Starting phenix.real_space_refine on Wed Sep 25 05:18:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1i_21012/09_2024/6v1i_21012_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1i_21012/09_2024/6v1i_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1i_21012/09_2024/6v1i_21012.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1i_21012/09_2024/6v1i_21012.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1i_21012/09_2024/6v1i_21012_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1i_21012/09_2024/6v1i_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-5461/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: 3.08, per 1000 atoms: 0.32 Number of scatterers: 9711 At special positions: 0 Unit cell: (133.434, 131.316, 67.776, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1827 8.00 N 1701 7.00 C 6129 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.00 Conformation dependent library (CDL) restraints added in 1.0 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: 0.77 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: 2.31 Time building geometry restraints manager: 2.36 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 19.650 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.190 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 322 time to evaluate : 1.086 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: 0.3622 time to fit residues: 142.7715 Evaluate side-chains 180 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.120 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 38 poor density : 207 time to evaluate : 1.192 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: 0.8563 (m-30) cc_final: 0.8304 (m-30) REVERT: A 117 ASP cc_start: 0.8532 (t0) cc_final: 0.8320 (t0) REVERT: A 120 MET cc_start: 0.8825 (mtp) cc_final: 0.8506 (mtp) REVERT: D 75 LYS cc_start: 0.9419 (mmmm) cc_final: 0.9162 (mmmt) REVERT: E 75 LYS cc_start: 0.9312 (mmmm) cc_final: 0.8964 (mmtt) REVERT: E 76 ASP cc_start: 0.8556 (m-30) cc_final: 0.8338 (m-30) REVERT: E 92 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.8016 (tmm) REVERT: F 72 ILE cc_start: 0.9473 (mm) cc_final: 0.9218 (tp) REVERT: F 117 ASP cc_start: 0.8514 (t0) cc_final: 0.8256 (t0) REVERT: F 120 MET cc_start: 0.8715 (mtp) cc_final: 0.8509 (mtp) REVERT: G 33 LYS cc_start: 0.8306 (ptmm) cc_final: 0.7973 (ttpp) REVERT: G 117 ASP cc_start: 0.8629 (t0) cc_final: 0.8333 (t0) REVERT: H 76 ASP cc_start: 0.8552 (m-30) cc_final: 0.8239 (m-30) REVERT: I 117 ASP cc_start: 0.8494 (t0) cc_final: 0.8225 (t0) outliers start: 38 outliers final: 30 residues processed: 234 average time/residue: 0.3198 time to fit residues: 93.9826 Evaluate side-chains 184 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 153 time to evaluate : 1.172 ------------------------------------------------------------------------------- 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 59 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 29 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 83 ASN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN E 83 ASN F 82 GLN F 83 ASN G 82 GLN ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN ** H 83 ASN ** 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.4180 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= 0.175 Angle : 0.495 6.125 13248 Z= 0.261 Chirality : 0.037 0.130 1584 Planarity : 0.004 0.027 1710 Dihedral : 3.404 10.395 1350 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 3.32 % Allowed : 11.78 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.12 (0.23), residues: 1215 helix: 2.28 (0.16), residues: 963 sheet: None (None), residues: 0 loop : 1.44 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS G 98 PHE 0.006 0.001 PHE F 73 TYR 0.006 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 fitting. rotamer outliers: 35 poor density : 164 time to evaluate : 1.228 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: A 75 LYS cc_start: 0.9412 (mmmt) cc_final: 0.9191 (tppt) REVERT: D 75 LYS cc_start: 0.9454 (mmmm) cc_final: 0.9129 (tppt) REVERT: E 75 LYS cc_start: 0.9372 (mmmm) cc_final: 0.9139 (mmtt) REVERT: E 76 ASP cc_start: 0.8556 (m-30) cc_final: 0.8319 (m-30) REVERT: E 92 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.8058 (tmm) REVERT: G 33 LYS cc_start: 0.8269 (ptmm) cc_final: 0.7914 (ttpp) REVERT: G 117 ASP cc_start: 0.8602 (t0) cc_final: 0.8334 (t0) REVERT: H 4 SER cc_start: 0.8672 (m) cc_final: 0.8394 (p) REVERT: H 72 ILE cc_start: 0.9543 (mm) cc_final: 0.9237 (tp) REVERT: H 75 LYS cc_start: 0.9423 (mmmm) cc_final: 0.9152 (tppt) REVERT: H 76 ASP cc_start: 0.8645 (m-30) cc_final: 0.8282 (m-30) REVERT: I 8 ARG cc_start: 0.9262 (mmm-85) cc_final: 0.8849 (mmm-85) REVERT: I 72 ILE cc_start: 0.9455 (mm) cc_final: 0.9242 (tp) REVERT: I 117 ASP cc_start: 0.8468 (t0) cc_final: 0.8214 (t0) outliers start: 35 outliers final: 33 residues processed: 189 average time/residue: 0.3259 time to fit residues: 77.4028 Evaluate side-chains 182 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 148 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 55 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 106 optimal weight: 0.9990 chunk 113 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 94 optimal weight: 6.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 ASN C 83 ASN ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 ASN I 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9819 Z= 0.151 Angle : 0.470 7.544 13248 Z= 0.242 Chirality : 0.036 0.130 1584 Planarity : 0.004 0.027 1710 Dihedral : 3.174 9.630 1350 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.32 % Allowed : 11.87 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.05 (0.24), residues: 1215 helix: 2.96 (0.16), residues: 963 sheet: None (None), residues: 0 loop : 1.60 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 98 PHE 0.005 0.001 PHE H 5 TYR 0.005 0.001 TYR E 81 ARG 0.005 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 201 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 166 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.9433 (mmmt) cc_final: 0.9154 (tppt) REVERT: A 120 MET cc_start: 0.8841 (mtp) cc_final: 0.8495 (mtp) REVERT: D 4 SER cc_start: 0.8566 (m) cc_final: 0.8327 (p) REVERT: E 92 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.8210 (tmm) REVERT: F 120 MET cc_start: 0.8720 (mtm) cc_final: 0.8437 (mpp) REVERT: G 117 ASP cc_start: 0.8585 (t0) cc_final: 0.8294 (t0) REVERT: H 4 SER cc_start: 0.8699 (m) cc_final: 0.8455 (p) REVERT: H 8 ARG cc_start: 0.9325 (mmm-85) cc_final: 0.9025 (mmm-85) REVERT: H 72 ILE cc_start: 0.9511 (mm) cc_final: 0.9286 (tp) REVERT: H 76 ASP cc_start: 0.8627 (m-30) cc_final: 0.8354 (m-30) REVERT: I 8 ARG cc_start: 0.9280 (mmm-85) cc_final: 0.8899 (mmm-85) REVERT: I 117 ASP cc_start: 0.8487 (t0) cc_final: 0.8206 (t0) REVERT: I 120 MET cc_start: 0.9008 (mtp) cc_final: 0.8783 (mtp) outliers start: 35 outliers final: 30 residues processed: 190 average time/residue: 0.3183 time to fit residues: 76.6165 Evaluate side-chains 171 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 140 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 55 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 0 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 ASN H 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.4698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9819 Z= 0.172 Angle : 0.502 9.326 13248 Z= 0.251 Chirality : 0.037 0.131 1584 Planarity : 0.004 0.027 1710 Dihedral : 3.043 10.064 1350 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 4.08 % Allowed : 11.59 % 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: 4.44 (0.24), residues: 1215 helix: 3.25 (0.16), residues: 963 sheet: None (None), residues: 0 loop : 1.68 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 98 PHE 0.009 0.001 PHE F 73 TYR 0.005 0.001 TYR C 81 ARG 0.005 0.000 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 142 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.9424 (mmmt) cc_final: 0.9168 (tppt) REVERT: A 120 MET cc_start: 0.8861 (mtp) cc_final: 0.8563 (mtp) REVERT: A 135 LYS cc_start: 0.9543 (tptp) cc_final: 0.9116 (ptpp) REVERT: D 4 SER cc_start: 0.8586 (m) cc_final: 0.8375 (p) REVERT: E 92 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8215 (tmm) REVERT: F 8 ARG cc_start: 0.9415 (mmm-85) cc_final: 0.9189 (mmm-85) REVERT: G 117 ASP cc_start: 0.8556 (t0) cc_final: 0.8341 (t0) REVERT: H 8 ARG cc_start: 0.9344 (mmm-85) cc_final: 0.9024 (mmm-85) REVERT: H 72 ILE cc_start: 0.9488 (mm) cc_final: 0.9287 (tp) REVERT: H 76 ASP cc_start: 0.8725 (m-30) cc_final: 0.8384 (m-30) REVERT: I 8 ARG cc_start: 0.9313 (mmm-85) cc_final: 0.8943 (mmm-85) REVERT: I 117 ASP cc_start: 0.8479 (t0) cc_final: 0.8266 (t0) REVERT: I 120 MET cc_start: 0.9002 (mtp) cc_final: 0.8739 (mtp) outliers start: 43 outliers final: 29 residues processed: 175 average time/residue: 0.2789 time to fit residues: 63.9820 Evaluate side-chains 168 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 138 time to evaluate : 1.160 ------------------------------------------------------------------------------- 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 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 101 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 113 optimal weight: 6.9990 chunk 93 optimal weight: 0.5980 chunk 52 optimal weight: 10.0000 chunk 9 optimal weight: 0.0030 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 109 optimal weight: 0.0000 overall best weight: 0.3994 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.5044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9819 Z= 0.133 Angle : 0.486 10.352 13248 Z= 0.240 Chirality : 0.035 0.127 1584 Planarity : 0.004 0.028 1710 Dihedral : 2.961 9.173 1350 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.04 % Allowed : 13.01 % Favored : 83.95 % 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: 3.45 (0.16), residues: 963 sheet: None (None), residues: 0 loop : 1.78 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 98 PHE 0.005 0.001 PHE E 73 TYR 0.003 0.000 TYR B 81 ARG 0.004 0.000 ARG F 108 *********************** 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 189 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 157 time to evaluate : 1.073 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: 0.9424 (mmmt) cc_final: 0.9005 (tppt) REVERT: A 135 LYS cc_start: 0.9442 (tptp) cc_final: 0.9011 (ptpp) REVERT: B 8 ARG cc_start: 0.9423 (mmm-85) cc_final: 0.9062 (mmm-85) REVERT: B 120 MET cc_start: 0.8819 (mtp) cc_final: 0.8318 (mtp) REVERT: C 120 MET cc_start: 0.8769 (mtp) cc_final: 0.8353 (mtp) REVERT: C 135 LYS cc_start: 0.9476 (tptp) cc_final: 0.9026 (ptpp) REVERT: D 8 ARG cc_start: 0.9401 (mmm-85) cc_final: 0.9118 (mmm-85) REVERT: F 8 ARG cc_start: 0.9391 (mmm-85) cc_final: 0.9183 (mmm-85) REVERT: F 75 LYS cc_start: 0.9436 (mmmt) cc_final: 0.8811 (tppt) REVERT: G 8 ARG cc_start: 0.9345 (mmm-85) cc_final: 0.9064 (mmm-85) REVERT: G 117 ASP cc_start: 0.8482 (t0) cc_final: 0.8202 (t0) REVERT: H 8 ARG cc_start: 0.9319 (mmm-85) cc_final: 0.9034 (mmm-85) REVERT: H 24 GLN cc_start: 0.8918 (mt0) cc_final: 0.8638 (mt0) REVERT: H 76 ASP cc_start: 0.8695 (m-30) cc_final: 0.8392 (m-30) REVERT: H 135 LYS cc_start: 0.9478 (tptp) cc_final: 0.9040 (ptpp) REVERT: I 8 ARG cc_start: 0.9280 (mmm-85) cc_final: 0.8968 (mmm-85) outliers start: 32 outliers final: 26 residues processed: 180 average time/residue: 0.2816 time to fit residues: 65.2834 Evaluate side-chains 166 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 140 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain E residue 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 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 2 SER Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 55 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 112 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9819 Z= 0.152 Angle : 0.520 10.958 13248 Z= 0.254 Chirality : 0.036 0.127 1584 Planarity : 0.004 0.027 1710 Dihedral : 2.915 9.250 1350 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.23 % Allowed : 13.49 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.82 (0.24), residues: 1215 helix: 3.52 (0.16), residues: 963 sheet: None (None), residues: 0 loop : 1.80 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 98 PHE 0.008 0.001 PHE E 73 TYR 0.005 0.001 TYR A 81 ARG 0.005 0.000 ARG E 108 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 142 time to evaluate : 1.245 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: A 75 LYS cc_start: 0.9434 (mmmt) cc_final: 0.9186 (tppt) REVERT: A 135 LYS cc_start: 0.9495 (tptp) cc_final: 0.9132 (ptpp) REVERT: B 8 ARG cc_start: 0.9412 (mmm-85) cc_final: 0.9092 (mmm-85) REVERT: E 75 LYS cc_start: 0.9393 (tppp) cc_final: 0.9129 (tppt) REVERT: F 8 ARG cc_start: 0.9415 (mmm-85) cc_final: 0.9206 (mmm-85) REVERT: G 8 ARG cc_start: 0.9335 (mmm-85) cc_final: 0.9062 (mmm-85) REVERT: G 117 ASP cc_start: 0.8432 (t0) cc_final: 0.8155 (t0) REVERT: H 8 ARG cc_start: 0.9333 (mmm-85) cc_final: 0.9039 (mmm-85) REVERT: H 135 LYS cc_start: 0.9486 (tptp) cc_final: 0.9038 (ptpp) REVERT: I 8 ARG cc_start: 0.9273 (mmm-85) cc_final: 0.8940 (mmm-85) outliers start: 34 outliers final: 30 residues processed: 166 average time/residue: 0.2871 time to fit residues: 61.8178 Evaluate side-chains 170 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 140 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 24 GLN 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 105 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain H residue 2 SER Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 55 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 0.0000 chunk 10 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN B 82 GLN E 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.5195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9819 Z= 0.149 Angle : 0.524 11.649 13248 Z= 0.255 Chirality : 0.036 0.126 1584 Planarity : 0.004 0.027 1710 Dihedral : 2.878 9.656 1350 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.85 % Allowed : 13.87 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.88 (0.23), residues: 1215 helix: 3.57 (0.16), residues: 963 sheet: None (None), residues: 0 loop : 1.82 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 98 PHE 0.008 0.001 PHE E 73 TYR 0.004 0.000 TYR B 81 ARG 0.005 0.000 ARG E 108 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 145 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.9445 (mmmt) cc_final: 0.9191 (tppt) REVERT: A 135 LYS cc_start: 0.9506 (tptp) cc_final: 0.9111 (ptpp) REVERT: B 8 ARG cc_start: 0.9410 (mmm-85) cc_final: 0.9097 (mmm-85) REVERT: F 8 ARG cc_start: 0.9432 (mmm-85) cc_final: 0.9231 (mmm-85) REVERT: F 75 LYS cc_start: 0.9412 (mmmt) cc_final: 0.8976 (tppt) REVERT: H 8 ARG cc_start: 0.9325 (mmm-85) cc_final: 0.9038 (mmm-85) REVERT: H 135 LYS cc_start: 0.9479 (tptp) cc_final: 0.9033 (ptpp) REVERT: I 8 ARG cc_start: 0.9282 (mmm-85) cc_final: 0.8936 (mmm-85) outliers start: 30 outliers final: 27 residues processed: 168 average time/residue: 0.3054 time to fit residues: 66.6397 Evaluate side-chains 168 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 141 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 24 GLN 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 55 SER Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain H residue 2 SER Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 55 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 94 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 69 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN I 83 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.5161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9819 Z= 0.189 Angle : 0.563 12.341 13248 Z= 0.276 Chirality : 0.037 0.133 1584 Planarity : 0.004 0.028 1710 Dihedral : 2.881 9.480 1350 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.94 % Allowed : 13.39 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.80 (0.23), residues: 1215 helix: 3.49 (0.16), residues: 963 sheet: None (None), residues: 0 loop : 1.86 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 98 PHE 0.009 0.001 PHE F 73 TYR 0.005 0.001 TYR I 81 ARG 0.005 0.000 ARG E 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 171 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 140 time to evaluate : 1.113 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: A 75 LYS cc_start: 0.9459 (mmmt) cc_final: 0.9206 (tppt) REVERT: A 117 ASP cc_start: 0.8418 (t0) cc_final: 0.8148 (m-30) REVERT: F 75 LYS cc_start: 0.9424 (mmmt) cc_final: 0.8797 (tppt) REVERT: H 135 LYS cc_start: 0.9525 (tptp) cc_final: 0.9099 (ptpp) REVERT: I 120 MET cc_start: 0.9001 (mtp) cc_final: 0.8735 (mpp) outliers start: 31 outliers final: 28 residues processed: 164 average time/residue: 0.2904 time to fit residues: 61.6264 Evaluate side-chains 166 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 138 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain A residue 24 GLN 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 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 G residue 7 ASP Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain H residue 2 SER Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 55 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN I 83 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.5198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9819 Z= 0.186 Angle : 0.592 12.997 13248 Z= 0.290 Chirality : 0.037 0.132 1584 Planarity : 0.004 0.028 1710 Dihedral : 2.884 9.576 1350 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.94 % Allowed : 13.49 % Favored : 83.57 % 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: 4.76 (0.23), residues: 1215 helix: 3.45 (0.16), residues: 963 sheet: None (None), residues: 0 loop : 1.92 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 98 PHE 0.010 0.001 PHE D 73 TYR 0.004 0.001 TYR B 81 ARG 0.004 0.000 ARG E 108 ********************** 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 169 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 138 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.9457 (mmmt) cc_final: 0.9201 (tppt) REVERT: A 117 ASP cc_start: 0.8425 (t0) cc_final: 0.8151 (m-30) REVERT: B 8 ARG cc_start: 0.9413 (mmm-85) cc_final: 0.9061 (mmm-85) REVERT: E 120 MET cc_start: 0.9183 (mpp) cc_final: 0.8865 (mpp) REVERT: F 75 LYS cc_start: 0.9425 (mmmt) cc_final: 0.9004 (tppt) REVERT: H 8 ARG cc_start: 0.9341 (mmm-85) cc_final: 0.9040 (mmm-85) REVERT: H 135 LYS cc_start: 0.9538 (tptp) cc_final: 0.9125 (ptpp) REVERT: I 8 ARG cc_start: 0.9243 (mmm-85) cc_final: 0.9000 (mmm-85) REVERT: I 120 MET cc_start: 0.8984 (mtp) cc_final: 0.8681 (mpp) REVERT: I 135 LYS cc_start: 0.9070 (ptpp) cc_final: 0.8869 (ptpp) outliers start: 31 outliers final: 29 residues processed: 162 average time/residue: 0.3156 time to fit residues: 66.5527 Evaluate side-chains 167 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 138 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain A residue 24 GLN 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 105 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain 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 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 98 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 13 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 81 optimal weight: 8.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.039664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.028740 restraints weight = 57729.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.029706 restraints weight = 34695.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.030337 restraints weight = 25748.061| |-----------------------------------------------------------------------------| r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.5212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9819 Z= 0.182 Angle : 0.586 12.827 13248 Z= 0.288 Chirality : 0.037 0.129 1584 Planarity : 0.004 0.027 1710 Dihedral : 2.885 9.506 1350 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.75 % Allowed : 13.68 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.80 (0.23), residues: 1215 helix: 3.48 (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 0.009 0.001 PHE G 73 TYR 0.004 0.001 TYR I 81 ARG 0.005 0.000 ARG F 8 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2095.98 seconds wall clock time: 38 minutes 27.50 seconds (2307.50 seconds total)