Starting phenix.real_space_refine on Fri Feb 14 00:57:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v1i_21012/02_2025/6v1i_21012_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v1i_21012/02_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_21012/02_2025/6v1i_21012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v1i_21012/02_2025/6v1i_21012.map" model { file = "/net/cci-nas-00/data/ceres_data/6v1i_21012/02_2025/6v1i_21012_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v1i_21012/02_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-5592/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: 3.29, per 1000 atoms: 0.34 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: 1.98 Conformation dependent library (CDL) restraints added in 1.2 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: 2.58 Time building geometry restraints manager: 2.37 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 20.330 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.840 ------------------------------------------------------------------------------- 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 : 1.211 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: 0.3803 time to fit residues: 149.8519 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 : 1.104 ------------------------------------------------------------------------------- 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 = 36)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.030657 restraints weight = 56603.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.031690 restraints weight = 33460.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.032378 restraints weight = 24537.793| |-----------------------------------------------------------------------------| 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 : 1.238 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: 0.8484 (m-30) cc_final: 0.8251 (m-30) REVERT: A 117 ASP cc_start: 0.8533 (t0) cc_final: 0.8309 (t0) REVERT: A 120 MET cc_start: 0.8878 (mtp) cc_final: 0.8561 (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: 0.8261 (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: 0.8463 (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: 0.8320 (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: 0.3178 time to fit residues: 93.3954 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 : 1.232 ------------------------------------------------------------------------------- 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: 0.9990 chunk 55 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 4 optimal weight: 0.4980 chunk 2 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN ** H 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.040497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2550 r_free = 0.2550 target = 0.029803 restraints weight = 58339.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.030839 restraints weight = 34084.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.031519 restraints weight = 24852.191| |-----------------------------------------------------------------------------| r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.4227 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= 0.170 Angle : 0.492 6.267 13248 Z= 0.260 Chirality : 0.037 0.129 1584 Planarity : 0.004 0.027 1710 Dihedral : 3.378 10.411 1350 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 3.32 % Allowed : 11.59 % Favored : 85.09 % 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: 3.17 (0.23), residues: 1215 helix: 2.30 (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 0.004 0.000 HIS G 98 PHE 0.006 0.001 PHE I 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 : 1.260 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: A 75 LYS cc_start: 0.9382 (mmmt) cc_final: 0.9174 (tppt) REVERT: D 75 LYS cc_start: 0.9445 (mmmm) cc_final: 0.9127 (tppt) REVERT: D 120 MET cc_start: 0.8604 (mtp) cc_final: 0.8178 (mtt) REVERT: E 72 ILE cc_start: 0.9522 (mm) cc_final: 0.9314 (tp) REVERT: E 92 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.8059 (tmm) REVERT: G 33 LYS cc_start: 0.8149 (ptmm) cc_final: 0.7821 (ttpp) REVERT: G 117 ASP cc_start: 0.8563 (t0) cc_final: 0.8306 (t0) REVERT: H 4 SER cc_start: 0.8718 (m) cc_final: 0.8452 (p) REVERT: H 72 ILE cc_start: 0.9540 (mm) cc_final: 0.9256 (tp) REVERT: H 76 ASP cc_start: 0.8495 (m-30) cc_final: 0.8156 (m-30) REVERT: I 8 ARG cc_start: 0.9252 (mmm-85) cc_final: 0.8842 (mmm-85) REVERT: I 72 ILE cc_start: 0.9458 (mm) cc_final: 0.9256 (tp) REVERT: I 117 ASP cc_start: 0.8430 (t0) cc_final: 0.8179 (t0) outliers start: 35 outliers final: 32 residues processed: 189 average time/residue: 0.3449 time to fit residues: 82.0094 Evaluate side-chains 175 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 1.210 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 53 optimal weight: 0.0040 chunk 83 optimal weight: 0.2980 chunk 3 optimal weight: 10.0000 chunk 79 optimal weight: 0.7980 chunk 87 optimal weight: 0.4980 chunk 109 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 ASN C 83 ASN G 82 GLN G 83 ASN H 83 ASN I 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.041098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.030308 restraints weight = 57858.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.031340 restraints weight = 34246.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.032031 restraints weight = 25104.174| |-----------------------------------------------------------------------------| r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.4637 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= 0.132 Angle : 0.464 7.930 13248 Z= 0.236 Chirality : 0.036 0.128 1584 Planarity : 0.004 0.027 1710 Dihedral : 3.143 9.405 1350 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.32 % Allowed : 11.30 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.13 (0.24), residues: 1215 helix: 3.01 (0.16), residues: 963 sheet: None (None), residues: 0 loop : 1.64 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS F 98 PHE 0.004 0.001 PHE H 5 TYR 0.004 0.000 TYR I 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 200 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 165 time to evaluate : 1.107 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: 0.9405 (mmmt) cc_final: 0.9140 (tppt) REVERT: D 4 SER cc_start: 0.8545 (m) cc_final: 0.8306 (p) REVERT: D 8 ARG cc_start: 0.9387 (mmm-85) cc_final: 0.9055 (mmm-85) REVERT: E 92 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.8208 (tmm) REVERT: G 8 ARG cc_start: 0.9346 (mmm-85) cc_final: 0.9033 (mmm-85) REVERT: G 117 ASP cc_start: 0.8542 (t0) cc_final: 0.8268 (t0) REVERT: H 4 SER cc_start: 0.8688 (m) cc_final: 0.8460 (p) REVERT: H 8 ARG cc_start: 0.9316 (mmm-85) cc_final: 0.9011 (mmm-85) REVERT: H 76 ASP cc_start: 0.8491 (m-30) cc_final: 0.8235 (m-30) REVERT: I 8 ARG cc_start: 0.9268 (mmm-85) cc_final: 0.8889 (mmm-85) REVERT: I 117 ASP cc_start: 0.8434 (t0) cc_final: 0.8159 (t0) REVERT: I 120 MET cc_start: 0.9014 (mtp) cc_final: 0.8765 (mtp) outliers start: 35 outliers final: 29 residues processed: 189 average time/residue: 0.3198 time to fit residues: 76.9952 Evaluate side-chains 163 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 1.219 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 55 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 23 optimal weight: 0.0070 chunk 73 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 16 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 overall best weight: 1.7804 ------------------------------------------------------------------------------- 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** H 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.039807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.028761 restraints weight = 57569.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.029767 restraints weight = 34725.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.030390 restraints weight = 25679.518| |-----------------------------------------------------------------------------| r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9819 Z= 0.220 Angle : 0.530 9.701 13248 Z= 0.264 Chirality : 0.037 0.128 1584 Planarity : 0.004 0.027 1710 Dihedral : 3.067 10.502 1350 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 4.18 % Allowed : 11.49 % Favored : 84.33 % 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: 4.35 (0.24), residues: 1215 helix: 3.18 (0.16), residues: 963 sheet: None (None), residues: 0 loop : 1.69 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 98 PHE 0.012 0.002 PHE F 73 TYR 0.007 0.001 TYR B 81 ARG 0.005 0.000 ARG F 8 *********************** 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 181 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 137 time to evaluate : 1.184 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: 0.9405 (mmmt) cc_final: 0.9166 (tppt) REVERT: C 120 MET cc_start: 0.9010 (mtp) cc_final: 0.8655 (mtp) REVERT: C 135 LYS cc_start: 0.9473 (tptp) cc_final: 0.8994 (ptpp) REVERT: D 4 SER cc_start: 0.8630 (m) cc_final: 0.8415 (p) REVERT: E 92 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.8182 (tmm) REVERT: G 117 ASP cc_start: 0.8553 (t0) cc_final: 0.8352 (t0) REVERT: H 4 SER cc_start: 0.8674 (m) cc_final: 0.8470 (p) REVERT: H 76 ASP cc_start: 0.8576 (m-30) cc_final: 0.8287 (m-30) REVERT: I 117 ASP cc_start: 0.8445 (t0) cc_final: 0.8231 (t0) REVERT: I 120 MET cc_start: 0.9052 (mtp) cc_final: 0.8818 (mtp) outliers start: 44 outliers final: 30 residues processed: 170 average time/residue: 0.2894 time to fit residues: 64.1436 Evaluate side-chains 167 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 1.241 ------------------------------------------------------------------------------- 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 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 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 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 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: 0.7980 chunk 0 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.040286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.029475 restraints weight = 57769.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.030464 restraints weight = 34156.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.031124 restraints weight = 25149.800| |-----------------------------------------------------------------------------| r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.4974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9819 Z= 0.141 Angle : 0.493 10.213 13248 Z= 0.244 Chirality : 0.036 0.135 1584 Planarity : 0.004 0.027 1710 Dihedral : 2.991 9.314 1350 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.04 % Allowed : 12.73 % Favored : 84.24 % 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: 4.63 (0.24), residues: 1215 helix: 3.38 (0.16), residues: 963 sheet: None (None), residues: 0 loop : 1.77 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 98 PHE 0.006 0.001 PHE I 73 TYR 0.003 0.000 TYR B 81 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 179 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 1.295 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: 0.9397 (mmmt) cc_final: 0.9156 (tppt) REVERT: A 135 LYS cc_start: 0.9451 (tptp) cc_final: 0.9077 (ptpp) REVERT: B 8 ARG cc_start: 0.9412 (mmm-85) cc_final: 0.9039 (mmm-85) REVERT: C 120 MET cc_start: 0.8876 (mtp) cc_final: 0.8455 (mtp) REVERT: D 120 MET cc_start: 0.9071 (mpp) cc_final: 0.8801 (mpp) REVERT: E 92 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8271 (tmm) REVERT: F 75 LYS cc_start: 0.9417 (mmmt) cc_final: 0.8982 (tppt) REVERT: G 8 ARG cc_start: 0.9346 (mmm-85) cc_final: 0.9063 (mmm-85) REVERT: G 117 ASP cc_start: 0.8516 (t0) cc_final: 0.8235 (t0) REVERT: H 8 ARG cc_start: 0.9311 (mmm-85) cc_final: 0.9021 (mmm-85) REVERT: H 24 GLN cc_start: 0.8910 (mt0) cc_final: 0.8577 (mt0) REVERT: H 76 ASP cc_start: 0.8517 (m-30) cc_final: 0.8261 (m-30) REVERT: I 8 ARG cc_start: 0.9261 (mmm-85) cc_final: 0.9013 (mmm-85) REVERT: I 120 MET cc_start: 0.9031 (mtp) cc_final: 0.8760 (mtp) outliers start: 32 outliers final: 24 residues processed: 167 average time/residue: 0.3148 time to fit residues: 68.5814 Evaluate side-chains 161 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 1.102 ------------------------------------------------------------------------------- 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 2 SER 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 3 VAL 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 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 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: 0.9990 chunk 42 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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** I 83 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.039037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.028054 restraints weight = 58744.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.029017 restraints weight = 35269.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.029635 restraints weight = 26157.784| |-----------------------------------------------------------------------------| r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9819 Z= 0.261 Angle : 0.575 10.560 13248 Z= 0.283 Chirality : 0.039 0.128 1584 Planarity : 0.004 0.026 1710 Dihedral : 3.036 10.100 1350 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.70 % Allowed : 13.39 % 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: 4.41 (0.23), residues: 1215 helix: 3.21 (0.16), residues: 963 sheet: None (None), residues: 0 loop : 1.75 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 98 PHE 0.011 0.002 PHE G 73 TYR 0.007 0.001 TYR I 81 ARG 0.005 0.000 ARG F 8 *********************** 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: 39 poor density : 139 time to evaluate : 1.271 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: A 75 LYS cc_start: 0.9417 (mmmt) cc_final: 0.9178 (tppt) REVERT: C 120 MET cc_start: 0.8992 (mtp) cc_final: 0.8652 (mtp) REVERT: E 92 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.8138 (tmm) REVERT: H 76 ASP cc_start: 0.8503 (m-30) cc_final: 0.8250 (m-30) REVERT: I 8 ARG cc_start: 0.9347 (mmm-85) cc_final: 0.8987 (mmm-85) REVERT: I 120 MET cc_start: 0.9090 (mtp) cc_final: 0.8830 (mtp) outliers start: 39 outliers final: 28 residues processed: 161 average time/residue: 0.3020 time to fit residues: 63.4138 Evaluate side-chains 161 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 SER 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 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 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 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 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: 0.8980 chunk 24 optimal weight: 0.3980 chunk 4 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.040187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.029287 restraints weight = 58358.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.030320 restraints weight = 34371.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.030976 restraints weight = 25283.414| |-----------------------------------------------------------------------------| r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.5142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9819 Z= 0.154 Angle : 0.531 11.585 13248 Z= 0.266 Chirality : 0.037 0.151 1584 Planarity : 0.004 0.027 1710 Dihedral : 2.946 10.013 1350 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.75 % Allowed : 14.06 % 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: 4.72 (0.24), residues: 1215 helix: 3.43 (0.16), residues: 963 sheet: None (None), residues: 0 loop : 1.84 (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 I 73 TYR 0.003 0.000 TYR H 88 ARG 0.004 0.000 ARG F 8 *********************** 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 167 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 1.175 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: 0.9420 (mmmt) cc_final: 0.9165 (tppt) REVERT: A 135 LYS cc_start: 0.9563 (tptp) cc_final: 0.9122 (ptpp) REVERT: B 8 ARG cc_start: 0.9400 (mmm-85) cc_final: 0.9063 (mmm-85) REVERT: E 92 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8257 (tmm) REVERT: G 8 ARG cc_start: 0.9352 (mmm-85) cc_final: 0.9052 (mmm-85) REVERT: H 8 ARG cc_start: 0.9338 (mmm-85) cc_final: 0.9051 (mmm-85) REVERT: I 8 ARG cc_start: 0.9323 (mmm-85) cc_final: 0.9041 (mmm-85) REVERT: I 120 MET cc_start: 0.9055 (mtp) cc_final: 0.8761 (mtp) outliers start: 29 outliers final: 26 residues processed: 162 average time/residue: 0.2891 time to fit residues: 61.2028 Evaluate side-chains 159 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 1.243 ------------------------------------------------------------------------------- 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 2 SER 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 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 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: 6.9990 chunk 49 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 38 optimal weight: 0.0010 chunk 7 optimal weight: 0.3980 chunk 23 optimal weight: 0.4980 chunk 91 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 chunk 97 optimal weight: 0.9980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.040448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.029554 restraints weight = 58089.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.030588 restraints weight = 34425.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.031243 restraints weight = 25283.414| |-----------------------------------------------------------------------------| r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.5284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9819 Z= 0.148 Angle : 0.548 12.540 13248 Z= 0.273 Chirality : 0.037 0.149 1584 Planarity : 0.004 0.027 1710 Dihedral : 2.894 9.745 1350 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.94 % Allowed : 13.96 % Favored : 83.10 % 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: 4.87 (0.24), residues: 1215 helix: 3.53 (0.16), residues: 963 sheet: None (None), residues: 0 loop : 1.94 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 98 PHE 0.006 0.001 PHE B 73 TYR 0.003 0.000 TYR B 81 ARG 0.004 0.000 ARG F 108 *********************** 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 172 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 1.124 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: A 75 LYS cc_start: 0.9430 (mmmt) cc_final: 0.9184 (tppt) REVERT: A 117 ASP cc_start: 0.8326 (t0) cc_final: 0.8081 (m-30) REVERT: B 8 ARG cc_start: 0.9389 (mmm-85) cc_final: 0.9066 (mmm-85) REVERT: E 8 ARG cc_start: 0.9323 (mmm-85) cc_final: 0.8963 (mmm-85) REVERT: H 8 ARG cc_start: 0.9307 (mmm-85) cc_final: 0.9026 (mmm-85) REVERT: I 8 ARG cc_start: 0.9307 (mmm-85) cc_final: 0.9030 (mmm-85) REVERT: I 120 MET cc_start: 0.9017 (mtp) cc_final: 0.8723 (mtp) outliers start: 31 outliers final: 26 residues processed: 165 average time/residue: 0.2831 time to fit residues: 61.3744 Evaluate side-chains 158 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 1.277 ------------------------------------------------------------------------------- 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 105 ILE Chi-restraints excluded: chain F residue 2 SER 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 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 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: 0.5980 chunk 115 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 104 optimal weight: 10.0000 chunk 36 optimal weight: 0.2980 chunk 108 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 106 optimal weight: 0.0000 chunk 20 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.040487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.029747 restraints weight = 58459.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.030760 restraints weight = 34387.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.031431 restraints weight = 25199.551| |-----------------------------------------------------------------------------| r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.5399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9819 Z= 0.155 Angle : 0.594 13.247 13248 Z= 0.294 Chirality : 0.037 0.146 1584 Planarity : 0.004 0.027 1710 Dihedral : 2.864 9.568 1350 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.28 % Allowed : 14.62 % Favored : 83.10 % 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: 3.44 (0.16), residues: 972 sheet: None (None), residues: 0 loop : 1.78 (0.42), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 98 PHE 0.007 0.001 PHE F 73 TYR 0.003 0.000 TYR D 81 ARG 0.004 0.000 ARG D 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 164 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 1.088 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: A 75 LYS cc_start: 0.9428 (mmmt) cc_final: 0.9189 (tppt) REVERT: A 117 ASP cc_start: 0.8344 (t0) cc_final: 0.8100 (m-30) REVERT: A 135 LYS cc_start: 0.9493 (tptp) cc_final: 0.9100 (ptpp) REVERT: B 8 ARG cc_start: 0.9377 (mmm-85) cc_final: 0.9057 (mmm-85) REVERT: B 135 LYS cc_start: 0.9110 (ptpp) cc_final: 0.8889 (ptpp) REVERT: E 8 ARG cc_start: 0.9312 (mmm-85) cc_final: 0.8954 (mmm-85) REVERT: G 117 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7830 (m-30) REVERT: H 8 ARG cc_start: 0.9296 (mmm-85) cc_final: 0.9026 (mmm-85) REVERT: I 8 ARG cc_start: 0.9305 (mmm-85) cc_final: 0.9033 (mmm-85) outliers start: 24 outliers final: 22 residues processed: 160 average time/residue: 0.2794 time to fit residues: 58.3426 Evaluate side-chains 158 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 1.074 ------------------------------------------------------------------------------- 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 105 ILE Chi-restraints excluded: chain C residue 35 THR 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 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 2 SER Chi-restraints excluded: chain H residue 3 VAL 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: 0.7980 chunk 110 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 64 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 48 optimal weight: 0.0270 chunk 7 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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 = 0.2966 r_free = 0.2966 target = 0.040234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.029357 restraints weight = 57525.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.030330 restraints weight = 34116.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.030983 restraints weight = 25178.437| |-----------------------------------------------------------------------------| r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.5421 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= 0.163 Angle : 0.608 12.996 13248 Z= 0.302 Chirality : 0.038 0.188 1584 Planarity : 0.004 0.027 1710 Dihedral : 2.854 9.751 1350 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.28 % Allowed : 14.62 % Favored : 83.10 % 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: 4.64 (0.24), residues: 1215 helix: 3.36 (0.16), residues: 972 sheet: None (None), residues: 0 loop : 1.82 (0.42), residues: 243 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 B 81 ARG 0.008 0.000 ARG A 8 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2855.70 seconds wall clock time: 52 minutes 11.69 seconds (3131.69 seconds total)