Starting phenix.real_space_refine on Fri Mar 14 04:51:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v1i_21012/03_2025/6v1i_21012_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v1i_21012/03_2025/6v1i_21012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6v1i_21012/03_2025/6v1i_21012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v1i_21012/03_2025/6v1i_21012.map" model { file = "/net/cci-nas-00/data/ceres_data/6v1i_21012/03_2025/6v1i_21012_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v1i_21012/03_2025/6v1i_21012_neut.cif" } resolution = 3.8 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= 0.001 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 54 5.16 5 C 6129 2.51 5 N 1701 2.21 5 O 1827 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9711 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1079 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 5, 'TRANS': 131} Restraints were copied for chains: C, B, E, D, G, F, I, H Time building chain proxies: 3.21, per 1000 atoms: 0.33 Number of scatterers: 9711 At special positions: 0 Unit cell: (133.434, 131.316, 67.776, 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 54 16.00 O 1827 8.00 N 1701 7.00 C 6129 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: 2.22 Conformation dependent library (CDL) restraints added in 1.1 seconds 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2376 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 0 sheets defined 79.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 5 through 15 Processing helix chain 'A' and resid 18 through 28 removed outlier: 3.840A pdb=" N LEU A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 51 removed outlier: 3.715A pdb=" N VAL A 42 " --> pdb=" O GLU A 38 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 49 " --> pdb=" O GLU A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 94 removed outlier: 3.859A pdb=" N GLU A 62 " --> pdb=" O ASP A 58 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 79 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN A 87 " --> pdb=" O ASN A 83 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 137 removed outlier: 3.612A pdb=" N ILE A 112 " --> pdb=" O ARG A 108 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 113 " --> pdb=" O PRO A 109 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A 127 " --> pdb=" O ASP A 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 15 Processing helix chain 'B' and resid 18 through 28 removed outlier: 3.839A pdb=" N LEU B 28 " --> pdb=" O GLN B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 51 removed outlier: 3.716A pdb=" N VAL B 42 " --> pdb=" O GLU B 38 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU B 48 " --> pdb=" O ALA B 44 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 49 " --> pdb=" O GLU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 94 removed outlier: 3.858A pdb=" N GLU B 62 " --> pdb=" O ASP B 58 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA B 79 " --> pdb=" O LYS B 75 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN B 87 " --> pdb=" O ASN B 83 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 137 removed outlier: 3.611A pdb=" N ILE B 112 " --> pdb=" O ARG B 108 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B 113 " --> pdb=" O PRO B 109 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE B 127 " --> pdb=" O ASP B 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 15 Processing helix chain 'C' and resid 18 through 28 removed outlier: 3.840A pdb=" N LEU C 28 " --> pdb=" O GLN C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 51 removed outlier: 3.716A pdb=" N VAL C 42 " --> pdb=" O GLU C 38 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU C 48 " --> pdb=" O ALA C 44 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU C 49 " --> pdb=" O GLU C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 94 removed outlier: 3.859A pdb=" N GLU C 62 " --> pdb=" O ASP C 58 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA C 79 " --> pdb=" O LYS C 75 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN C 87 " --> pdb=" O ASN C 83 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY C 94 " --> pdb=" O ALA C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 137 removed outlier: 3.612A pdb=" N ILE C 112 " --> pdb=" O ARG C 108 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA C 113 " --> pdb=" O PRO C 109 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE C 127 " --> pdb=" O ASP C 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 15 Processing helix chain 'D' and resid 18 through 28 removed outlier: 3.839A pdb=" N LEU D 28 " --> pdb=" O GLN D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 51 removed outlier: 3.716A pdb=" N VAL D 42 " --> pdb=" O GLU D 38 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU D 48 " --> pdb=" O ALA D 44 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU D 49 " --> pdb=" O GLU D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 94 removed outlier: 3.859A pdb=" N GLU D 62 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA D 79 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN D 87 " --> pdb=" O ASN D 83 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 137 removed outlier: 3.611A pdb=" N ILE D 112 " --> pdb=" O ARG D 108 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA D 113 " --> pdb=" O PRO D 109 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE D 127 " --> pdb=" O ASP D 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 15 Processing helix chain 'E' and resid 18 through 28 removed outlier: 3.840A pdb=" N LEU E 28 " --> pdb=" O GLN E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 51 removed outlier: 3.716A pdb=" N VAL E 42 " --> pdb=" O GLU E 38 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU E 48 " --> pdb=" O ALA E 44 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU E 49 " --> pdb=" O GLU E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 94 removed outlier: 3.859A pdb=" N GLU E 62 " --> pdb=" O ASP E 58 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA E 79 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN E 87 " --> pdb=" O ASN E 83 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY E 94 " --> pdb=" O ALA E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 137 removed outlier: 3.611A pdb=" N ILE E 112 " --> pdb=" O ARG E 108 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA E 113 " --> pdb=" O PRO E 109 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE E 127 " --> pdb=" O ASP E 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 15 Processing helix chain 'F' and resid 18 through 28 removed outlier: 3.840A pdb=" N LEU F 28 " --> pdb=" O GLN F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 51 removed outlier: 3.715A pdb=" N VAL F 42 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU F 48 " --> pdb=" O ALA F 44 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU F 49 " --> pdb=" O GLU F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 94 removed outlier: 3.859A pdb=" N GLU F 62 " --> pdb=" O ASP F 58 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA F 79 " --> pdb=" O LYS F 75 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN F 87 " --> pdb=" O ASN F 83 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY F 94 " --> pdb=" O ALA F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 137 removed outlier: 3.611A pdb=" N ILE F 112 " --> pdb=" O ARG F 108 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA F 113 " --> pdb=" O PRO F 109 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE F 127 " --> pdb=" O ASP F 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 15 Processing helix chain 'G' and resid 18 through 28 removed outlier: 3.840A pdb=" N LEU G 28 " --> pdb=" O GLN G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 51 removed outlier: 3.715A pdb=" N VAL G 42 " --> pdb=" O GLU G 38 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU G 48 " --> pdb=" O ALA G 44 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU G 49 " --> pdb=" O GLU G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 94 removed outlier: 3.859A pdb=" N GLU G 62 " --> pdb=" O ASP G 58 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA G 79 " --> pdb=" O LYS G 75 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN G 87 " --> pdb=" O ASN G 83 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY G 94 " --> pdb=" O ALA G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 137 removed outlier: 3.612A pdb=" N ILE G 112 " --> pdb=" O ARG G 108 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA G 113 " --> pdb=" O PRO G 109 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE G 127 " --> pdb=" O ASP G 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 15 Processing helix chain 'H' and resid 18 through 28 removed outlier: 3.840A pdb=" N LEU H 28 " --> pdb=" O GLN H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 51 removed outlier: 3.716A pdb=" N VAL H 42 " --> pdb=" O GLU H 38 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU H 49 " --> pdb=" O GLU H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 94 removed outlier: 3.858A pdb=" N GLU H 62 " --> pdb=" O ASP H 58 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA H 79 " --> pdb=" O LYS H 75 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN H 87 " --> pdb=" O ASN H 83 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 137 removed outlier: 3.611A pdb=" N ILE H 112 " --> pdb=" O ARG H 108 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA H 113 " --> pdb=" O PRO H 109 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE H 127 " --> pdb=" O ASP H 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 15 Processing helix chain 'I' and resid 18 through 28 removed outlier: 3.840A pdb=" N LEU I 28 " --> pdb=" O GLN I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 51 removed outlier: 3.716A pdb=" N VAL I 42 " --> pdb=" O GLU I 38 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU I 48 " --> pdb=" O ALA I 44 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU I 49 " --> pdb=" O GLU I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 94 removed outlier: 3.859A pdb=" N GLU I 62 " --> pdb=" O ASP I 58 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA I 79 " --> pdb=" O LYS I 75 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASN I 87 " --> pdb=" O ASN I 83 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY I 94 " --> pdb=" O ALA I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 137 removed outlier: 3.612A pdb=" N ILE I 112 " --> pdb=" O ARG I 108 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA I 113 " --> pdb=" O PRO I 109 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE I 127 " --> pdb=" O ASP I 123 " (cutoff:3.500A) 702 hydrogen bonds defined for protein. 2106 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.36 Time building geometry restraints manager: 2.65 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: 3313 1.34 - 1.46: 1038 1.46 - 1.57: 5360 1.57 - 1.68: 0 1.68 - 1.80: 108 Bond restraints: 9819 Sorted by residual: bond pdb=" C SER I 4 " pdb=" N PHE I 5 " ideal model delta sigma weight residual 1.332 1.302 0.030 1.35e-02 5.49e+03 4.82e+00 bond pdb=" C SER E 4 " pdb=" N PHE E 5 " ideal model delta sigma weight residual 1.331 1.301 0.029 1.38e-02 5.25e+03 4.46e+00 bond pdb=" C SER D 4 " pdb=" N PHE D 5 " ideal model delta sigma weight residual 1.331 1.302 0.029 1.38e-02 5.25e+03 4.41e+00 bond pdb=" C SER G 4 " pdb=" N PHE G 5 " ideal model delta sigma weight residual 1.331 1.302 0.029 1.38e-02 5.25e+03 4.34e+00 bond pdb=" C SER C 4 " pdb=" N PHE C 5 " ideal model delta sigma weight residual 1.331 1.302 0.029 1.38e-02 5.25e+03 4.32e+00 ... (remaining 9814 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 11472 1.16 - 2.33: 1305 2.33 - 3.49: 336 3.49 - 4.65: 117 4.65 - 5.82: 18 Bond angle restraints: 13248 Sorted by residual: angle pdb=" C GLU B 97 " pdb=" N HIS B 98 " pdb=" CA HIS B 98 " ideal model delta sigma weight residual 121.03 124.60 -3.57 1.60e+00 3.91e-01 4.99e+00 angle pdb=" C GLU F 97 " pdb=" N HIS F 98 " pdb=" CA HIS F 98 " ideal model delta sigma weight residual 121.03 124.59 -3.56 1.60e+00 3.91e-01 4.96e+00 angle pdb=" C GLU I 97 " pdb=" N HIS I 98 " pdb=" CA HIS I 98 " ideal model delta sigma weight residual 121.03 124.59 -3.56 1.60e+00 3.91e-01 4.96e+00 angle pdb=" C GLU A 97 " pdb=" N HIS A 98 " pdb=" CA HIS A 98 " ideal model delta sigma weight residual 121.03 124.58 -3.55 1.60e+00 3.91e-01 4.93e+00 angle pdb=" C GLU G 97 " pdb=" N HIS G 98 " pdb=" CA HIS G 98 " ideal model delta sigma weight residual 121.03 124.57 -3.54 1.60e+00 3.91e-01 4.89e+00 ... (remaining 13243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.54: 5850 13.54 - 27.08: 216 27.08 - 40.62: 126 40.62 - 54.16: 0 54.16 - 67.70: 9 Dihedral angle restraints: 6201 sinusoidal: 2574 harmonic: 3627 Sorted by residual: dihedral pdb=" CA LEU F 15 " pdb=" C LEU F 15 " pdb=" N GLY F 16 " pdb=" CA GLY F 16 " ideal model delta harmonic sigma weight residual 180.00 164.10 15.90 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA LEU H 15 " pdb=" C LEU H 15 " pdb=" N GLY H 16 " pdb=" CA GLY H 16 " ideal model delta harmonic sigma weight residual 180.00 164.11 15.89 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA LEU C 15 " pdb=" C LEU C 15 " pdb=" N GLY C 16 " pdb=" CA GLY C 16 " ideal model delta harmonic sigma weight residual 180.00 164.12 15.88 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 6198 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 753 0.026 - 0.051: 446 0.051 - 0.076: 250 0.076 - 0.102: 83 0.102 - 0.127: 52 Chirality restraints: 1584 Sorted by residual: chirality pdb=" CA ILE I 105 " pdb=" N ILE I 105 " pdb=" C ILE I 105 " pdb=" CB ILE I 105 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA ILE C 105 " pdb=" N ILE C 105 " pdb=" C ILE C 105 " pdb=" CB ILE C 105 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.03e-01 chirality pdb=" CA ILE A 105 " pdb=" N ILE A 105 " pdb=" C ILE A 105 " pdb=" CB ILE A 105 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.00e-01 ... (remaining 1581 not shown) Planarity restraints: 1710 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS C 98 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO C 99 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO C 99 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 99 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS D 98 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO D 99 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO D 99 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 99 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS E 98 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO E 99 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO E 99 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 99 " -0.023 5.00e-02 4.00e+02 ... (remaining 1707 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 3982 2.98 - 3.46: 10365 3.46 - 3.94: 14573 3.94 - 4.42: 17338 4.42 - 4.90: 26850 Nonbonded interactions: 73108 Sorted by model distance: nonbonded pdb=" OD1 ASN E 87 " pdb=" NE2 HIS E 98 " model vdw 2.505 3.120 nonbonded pdb=" OD1 ASN G 87 " pdb=" NE2 HIS G 98 " model vdw 2.505 3.120 nonbonded pdb=" OD1 ASN F 87 " pdb=" NE2 HIS F 98 " model vdw 2.505 3.120 nonbonded pdb=" OD1 ASN A 87 " pdb=" NE2 HIS A 98 " model vdw 2.505 3.120 nonbonded pdb=" OD1 ASN I 87 " pdb=" NE2 HIS I 98 " model vdw 2.505 3.120 ... (remaining 73103 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' } 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 20.480 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 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 : 0.007 0.042 9819 Z= 0.452 Angle : 0.905 5.817 13248 Z= 0.507 Chirality : 0.044 0.127 1584 Planarity : 0.006 0.042 1710 Dihedral : 9.434 67.700 3825 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % 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: -3.88 (0.19), residues: 1215 helix: -2.88 (0.11), residues: 972 sheet: None (None), residues: 0 loop : 0.17 (0.39), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS G 98 PHE 0.008 0.002 PHE C 73 TYR 0.006 0.002 TYR E 13 ARG 0.009 0.001 ARG F 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 1.118 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASP cc_start: 0.8579 (m-30) cc_final: 0.8298 (m-30) REVERT: A 117 ASP cc_start: 0.8466 (t0) cc_final: 0.8215 (t0) REVERT: B 72 ILE cc_start: 0.9547 (mm) cc_final: 0.9300 (mm) REVERT: C 72 ILE cc_start: 0.9479 (mm) cc_final: 0.9255 (mm) REVERT: D 72 ILE cc_start: 0.9506 (mm) cc_final: 0.9236 (mm) REVERT: E 76 ASP cc_start: 0.8587 (m-30) cc_final: 0.8345 (m-30) REVERT: F 72 ILE cc_start: 0.9539 (mm) cc_final: 0.9300 (mt) REVERT: F 123 ASP cc_start: 0.8895 (t0) cc_final: 0.8582 (t0) REVERT: G 72 ILE cc_start: 0.9494 (mm) cc_final: 0.9263 (mt) REVERT: G 117 ASP cc_start: 0.8604 (t0) cc_final: 0.8201 (t0) REVERT: H 72 ILE cc_start: 0.9501 (mm) cc_final: 0.9294 (mm) REVERT: H 76 ASP cc_start: 0.8573 (m-30) cc_final: 0.8276 (m-30) REVERT: I 1 MET cc_start: 0.6519 (ttm) cc_final: 0.4992 (mtp) REVERT: I 24 GLN cc_start: 0.9317 (mt0) cc_final: 0.9083 (mt0) REVERT: I 72 ILE cc_start: 0.9536 (mm) cc_final: 0.9292 (mm) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.3798 time to fit residues: 149.6711 Evaluate side-chains 180 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 30 optimal weight: 8.9990 chunk 59 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 ASN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 ASN ** I 82 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 = 0.2993 r_free = 0.2993 target = 0.041274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.030656 restraints weight = 56603.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.031690 restraints weight = 33462.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.032378 restraints weight = 24536.464| |-----------------------------------------------------------------------------| r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9819 Z= 0.198 Angle : 0.564 4.540 13248 Z= 0.306 Chirality : 0.040 0.119 1584 Planarity : 0.005 0.032 1710 Dihedral : 3.865 11.341 1350 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.61 % Allowed : 10.07 % Favored : 86.32 % 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: 1.00 (0.22), residues: 1215 helix: 0.78 (0.15), residues: 963 sheet: None (None), residues: 0 loop : 0.73 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 41 PHE 0.007 0.001 PHE E 73 TYR 0.005 0.001 TYR C 88 ARG 0.007 0.001 ARG G 108 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 207 time to evaluate : 1.260 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: symmetry clash 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: symmetry clash 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: symmetry clash REVERT: A 76 ASP cc_start: 0.8485 (m-30) cc_final: 0.8251 (m-30) REVERT: A 117 ASP cc_start: 0.8532 (t0) cc_final: 0.8309 (t0) REVERT: A 120 MET cc_start: 0.8879 (mtp) cc_final: 0.8560 (mtp) REVERT: D 75 LYS cc_start: 0.9409 (mmmm) cc_final: 0.9158 (mmmt) REVERT: E 75 LYS cc_start: 0.9316 (mmmm) cc_final: 0.8969 (mmtt) REVERT: E 76 ASP cc_start: 0.8496 (m-30) cc_final: 0.8287 (m-30) REVERT: E 92 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.8008 (tmm) REVERT: F 72 ILE cc_start: 0.9476 (mm) cc_final: 0.9228 (tp) REVERT: F 117 ASP cc_start: 0.8462 (t0) cc_final: 0.8211 (t0) REVERT: F 120 MET cc_start: 0.8747 (mtp) cc_final: 0.8537 (mtp) REVERT: G 33 LYS cc_start: 0.8327 (ptmm) cc_final: 0.7991 (ttpp) REVERT: G 117 ASP cc_start: 0.8618 (t0) cc_final: 0.8321 (t0) REVERT: H 76 ASP cc_start: 0.8450 (m-30) cc_final: 0.8157 (m-30) REVERT: I 117 ASP cc_start: 0.8454 (t0) cc_final: 0.8191 (t0) outliers start: 38 outliers final: 30 residues processed: 234 average time/residue: 0.3346 time to fit residues: 98.0410 Evaluate side-chains 184 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 55 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 56 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 55 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 83 ASN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN E 83 ASN F 82 GLN F 83 ASN G 82 GLN ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN H 83 ASN ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.040342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.029693 restraints weight = 58294.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.030720 restraints weight = 33862.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.031397 restraints weight = 24678.709| |-----------------------------------------------------------------------------| r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9819 Z= 0.177 Angle : 0.497 6.294 13248 Z= 0.263 Chirality : 0.037 0.131 1584 Planarity : 0.004 0.027 1710 Dihedral : 3.403 10.395 1350 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 3.32 % Allowed : 11.87 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.11 (0.23), residues: 1215 helix: 2.27 (0.16), residues: 963 sheet: None (None), residues: 0 loop : 1.42 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.000 HIS G 98 PHE 0.006 0.001 PHE F 73 TYR 0.005 0.001 TYR H 81 ARG 0.004 0.000 ARG G 108 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 164 time to evaluate : 1.191 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: symmetry clash 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: symmetry clash 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: A 75 LYS cc_start: 0.9396 (mmmt) cc_final: 0.9178 (tppt) REVERT: D 75 LYS cc_start: 0.9438 (mmmm) cc_final: 0.9116 (tppt) REVERT: E 75 LYS cc_start: 0.9369 (mmmm) cc_final: 0.9140 (mmtt) REVERT: E 76 ASP cc_start: 0.8455 (m-30) cc_final: 0.8234 (m-30) REVERT: E 92 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.8023 (tmm) REVERT: G 33 LYS cc_start: 0.8259 (ptmm) cc_final: 0.7906 (ttpp) REVERT: G 117 ASP cc_start: 0.8577 (t0) cc_final: 0.8311 (t0) REVERT: H 4 SER cc_start: 0.8725 (m) cc_final: 0.8453 (p) REVERT: H 72 ILE cc_start: 0.9544 (mm) cc_final: 0.9252 (tp) REVERT: H 75 LYS cc_start: 0.9407 (mmmm) cc_final: 0.9146 (tppt) REVERT: H 76 ASP cc_start: 0.8513 (m-30) cc_final: 0.8172 (m-30) REVERT: I 8 ARG cc_start: 0.9251 (mmm-85) cc_final: 0.9034 (mmm-85) REVERT: I 117 ASP cc_start: 0.8427 (t0) cc_final: 0.8182 (t0) outliers start: 35 outliers final: 33 residues processed: 189 average time/residue: 0.3353 time to fit residues: 79.3459 Evaluate side-chains 181 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 55 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 0.7980 chunk 53 optimal weight: 0.4980 chunk 83 optimal weight: 0.0970 chunk 3 optimal weight: 9.9990 chunk 79 optimal weight: 0.4980 chunk 87 optimal weight: 9.9990 chunk 109 optimal weight: 20.0000 chunk 97 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 ASN C 83 ASN ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.041026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.030222 restraints weight = 57657.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.031253 restraints weight = 34213.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.031946 restraints weight = 25094.377| |-----------------------------------------------------------------------------| r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9819 Z= 0.135 Angle : 0.455 7.841 13248 Z= 0.234 Chirality : 0.036 0.124 1584 Planarity : 0.004 0.028 1710 Dihedral : 3.157 9.531 1350 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.23 % Allowed : 11.59 % Favored : 85.19 % 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: 4.07 (0.24), residues: 1215 helix: 2.98 (0.16), residues: 963 sheet: None (None), residues: 0 loop : 1.61 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 98 PHE 0.005 0.001 PHE H 5 TYR 0.004 0.001 TYR A 81 ARG 0.006 0.000 ARG F 8 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 174 time to evaluate : 1.231 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: symmetry clash 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: A 75 LYS cc_start: 0.9410 (mmmt) cc_final: 0.9147 (tppt) REVERT: D 4 SER cc_start: 0.8542 (m) cc_final: 0.8302 (p) REVERT: D 8 ARG cc_start: 0.9397 (mmm-85) cc_final: 0.9063 (mmm-85) REVERT: E 92 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.8157 (tmm) REVERT: G 8 ARG cc_start: 0.9353 (mmm-85) cc_final: 0.9035 (mmm-85) REVERT: G 33 LYS cc_start: 0.8190 (ptmm) cc_final: 0.7866 (ttpp) REVERT: G 117 ASP cc_start: 0.8541 (t0) cc_final: 0.8265 (t0) REVERT: H 4 SER cc_start: 0.8688 (m) cc_final: 0.8461 (p) REVERT: H 8 ARG cc_start: 0.9337 (mmm-85) cc_final: 0.9029 (mmm-85) REVERT: H 72 ILE cc_start: 0.9485 (mm) cc_final: 0.9277 (tp) REVERT: H 75 LYS cc_start: 0.9401 (mmmm) cc_final: 0.9159 (tppt) REVERT: H 76 ASP cc_start: 0.8489 (m-30) cc_final: 0.8246 (m-30) REVERT: I 8 ARG cc_start: 0.9257 (mmm-85) cc_final: 0.8873 (mmm-85) REVERT: I 117 ASP cc_start: 0.8430 (t0) cc_final: 0.8158 (t0) REVERT: I 120 MET cc_start: 0.9006 (mtp) cc_final: 0.8743 (mtp) outliers start: 34 outliers final: 30 residues processed: 197 average time/residue: 0.3399 time to fit residues: 83.6640 Evaluate side-chains 172 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 55 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 107 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 31 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 ASN H 124 GLN I 83 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.038291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2464 r_free = 0.2464 target = 0.027501 restraints weight = 58234.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.028428 restraints weight = 35573.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2529 r_free = 0.2529 target = 0.029010 restraints weight = 26592.243| |-----------------------------------------------------------------------------| r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 9819 Z= 0.359 Angle : 0.637 9.475 13248 Z= 0.314 Chirality : 0.040 0.128 1584 Planarity : 0.004 0.025 1710 Dihedral : 3.229 12.427 1350 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 4.75 % Allowed : 11.59 % Favored : 83.67 % 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: 3.86 (0.23), residues: 1215 helix: 2.84 (0.16), residues: 963 sheet: None (None), residues: 0 loop : 1.50 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 98 PHE 0.017 0.002 PHE F 73 TYR 0.009 0.001 TYR I 81 ARG 0.005 0.001 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 140 time to evaluate : 1.307 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.9407 (mmmt) cc_final: 0.9169 (tppt) REVERT: C 120 MET cc_start: 0.9100 (mtp) cc_final: 0.8778 (mtp) REVERT: E 92 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8134 (tmm) REVERT: G 117 ASP cc_start: 0.8545 (t0) cc_final: 0.8220 (t0) REVERT: H 4 SER cc_start: 0.8665 (m) cc_final: 0.8456 (p) REVERT: H 76 ASP cc_start: 0.8534 (m-30) cc_final: 0.8288 (m-30) REVERT: I 117 ASP cc_start: 0.8445 (t0) cc_final: 0.8236 (t0) REVERT: I 120 MET cc_start: 0.9028 (mtp) cc_final: 0.8811 (mtp) outliers start: 50 outliers final: 31 residues processed: 174 average time/residue: 0.3101 time to fit residues: 69.2897 Evaluate side-chains 169 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain H residue 2 SER Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 55 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 1 optimal weight: 0.8980 chunk 0 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.039826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.028985 restraints weight = 57780.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.029999 restraints weight = 34216.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.030640 restraints weight = 25141.955| |-----------------------------------------------------------------------------| r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9819 Z= 0.149 Angle : 0.499 10.319 13248 Z= 0.251 Chirality : 0.036 0.130 1584 Planarity : 0.004 0.026 1710 Dihedral : 3.062 9.800 1350 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.85 % Allowed : 12.73 % Favored : 84.43 % 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: 4.49 (0.24), residues: 1215 helix: 3.28 (0.16), residues: 963 sheet: None (None), residues: 0 loop : 1.72 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 98 PHE 0.007 0.001 PHE H 73 TYR 0.003 0.000 TYR H 88 ARG 0.005 0.000 ARG E 8 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 1.224 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: symmetry clash 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: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.9396 (mmmt) cc_final: 0.9152 (tppt) REVERT: A 135 LYS cc_start: 0.9501 (tptp) cc_final: 0.9118 (ptpp) REVERT: B 8 ARG cc_start: 0.9409 (mmm-85) cc_final: 0.9051 (mmm-85) REVERT: E 92 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8199 (tmm) REVERT: E 120 MET cc_start: 0.9215 (mpp) cc_final: 0.8935 (mpp) REVERT: F 8 ARG cc_start: 0.9391 (mmm-85) cc_final: 0.9180 (mmm-85) REVERT: F 120 MET cc_start: 0.9131 (mpp) cc_final: 0.8898 (mpp) REVERT: G 8 ARG cc_start: 0.9338 (mmm-85) cc_final: 0.9044 (mmm-85) REVERT: G 117 ASP cc_start: 0.8482 (t0) cc_final: 0.8232 (t0) REVERT: H 8 ARG cc_start: 0.9311 (mmm-85) cc_final: 0.9029 (mmm-85) REVERT: H 76 ASP cc_start: 0.8515 (m-30) cc_final: 0.8205 (m-30) REVERT: H 135 LYS cc_start: 0.9534 (tptp) cc_final: 0.9094 (ptpp) REVERT: I 8 ARG cc_start: 0.9267 (mmm-85) cc_final: 0.9020 (mmm-85) REVERT: I 117 ASP cc_start: 0.8450 (t0) cc_final: 0.8236 (t0) REVERT: I 120 MET cc_start: 0.9041 (mtp) cc_final: 0.8760 (mtp) outliers start: 30 outliers final: 24 residues processed: 174 average time/residue: 0.3037 time to fit residues: 68.7906 Evaluate side-chains 169 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 55 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 62 optimal weight: 0.4980 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 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 = 0.2932 r_free = 0.2932 target = 0.039413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2510 r_free = 0.2510 target = 0.028543 restraints weight = 58418.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.029512 restraints weight = 34463.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.030135 restraints weight = 25466.726| |-----------------------------------------------------------------------------| r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.4936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9819 Z= 0.175 Angle : 0.512 11.218 13248 Z= 0.252 Chirality : 0.037 0.128 1584 Planarity : 0.004 0.026 1710 Dihedral : 2.990 9.842 1350 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.94 % Allowed : 13.39 % Favored : 83.67 % 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: 4.60 (0.24), residues: 1215 helix: 3.36 (0.16), residues: 963 sheet: None (None), residues: 0 loop : 1.76 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 98 PHE 0.010 0.001 PHE E 73 TYR 0.004 0.001 TYR I 81 ARG 0.003 0.000 ARG F 108 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 1.131 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.9435 (mmmt) cc_final: 0.9181 (tppt) REVERT: B 8 ARG cc_start: 0.9412 (mmm-85) cc_final: 0.9092 (mmm-85) REVERT: E 92 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8214 (tmm) REVERT: F 8 ARG cc_start: 0.9407 (mmm-85) cc_final: 0.9191 (mmm-85) REVERT: F 75 LYS cc_start: 0.9428 (mmmt) cc_final: 0.8991 (tppt) REVERT: F 120 MET cc_start: 0.9113 (mpp) cc_final: 0.8855 (mpp) REVERT: G 8 ARG cc_start: 0.9345 (mmm-85) cc_final: 0.9052 (mmm-85) REVERT: H 8 ARG cc_start: 0.9345 (mmm-85) cc_final: 0.9059 (mmm-85) REVERT: H 76 ASP cc_start: 0.8559 (m-30) cc_final: 0.8269 (m-30) REVERT: H 117 ASP cc_start: 0.8105 (m-30) cc_final: 0.7840 (m-30) REVERT: H 135 LYS cc_start: 0.9523 (tptp) cc_final: 0.9116 (ptpp) REVERT: I 8 ARG cc_start: 0.9294 (mmm-85) cc_final: 0.9034 (mmm-85) REVERT: I 120 MET cc_start: 0.9036 (mtp) cc_final: 0.8747 (mtp) outliers start: 31 outliers final: 25 residues processed: 170 average time/residue: 0.3234 time to fit residues: 71.0655 Evaluate side-chains 164 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 117 ASP Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 55 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 68 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 43 optimal weight: 0.0770 chunk 64 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.039996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.029128 restraints weight = 58213.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.030121 restraints weight = 34183.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.030781 restraints weight = 25073.832| |-----------------------------------------------------------------------------| r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9819 Z= 0.148 Angle : 0.531 11.678 13248 Z= 0.260 Chirality : 0.036 0.126 1584 Planarity : 0.004 0.026 1710 Dihedral : 2.958 9.854 1350 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.85 % Allowed : 14.25 % Favored : 82.91 % 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: 4.80 (0.24), residues: 1215 helix: 3.50 (0.16), residues: 963 sheet: None (None), residues: 0 loop : 1.81 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 98 PHE 0.007 0.001 PHE E 73 TYR 0.003 0.000 TYR H 88 ARG 0.004 0.000 ARG F 108 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 1.018 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.9428 (mmmt) cc_final: 0.9181 (tppt) REVERT: B 8 ARG cc_start: 0.9384 (mmm-85) cc_final: 0.9072 (mmm-85) REVERT: C 120 MET cc_start: 0.8841 (mtp) cc_final: 0.8398 (mtp) REVERT: E 92 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.8226 (tmm) REVERT: G 8 ARG cc_start: 0.9337 (mmm-85) cc_final: 0.9047 (mmm-85) REVERT: H 8 ARG cc_start: 0.9320 (mmm-85) cc_final: 0.9045 (mmm-85) REVERT: H 117 ASP cc_start: 0.8112 (m-30) cc_final: 0.7851 (m-30) REVERT: H 135 LYS cc_start: 0.9522 (tptp) cc_final: 0.9151 (ptpp) REVERT: I 8 ARG cc_start: 0.9286 (mmm-85) cc_final: 0.9027 (mmm-85) REVERT: I 120 MET cc_start: 0.9045 (mtp) cc_final: 0.8715 (mtp) outliers start: 30 outliers final: 25 residues processed: 169 average time/residue: 0.3727 time to fit residues: 81.0744 Evaluate side-chains 165 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 117 ASP Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 55 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 110 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 70 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 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 = 0.2931 r_free = 0.2931 target = 0.039302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2501 r_free = 0.2501 target = 0.028326 restraints weight = 58268.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.029282 restraints weight = 34944.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.029915 restraints weight = 25904.270| |-----------------------------------------------------------------------------| r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.5122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9819 Z= 0.205 Angle : 0.563 12.356 13248 Z= 0.276 Chirality : 0.038 0.128 1584 Planarity : 0.004 0.026 1710 Dihedral : 2.939 9.894 1350 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.56 % Allowed : 14.15 % Favored : 83.29 % 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: 4.67 (0.23), residues: 1215 helix: 3.39 (0.16), residues: 963 sheet: None (None), residues: 0 loop : 1.85 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 98 PHE 0.010 0.001 PHE E 73 TYR 0.005 0.001 TYR B 81 ARG 0.008 0.000 ARG F 8 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 1.167 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.9428 (mmmt) cc_final: 0.9194 (tppt) REVERT: E 92 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8214 (tmm) REVERT: H 8 ARG cc_start: 0.9340 (mmm-85) cc_final: 0.9052 (mmm-85) REVERT: H 117 ASP cc_start: 0.8084 (m-30) cc_final: 0.7811 (m-30) REVERT: H 135 LYS cc_start: 0.9531 (tptp) cc_final: 0.9151 (ptpp) REVERT: I 8 ARG cc_start: 0.9321 (mmm-85) cc_final: 0.9036 (mmm-85) REVERT: I 120 MET cc_start: 0.9084 (mtp) cc_final: 0.8787 (mtp) outliers start: 27 outliers final: 25 residues processed: 163 average time/residue: 0.3429 time to fit residues: 72.5159 Evaluate side-chains 161 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 117 ASP Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 55 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 37 optimal weight: 0.6980 chunk 115 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 104 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 42 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 106 optimal weight: 0.2980 chunk 20 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 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 = 0.2953 r_free = 0.2953 target = 0.039979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.029112 restraints weight = 58199.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.030101 restraints weight = 34577.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.030745 restraints weight = 25542.587| |-----------------------------------------------------------------------------| r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.5274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9819 Z= 0.159 Angle : 0.588 13.404 13248 Z= 0.293 Chirality : 0.037 0.134 1584 Planarity : 0.004 0.026 1710 Dihedral : 2.904 9.646 1350 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.47 % Allowed : 14.53 % Favored : 83.00 % 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: 4.74 (0.24), residues: 1215 helix: 3.43 (0.16), residues: 963 sheet: None (None), residues: 0 loop : 1.94 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 98 PHE 0.007 0.001 PHE G 73 TYR 0.003 0.000 TYR H 88 ARG 0.008 0.000 ARG F 8 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 2.169 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.9425 (mmmt) cc_final: 0.9180 (tppt) REVERT: B 8 ARG cc_start: 0.9383 (mmm-85) cc_final: 0.9042 (mmm-85) REVERT: C 120 MET cc_start: 0.8829 (mtp) cc_final: 0.8341 (mtp) REVERT: E 8 ARG cc_start: 0.9313 (mmm-85) cc_final: 0.8945 (mmm-85) REVERT: E 92 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.8187 (tmm) REVERT: E 120 MET cc_start: 0.9333 (mpp) cc_final: 0.8922 (mpp) REVERT: G 117 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7879 (m-30) REVERT: H 8 ARG cc_start: 0.9304 (mmm-85) cc_final: 0.9018 (mmm-85) REVERT: H 117 ASP cc_start: 0.8044 (m-30) cc_final: 0.7769 (m-30) REVERT: H 135 LYS cc_start: 0.9521 (tptp) cc_final: 0.9143 (ptpp) REVERT: I 8 ARG cc_start: 0.9283 (mmm-85) cc_final: 0.9007 (mmm-85) REVERT: I 120 MET cc_start: 0.9025 (mtp) cc_final: 0.8708 (mtp) outliers start: 26 outliers final: 23 residues processed: 161 average time/residue: 0.4676 time to fit residues: 99.8108 Evaluate side-chains 160 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 117 ASP Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 55 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 85 optimal weight: 0.8980 chunk 110 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 chunk 64 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 48 optimal weight: 0.0020 chunk 7 optimal weight: 0.9990 chunk 112 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.040126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.029276 restraints weight = 57894.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.030273 restraints weight = 34456.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.030922 restraints weight = 25422.474| |-----------------------------------------------------------------------------| r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.5367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9819 Z= 0.159 Angle : 0.604 13.128 13248 Z= 0.303 Chirality : 0.038 0.197 1584 Planarity : 0.004 0.026 1710 Dihedral : 2.871 9.355 1350 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.56 % Allowed : 14.25 % Favored : 83.19 % 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: 4.80 (0.23), residues: 1215 helix: 3.46 (0.16), residues: 963 sheet: None (None), residues: 0 loop : 2.00 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 98 PHE 0.007 0.001 PHE C 73 TYR 0.003 0.000 TYR H 88 ARG 0.007 0.000 ARG F 8 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3102.92 seconds wall clock time: 55 minutes 58.65 seconds (3358.65 seconds total)