) cc_final: 0.7661 (ttm) REVERT: H 16 GLN cc_start: 0.8246 (tm-30) cc_final: 0.7891 (tm-30) REVERT: D 107 MET cc_start: 0.8907 (ptp) cc_final: 0.8638 (ptp) REVERT: I 16 GLN cc_start: 0.8194 (tm-30) cc_final: 0.7873 (tm-30) REVERT: G 31 ASN cc_start: 0.8552 (t0) cc_final: 0.8160 (t0) outliers start: 11 outliers final: 10 residues processed: 119 average time/residue: 0.0877 time to fit residues: 14.5798 Evaluate side-chains 122 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain G residue 43 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 23 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** 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 = 0.3586 r_free = 0.3586 target = 0.141864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.120754 restraints weight = 11449.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.119227 restraints weight = 15314.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.119473 restraints weight = 17214.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.119689 restraints weight = 14602.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.119702 restraints weight = 13668.516| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8988 Z= 0.138 Angle : 0.516 6.907 12192 Z= 0.270 Chirality : 0.042 0.132 1335 Planarity : 0.003 0.026 1551 Dihedral : 3.835 19.030 1212 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.03 % Favored : 92.88 % Rotamer: Outliers : 1.55 % Allowed : 12.59 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.26), residues: 1110 helix: 1.25 (0.45), residues: 153 sheet: -0.42 (0.28), residues: 393 loop : -1.57 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 132 TYR 0.031 0.002 TYR G 49 PHE 0.005 0.001 PHE D 64 TRP 0.006 0.001 TRP H 137 HIS 0.003 0.001 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 8982) covalent geometry : angle 0.51599 (12180) SS BOND : bond 0.00249 ( 6) SS BOND : angle 0.67818 ( 12) hydrogen bonds : bond 0.03138 ( 233) hydrogen bonds : angle 4.50196 ( 627) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1301.98 seconds wall clock time: 23 minutes 18.85 seconds (1398.85 seconds total)