Starting phenix.real_space_refine on Wed Sep 17 03:22:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ve4_43164/09_2025/8ve4_43164.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ve4_43164/09_2025/8ve4_43164.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ve4_43164/09_2025/8ve4_43164.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ve4_43164/09_2025/8ve4_43164.map" model { file = "/net/cci-nas-00/data/ceres_data/8ve4_43164/09_2025/8ve4_43164.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ve4_43164/09_2025/8ve4_43164.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 3 5.16 5 C 2067 2.51 5 N 548 2.21 5 O 530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3148 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 807 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 7, 'TRANS': 109} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 4, 'GLU:plan': 8, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 60 Chain: "B" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 791 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 7, 'TRANS': 109} Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 4, 'GLU:plan': 10, 'HIS:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 71 Chain: "C" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 781 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 7, 'TRANS': 108} Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 5, 'ASN:plan1': 2, 'GLU:plan': 8, 'HIS:plan': 1, 'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "D" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 769 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 6, 'TRANS': 108} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 5, 'ASN:plan1': 1, 'ARG:plan': 3, 'GLU:plan': 10, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 78 Time building chain proxies: 1.01, per 1000 atoms: 0.32 Number of scatterers: 3148 At special positions: 0 Unit cell: (75.308, 71.936, 62.382, 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 3 16.00 O 530 8.00 N 548 7.00 C 2067 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: 0.23 Conformation dependent library (CDL) restraints added in 145.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 874 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 6 sheets defined 8.4% alpha, 61.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 74 through 83 Processing helix chain 'B' and resid 75 through 83 removed outlier: 3.551A pdb=" N TRP B 79 " --> pdb=" O THR B 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 83 removed outlier: 3.850A pdb=" N TYR C 78 " --> pdb=" O ASP C 74 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TRP C 79 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS C 80 " --> pdb=" O LYS C 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 83 removed outlier: 3.533A pdb=" N TYR D 78 " --> pdb=" O ASP D 74 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 55 removed outlier: 6.336A pdb=" N MET A 13 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ALA A 109 " --> pdb=" O MET A 13 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LYS A 15 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N LEU A 111 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU A 17 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N MET B 13 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ALA B 109 " --> pdb=" O MET B 13 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LYS B 15 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU B 111 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU B 17 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 55 removed outlier: 6.336A pdb=" N MET A 13 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ALA A 109 " --> pdb=" O MET A 13 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LYS A 15 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N LEU A 111 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU A 17 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N MET B 13 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ALA B 109 " --> pdb=" O MET B 13 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LYS B 15 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU B 111 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU B 17 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL B 14 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 55 " --> pdb=" O VAL B 14 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 48 removed outlier: 6.224A pdb=" N ARG A 34 " --> pdb=" O PRO A 43 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ILE A 68 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE A 95 " --> pdb=" O TYR A 69 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N VAL B 94 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA A 91 " --> pdb=" O GLU B 92 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N GLU B 92 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL A 93 " --> pdb=" O HIS B 90 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N HIS B 90 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N PHE A 95 " --> pdb=" O HIS B 88 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N HIS B 88 " --> pdb=" O PHE A 95 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ALA B 29 " --> pdb=" O ASP B 74 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ARG B 34 " --> pdb=" O PRO B 43 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 54 through 56 removed outlier: 6.297A pdb=" N MET C 13 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ALA C 109 " --> pdb=" O MET C 13 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LYS C 15 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N LEU C 111 " --> pdb=" O LYS C 15 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU C 17 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR C 106 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N MET D 13 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ALA D 109 " --> pdb=" O MET D 13 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LYS D 15 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N LEU D 111 " --> pdb=" O LYS D 15 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU D 17 " --> pdb=" O LEU D 111 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 54 through 56 removed outlier: 6.297A pdb=" N MET C 13 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ALA C 109 " --> pdb=" O MET C 13 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LYS C 15 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N LEU C 111 " --> pdb=" O LYS C 15 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU C 17 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR C 106 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N MET D 13 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ALA D 109 " --> pdb=" O MET D 13 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LYS D 15 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N LEU D 111 " --> pdb=" O LYS D 15 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU D 17 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL D 14 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 41 through 48 removed outlier: 6.655A pdb=" N VAL C 32 " --> pdb=" O PHE C 44 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER C 46 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL C 30 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE C 68 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY C 67 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE C 95 " --> pdb=" O TYR C 69 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N HIS C 88 " --> pdb=" O PHE D 95 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N PHE D 95 " --> pdb=" O HIS C 88 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N HIS C 90 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL D 93 " --> pdb=" O HIS C 90 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N GLU C 92 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA D 91 " --> pdb=" O GLU C 92 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N VAL C 94 " --> pdb=" O GLU D 89 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ILE D 68 " --> pdb=" O LYS D 35 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ARG D 34 " --> pdb=" O PRO D 43 " (cutoff:3.500A) 178 hydrogen bonds defined for protein. 489 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: 0.52 Time building geometry restraints manager: 0.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 997 1.35 - 1.46: 822 1.46 - 1.58: 1416 1.58 - 1.70: 0 1.70 - 1.81: 3 Bond restraints: 3238 Sorted by residual: bond pdb=" CB ASP A 18 " pdb=" CG ASP A 18 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.88e-01 bond pdb=" CG ARG A 21 " pdb=" CD ARG A 21 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 6.03e-01 bond pdb=" N PHE A 44 " pdb=" CA PHE A 44 " ideal model delta sigma weight residual 1.458 1.467 -0.009 1.27e-02 6.20e+03 4.78e-01 bond pdb=" CB VAL C 28 " pdb=" CG1 VAL C 28 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.18e-01 bond pdb=" N GLU C 42 " pdb=" CA GLU C 42 " ideal model delta sigma weight residual 1.458 1.447 0.011 1.69e-02 3.50e+03 4.09e-01 ... (remaining 3233 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 4286 1.24 - 2.48: 143 2.48 - 3.72: 33 3.72 - 4.96: 3 4.96 - 6.19: 2 Bond angle restraints: 4467 Sorted by residual: angle pdb=" N PHE A 44 " pdb=" CA PHE A 44 " pdb=" C PHE A 44 " ideal model delta sigma weight residual 112.68 110.26 2.42 1.33e+00 5.65e-01 3.30e+00 angle pdb=" CB ARG A 21 " pdb=" CG ARG A 21 " pdb=" CD ARG A 21 " ideal model delta sigma weight residual 111.30 115.41 -4.11 2.30e+00 1.89e-01 3.19e+00 angle pdb=" N ASP A 18 " pdb=" CA ASP A 18 " pdb=" C ASP A 18 " ideal model delta sigma weight residual 109.59 106.76 2.83 1.61e+00 3.86e-01 3.10e+00 angle pdb=" CA PRO A 86 " pdb=" C PRO A 86 " pdb=" N PHE A 87 " ideal model delta sigma weight residual 114.58 116.48 -1.90 1.16e+00 7.43e-01 2.68e+00 angle pdb=" N LEU C 82 " pdb=" CA LEU C 82 " pdb=" C LEU C 82 " ideal model delta sigma weight residual 113.18 111.23 1.95 1.21e+00 6.83e-01 2.60e+00 ... (remaining 4462 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.47: 1664 10.47 - 20.94: 106 20.94 - 31.41: 53 31.41 - 41.87: 19 41.87 - 52.34: 4 Dihedral angle restraints: 1846 sinusoidal: 492 harmonic: 1354 Sorted by residual: dihedral pdb=" CG ARG C 21 " pdb=" CD ARG C 21 " pdb=" NE ARG C 21 " pdb=" CZ ARG C 21 " ideal model delta sinusoidal sigma weight residual 90.00 50.92 39.08 2 1.50e+01 4.44e-03 8.48e+00 dihedral pdb=" CG ARG B 34 " pdb=" CD ARG B 34 " pdb=" NE ARG B 34 " pdb=" CZ ARG B 34 " ideal model delta sinusoidal sigma weight residual 90.00 51.02 38.98 2 1.50e+01 4.44e-03 8.44e+00 dihedral pdb=" CA LYS A 15 " pdb=" CB LYS A 15 " pdb=" CG LYS A 15 " pdb=" CD LYS A 15 " ideal model delta sinusoidal sigma weight residual -180.00 -137.83 -42.17 3 1.50e+01 4.44e-03 7.56e+00 ... (remaining 1843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 281 0.025 - 0.049: 142 0.049 - 0.074: 46 0.074 - 0.098: 29 0.098 - 0.123: 40 Chirality restraints: 538 Sorted by residual: chirality pdb=" CA ILE C 73 " pdb=" N ILE C 73 " pdb=" C ILE C 73 " pdb=" CB ILE C 73 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.78e-01 chirality pdb=" CA ILE B 73 " pdb=" N ILE B 73 " pdb=" C ILE B 73 " pdb=" CB ILE B 73 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.74e-01 chirality pdb=" CA ILE A 107 " pdb=" N ILE A 107 " pdb=" C ILE A 107 " pdb=" CB ILE A 107 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.67e-01 ... (remaining 535 not shown) Planarity restraints: 566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 85 " 0.035 5.00e-02 4.00e+02 5.39e-02 4.64e+00 pdb=" N PRO B 86 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 86 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 86 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 21 " 0.146 9.50e-02 1.11e+02 6.58e-02 3.13e+00 pdb=" NE ARG A 21 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 21 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 21 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 21 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 85 " -0.022 5.00e-02 4.00e+02 3.35e-02 1.79e+00 pdb=" N PRO A 86 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 86 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 86 " -0.019 5.00e-02 4.00e+02 ... (remaining 563 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 968 2.82 - 3.34: 2518 3.34 - 3.86: 4949 3.86 - 4.38: 5316 4.38 - 4.90: 10111 Nonbonded interactions: 23862 Sorted by model distance: nonbonded pdb=" O VAL B 65 " pdb=" OH TYR B 69 " model vdw 2.302 3.040 nonbonded pdb=" N VAL B 28 " pdb=" OG1 THR B 49 " model vdw 2.329 3.120 nonbonded pdb=" O PHE B 64 " pdb=" ND2 ASN B 98 " model vdw 2.335 3.120 nonbonded pdb=" O VAL C 65 " pdb=" OH TYR C 69 " model vdw 2.398 3.040 nonbonded pdb=" O TRP C 79 " pdb=" N ILE C 84 " model vdw 2.414 3.120 ... (remaining 23857 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' and ((resid 10 and (name N or name CA or name C or name O or name CB \ )) or resid 11 or (resid 12 through 13 and (name N or name CA or name C or name \ O or name CB )) or resid 14 or (resid 15 and (name N or name CA or name C or nam \ e O or name CB )) or resid 16 through 17 or (resid 18 through 20 and (name N or \ name CA or name C or name O or name CB )) or resid 21 through 33 or (resid 34 an \ d (name N or name CA or name C or name O or name CB )) or resid 35 through 41 or \ (resid 42 and (name N or name CA or name C or name O or name CB )) or resid 43 \ through 54 or (resid 55 through 56 and (name N or name CA or name C or name O or \ name CB )) or resid 57 through 58 or (resid 59 through 63 and (name N or name C \ A or name C or name O or name CB )) or resid 64 through 67 or (resid 68 and (nam \ e N or name CA or name C or name O or name CB )) or resid 69 through 71 or (resi \ d 72 and (name N or name CA or name C or name O or name CB )) or resid 73 throug \ h 74 or (resid 75 and (name N or name CA or name C or name O or name CB )) or re \ sid 76 through 79 or (resid 80 through 81 and (name N or name CA or name C or na \ me O or name CB )) or resid 82 through 86 or (resid 87 and (name N or name CA or \ name C or name O or name CB )) or resid 88 through 111 or (resid 112 and (name \ N or name CA or name C or name O or name CB )) or resid 113 or (resid 114 throug \ h 115 and (name N or name CA or name C or name O or name CB )) or resid 116 thro \ ugh 122 or (resid 123 and (name N or name CA or name C or name O or name CB )))) \ selection = (chain 'B' and (resid 10 through 17 or (resid 18 through 20 and (name N or name \ CA or name C or name O or name CB )) or resid 21 through 33 or (resid 34 and (na \ me N or name CA or name C or name O or name CB )) or resid 35 through 47 or (res \ id 48 and (name N or name CA or name C or name O or name CB )) or resid 49 throu \ gh 54 or (resid 55 through 56 and (name N or name CA or name C or name O or name \ CB )) or resid 57 through 67 or (resid 68 and (name N or name CA or name C or n \ ame O or name CB )) or resid 69 through 76 or (resid 77 and (name N or name CA o \ r name C or name O or name CB )) or resid 78 through 79 or (resid 80 through 81 \ and (name N or name CA or name C or name O or name CB )) or resid 82 through 95 \ or (resid 96 through 97 and (name N or name CA or name C or name O or name CB )) \ or resid 98 through 102 or (resid 103 through 104 and (name N or name CA or nam \ e C or name O or name CB )) or resid 105 through 113 or (resid 114 through 115 a \ nd (name N or name CA or name C or name O or name CB )) or resid 116 through 117 \ or (resid 118 through 120 and (name N or name CA or name C or name O or name CB \ )) or resid 121 through 122 or (resid 123 and (name N or name CA or name C or n \ ame O or name CB )))) selection = (chain 'C' and ((resid 10 and (name N or name CA or name C or name O or name CB \ )) or resid 11 or (resid 12 through 13 and (name N or name CA or name C or name \ O or name CB )) or resid 14 through 19 or (resid 20 and (name N or name CA or na \ me C or name O or name CB )) or resid 21 through 33 or (resid 34 and (name N or \ name CA or name C or name O or name CB )) or resid 35 through 47 or (resid 48 an \ d (name N or name CA or name C or name O or name CB )) or resid 49 through 53 or \ (resid 54 through 56 and (name N or name CA or name C or name O or name CB )) o \ r resid 57 through 58 or (resid 59 through 63 and (name N or name CA or name C o \ r name O or name CB )) or resid 64 through 65 or (resid 66 and (name N or name C \ A or name C or name O or name CB )) or resid 67 through 79 or (resid 80 through \ 81 and (name N or name CA or name C or name O or name CB )) or resid 82 through \ 86 or (resid 87 and (name N or name CA or name C or name O or name CB )) or resi \ d 88 through 95 or (resid 96 through 97 and (name N or name CA or name C or name \ O or name CB )) or resid 98 through 111 or (resid 112 and (name N or name CA or \ name C or name O or name CB )) or resid 113 through 122 or (resid 123 and (name \ N or name CA or name C or name O or name CB )))) selection = (chain 'D' and ((resid 10 and (name N or name CA or name C or name O or name CB \ )) or resid 11 or (resid 12 through 13 and (name N or name CA or name C or name \ O or name CB )) or resid 14 or (resid 15 and (name N or name CA or name C or nam \ e O or name CB )) or resid 16 through 47 or (resid 48 and (name N or name CA or \ name C or name O or name CB )) or resid 49 or (resid 50 through 52 and (name N o \ r name CA or name C or name O or name CB )) or (resid 53 through 56 and (name N \ or name CA or name C or name O or name CB )) or resid 57 through 58 or (resid 59 \ through 63 and (name N or name CA or name C or name O or name CB )) or resid 64 \ through 76 or (resid 77 and (name N or name CA or name C or name O or name CB ) \ ) or resid 78 through 86 or (resid 87 and (name N or name CA or name C or name O \ or name CB )) or resid 88 through 111 or (resid 112 and (name N or name CA or n \ ame C or name O or name CB )) or resid 113 or (resid 114 through 115 and (name N \ or name CA or name C or name O or name CB )) or resid 116 through 117 or (resid \ 118 through 120 and (name N or name CA or name C or name O or name CB )) or res \ id 121 through 123)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.830 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 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 : 0.003 0.023 3238 Z= 0.131 Angle : 0.564 6.194 4467 Z= 0.315 Chirality : 0.045 0.123 538 Planarity : 0.006 0.066 566 Dihedral : 10.449 52.342 972 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.40), residues: 457 helix: 1.17 (1.06), residues: 30 sheet: 2.08 (0.36), residues: 228 loop : 0.08 (0.43), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG A 21 TYR 0.017 0.002 TYR C 78 PHE 0.006 0.001 PHE C 87 TRP 0.014 0.001 TRP C 79 HIS 0.003 0.001 HIS C 90 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 3238) covalent geometry : angle 0.56352 ( 4467) hydrogen bonds : bond 0.24048 ( 131) hydrogen bonds : angle 9.56822 ( 489) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.133 Fit side-chains REVERT: A 34 ARG cc_start: 0.7894 (tmm-80) cc_final: 0.7631 (tpt-90) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1148 time to fit residues: 9.3459 Evaluate side-chains 60 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 0.3980 chunk 16 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.173974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.138534 restraints weight = 4793.181| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 3.81 r_work: 0.3873 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3238 Z= 0.188 Angle : 0.619 6.188 4467 Z= 0.321 Chirality : 0.050 0.146 538 Planarity : 0.005 0.036 566 Dihedral : 4.284 17.122 488 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.39 % Allowed : 9.75 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.40), residues: 457 helix: 0.33 (0.98), residues: 36 sheet: 1.87 (0.37), residues: 198 loop : -0.50 (0.39), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 21 TYR 0.023 0.002 TYR C 78 PHE 0.016 0.002 PHE B 64 TRP 0.018 0.002 TRP D 79 HIS 0.004 0.001 HIS D 90 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 3238) covalent geometry : angle 0.61942 ( 4467) hydrogen bonds : bond 0.04111 ( 131) hydrogen bonds : angle 6.41515 ( 489) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.134 Fit side-chains REVERT: C 34 ARG cc_start: 0.8232 (ttp80) cc_final: 0.7922 (ttp-170) REVERT: D 15 LYS cc_start: 0.8144 (tttt) cc_final: 0.7902 (ttpp) outliers start: 8 outliers final: 6 residues processed: 68 average time/residue: 0.1185 time to fit residues: 9.1177 Evaluate side-chains 66 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 106 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 43 optimal weight: 0.0050 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.175004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.140023 restraints weight = 4796.414| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 3.79 r_work: 0.3893 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3238 Z= 0.122 Angle : 0.554 6.774 4467 Z= 0.283 Chirality : 0.048 0.138 538 Planarity : 0.005 0.041 566 Dihedral : 3.957 16.247 488 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.97 % Allowed : 9.75 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.39), residues: 457 helix: 0.12 (0.96), residues: 36 sheet: 1.54 (0.37), residues: 199 loop : -0.57 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 21 TYR 0.014 0.001 TYR C 116 PHE 0.011 0.001 PHE B 64 TRP 0.016 0.001 TRP D 79 HIS 0.003 0.001 HIS C 90 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 3238) covalent geometry : angle 0.55410 ( 4467) hydrogen bonds : bond 0.03372 ( 131) hydrogen bonds : angle 5.71150 ( 489) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.131 Fit side-chains REVERT: D 15 LYS cc_start: 0.8143 (tttt) cc_final: 0.7934 (ttpp) outliers start: 7 outliers final: 5 residues processed: 66 average time/residue: 0.1201 time to fit residues: 9.0305 Evaluate side-chains 67 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 123 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 11 optimal weight: 0.0970 chunk 7 optimal weight: 7.9990 chunk 9 optimal weight: 0.2980 chunk 35 optimal weight: 6.9990 chunk 15 optimal weight: 0.0170 chunk 14 optimal weight: 7.9990 chunk 30 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 overall best weight: 2.4820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.170104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.134666 restraints weight = 4815.972| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 3.76 r_work: 0.3796 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3238 Z= 0.181 Angle : 0.600 7.796 4467 Z= 0.310 Chirality : 0.050 0.146 538 Planarity : 0.005 0.048 566 Dihedral : 4.207 16.416 488 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.24 % Allowed : 13.14 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.39), residues: 457 helix: -0.02 (0.94), residues: 36 sheet: 1.15 (0.38), residues: 199 loop : -0.73 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 21 TYR 0.015 0.002 TYR C 116 PHE 0.012 0.002 PHE A 95 TRP 0.018 0.002 TRP D 79 HIS 0.004 0.001 HIS C 90 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 3238) covalent geometry : angle 0.60034 ( 4467) hydrogen bonds : bond 0.03568 ( 131) hydrogen bonds : angle 5.88145 ( 489) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.103 Fit side-chains REVERT: D 15 LYS cc_start: 0.8114 (tttt) cc_final: 0.7836 (tttm) outliers start: 10 outliers final: 10 residues processed: 69 average time/residue: 0.1102 time to fit residues: 8.6926 Evaluate side-chains 70 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 123 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 0.3980 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 38 optimal weight: 20.0000 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.169836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.133862 restraints weight = 4820.310| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 3.78 r_work: 0.3773 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3238 Z= 0.179 Angle : 0.591 7.583 4467 Z= 0.307 Chirality : 0.050 0.148 538 Planarity : 0.005 0.055 566 Dihedral : 4.204 15.769 488 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 5.08 % Allowed : 11.02 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.39), residues: 457 helix: -0.07 (0.94), residues: 36 sheet: 1.01 (0.38), residues: 197 loop : -0.90 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 21 TYR 0.015 0.002 TYR C 116 PHE 0.011 0.002 PHE A 95 TRP 0.018 0.002 TRP D 79 HIS 0.004 0.001 HIS C 90 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 3238) covalent geometry : angle 0.59114 ( 4467) hydrogen bonds : bond 0.03376 ( 131) hydrogen bonds : angle 5.81323 ( 489) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.124 Fit side-chains REVERT: D 15 LYS cc_start: 0.8166 (tttt) cc_final: 0.7794 (tttm) outliers start: 12 outliers final: 10 residues processed: 70 average time/residue: 0.1125 time to fit residues: 8.9916 Evaluate side-chains 71 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 123 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 14 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 15 optimal weight: 0.0020 chunk 30 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.171872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.136862 restraints weight = 4841.876| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 3.73 r_work: 0.3818 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3238 Z= 0.119 Angle : 0.557 6.713 4467 Z= 0.284 Chirality : 0.048 0.141 538 Planarity : 0.005 0.056 566 Dihedral : 3.886 14.827 488 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.66 % Allowed : 13.98 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.40), residues: 457 helix: -0.14 (0.92), residues: 36 sheet: 1.06 (0.38), residues: 197 loop : -0.86 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 21 TYR 0.013 0.001 TYR C 116 PHE 0.011 0.001 PHE B 44 TRP 0.017 0.001 TRP D 79 HIS 0.003 0.001 HIS C 90 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 3238) covalent geometry : angle 0.55655 ( 4467) hydrogen bonds : bond 0.02897 ( 131) hydrogen bonds : angle 5.42477 ( 489) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.133 Fit side-chains REVERT: B 48 LYS cc_start: 0.7822 (tppt) cc_final: 0.7386 (tmtt) REVERT: D 15 LYS cc_start: 0.8177 (tttt) cc_final: 0.7813 (tttm) outliers start: 11 outliers final: 8 residues processed: 72 average time/residue: 0.1135 time to fit residues: 9.2985 Evaluate side-chains 71 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 123 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 16 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 0.0570 chunk 23 optimal weight: 7.9990 chunk 35 optimal weight: 0.0470 chunk 6 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 overall best weight: 2.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.170538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.134623 restraints weight = 4917.334| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 3.84 r_work: 0.3787 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3238 Z= 0.155 Angle : 0.586 7.454 4467 Z= 0.300 Chirality : 0.050 0.144 538 Planarity : 0.005 0.060 566 Dihedral : 4.024 16.244 488 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.24 % Allowed : 16.10 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.40), residues: 457 helix: -0.07 (0.93), residues: 36 sheet: 0.93 (0.38), residues: 198 loop : -0.87 (0.40), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 21 TYR 0.019 0.002 TYR C 78 PHE 0.019 0.002 PHE A 44 TRP 0.017 0.001 TRP D 79 HIS 0.003 0.001 HIS C 90 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 3238) covalent geometry : angle 0.58633 ( 4467) hydrogen bonds : bond 0.03117 ( 131) hydrogen bonds : angle 5.55281 ( 489) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.125 Fit side-chains REVERT: A 44 PHE cc_start: 0.8149 (t80) cc_final: 0.7877 (t80) REVERT: B 48 LYS cc_start: 0.7797 (tppt) cc_final: 0.7346 (tmtt) REVERT: D 15 LYS cc_start: 0.8165 (tttt) cc_final: 0.7802 (tttm) outliers start: 10 outliers final: 9 residues processed: 66 average time/residue: 0.1107 time to fit residues: 8.3239 Evaluate side-chains 69 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 123 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 8 optimal weight: 0.0870 chunk 32 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.168711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.131973 restraints weight = 5006.165| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 3.89 r_work: 0.3751 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3238 Z= 0.188 Angle : 0.609 7.588 4467 Z= 0.315 Chirality : 0.051 0.145 538 Planarity : 0.006 0.065 566 Dihedral : 4.246 17.110 488 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.24 % Allowed : 16.53 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.40), residues: 457 helix: -0.27 (0.92), residues: 36 sheet: 0.82 (0.39), residues: 197 loop : -1.00 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 21 TYR 0.019 0.002 TYR C 78 PHE 0.016 0.002 PHE A 44 TRP 0.017 0.002 TRP D 79 HIS 0.004 0.001 HIS D 90 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 3238) covalent geometry : angle 0.60936 ( 4467) hydrogen bonds : bond 0.03365 ( 131) hydrogen bonds : angle 5.83545 ( 489) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.130 Fit side-chains REVERT: A 44 PHE cc_start: 0.8211 (t80) cc_final: 0.7980 (t80) REVERT: D 15 LYS cc_start: 0.8201 (tttt) cc_final: 0.7973 (tttm) REVERT: D 48 LYS cc_start: 0.6055 (tptp) cc_final: 0.5175 (tmtt) outliers start: 10 outliers final: 9 residues processed: 65 average time/residue: 0.1110 time to fit residues: 8.2079 Evaluate side-chains 66 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 123 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 8 optimal weight: 0.0770 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.174333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.139006 restraints weight = 4882.166| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 3.76 r_work: 0.3847 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3238 Z= 0.099 Angle : 0.566 8.441 4467 Z= 0.280 Chirality : 0.048 0.138 538 Planarity : 0.005 0.063 566 Dihedral : 3.862 15.780 488 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.54 % Allowed : 18.22 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.40), residues: 457 helix: -0.47 (0.87), residues: 36 sheet: 0.97 (0.39), residues: 199 loop : -0.84 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 21 TYR 0.012 0.001 TYR B 116 PHE 0.021 0.001 PHE A 44 TRP 0.017 0.001 TRP C 79 HIS 0.002 0.001 HIS C 90 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 3238) covalent geometry : angle 0.56649 ( 4467) hydrogen bonds : bond 0.02545 ( 131) hydrogen bonds : angle 5.18643 ( 489) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.120 Fit side-chains REVERT: A 44 PHE cc_start: 0.8224 (t80) cc_final: 0.7853 (t80) REVERT: B 48 LYS cc_start: 0.7790 (tppt) cc_final: 0.7374 (tmtt) REVERT: D 15 LYS cc_start: 0.8205 (tttt) cc_final: 0.7968 (ttpp) outliers start: 6 outliers final: 6 residues processed: 65 average time/residue: 0.0957 time to fit residues: 7.1473 Evaluate side-chains 66 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 16 optimal weight: 10.0000 chunk 27 optimal weight: 0.4980 chunk 36 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.174133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.138898 restraints weight = 4827.849| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 3.77 r_work: 0.3847 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3238 Z= 0.099 Angle : 0.559 6.918 4467 Z= 0.281 Chirality : 0.048 0.136 538 Planarity : 0.006 0.068 566 Dihedral : 3.730 14.422 488 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.12 % Allowed : 19.92 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.40), residues: 457 helix: -0.31 (0.87), residues: 36 sheet: 0.98 (0.39), residues: 198 loop : -0.81 (0.40), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 21 TYR 0.014 0.001 TYR B 116 PHE 0.019 0.002 PHE A 44 TRP 0.033 0.002 TRP B 79 HIS 0.003 0.001 HIS C 90 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 3238) covalent geometry : angle 0.55922 ( 4467) hydrogen bonds : bond 0.02640 ( 131) hydrogen bonds : angle 5.07956 ( 489) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.116 Fit side-chains REVERT: A 44 PHE cc_start: 0.8119 (t80) cc_final: 0.7849 (t80) REVERT: A 55 LEU cc_start: 0.8111 (tp) cc_final: 0.7890 (tp) REVERT: B 48 LYS cc_start: 0.7754 (tppt) cc_final: 0.7350 (tmtt) REVERT: D 15 LYS cc_start: 0.8191 (tttt) cc_final: 0.7955 (ttpp) outliers start: 5 outliers final: 5 residues processed: 62 average time/residue: 0.1068 time to fit residues: 7.6081 Evaluate side-chains 64 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 14 optimal weight: 0.0070 chunk 31 optimal weight: 7.9990 chunk 38 optimal weight: 20.0000 chunk 42 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 overall best weight: 2.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.170154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.134514 restraints weight = 4936.180| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 3.79 r_work: 0.3783 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3238 Z= 0.159 Angle : 0.597 6.987 4467 Z= 0.305 Chirality : 0.050 0.139 538 Planarity : 0.006 0.071 566 Dihedral : 4.033 15.000 488 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.39 % Allowed : 18.22 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.40), residues: 457 helix: -0.41 (0.85), residues: 36 sheet: 0.83 (0.39), residues: 198 loop : -0.91 (0.40), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 21 TYR 0.016 0.002 TYR B 116 PHE 0.016 0.002 PHE A 44 TRP 0.029 0.002 TRP B 79 HIS 0.003 0.001 HIS D 90 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 3238) covalent geometry : angle 0.59702 ( 4467) hydrogen bonds : bond 0.03157 ( 131) hydrogen bonds : angle 5.53668 ( 489) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1078.15 seconds wall clock time: 19 minutes 7.90 seconds (1147.90 seconds total)