Starting phenix.real_space_refine on Sun Aug 4 22:14:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ybj_39119/08_2024/8ybj_39119.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ybj_39119/08_2024/8ybj_39119.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ybj_39119/08_2024/8ybj_39119.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ybj_39119/08_2024/8ybj_39119.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ybj_39119/08_2024/8ybj_39119.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ybj_39119/08_2024/8ybj_39119.cif" } resolution = 2.38 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= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians P 289 5.49 5 S 14 5.16 5 C 6606 2.51 5 N 2246 2.21 5 O 2798 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 40": "NH1" <-> "NH2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A ARG 49": "NH1" <-> "NH2" Residue "A ARG 52": "NH1" <-> "NH2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ARG 72": "NH1" <-> "NH2" Residue "A ARG 83": "NH1" <-> "NH2" Residue "A ARG 116": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "A ARG 131": "NH1" <-> "NH2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "B ARG 23": "NH1" <-> "NH2" Residue "B ARG 35": "NH1" <-> "NH2" Residue "B ARG 36": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 40": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 55": "NH1" <-> "NH2" Residue "B ARG 67": "NH1" <-> "NH2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B ARG 92": "NH1" <-> "NH2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "C ARG 11": "NH1" <-> "NH2" Residue "C ARG 17": "NH1" <-> "NH2" Residue "C ARG 20": "NH1" <-> "NH2" Residue "C ARG 29": "NH1" <-> "NH2" Residue "C ARG 32": "NH1" <-> "NH2" Residue "C ARG 35": "NH1" <-> "NH2" Residue "C ARG 42": "NH1" <-> "NH2" Residue "C ARG 71": "NH1" <-> "NH2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 99": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 72": "NH1" <-> "NH2" Residue "D ARG 79": "NH1" <-> "NH2" Residue "D ARG 86": "NH1" <-> "NH2" Residue "D ARG 92": "NH1" <-> "NH2" Residue "D ARG 99": "NH1" <-> "NH2" Residue "E ARG 40": "NH1" <-> "NH2" Residue "E ARG 42": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "E ARG 53": "NH1" <-> "NH2" Residue "E ARG 63": "NH1" <-> "NH2" Residue "E ARG 69": "NH1" <-> "NH2" Residue "E ARG 72": "NH1" <-> "NH2" Residue "E ARG 83": "NH1" <-> "NH2" Residue "E ARG 116": "NH1" <-> "NH2" Residue "E ARG 128": "NH1" <-> "NH2" Residue "E ARG 129": "NH1" <-> "NH2" Residue "E ARG 131": "NH1" <-> "NH2" Residue "E ARG 134": "NH1" <-> "NH2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "F ARG 35": "NH1" <-> "NH2" Residue "F ARG 36": "NH1" <-> "NH2" Residue "F ARG 39": "NH1" <-> "NH2" Residue "F ARG 40": "NH1" <-> "NH2" Residue "F ARG 45": "NH1" <-> "NH2" Residue "F ARG 55": "NH1" <-> "NH2" Residue "F ARG 67": "NH1" <-> "NH2" Residue "F ARG 78": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F ARG 95": "NH1" <-> "NH2" Residue "G ARG 11": "NH1" <-> "NH2" Residue "G ARG 17": "NH1" <-> "NH2" Residue "G ARG 20": "NH1" <-> "NH2" Residue "G ARG 29": "NH1" <-> "NH2" Residue "G ARG 32": "NH1" <-> "NH2" Residue "G ARG 35": "NH1" <-> "NH2" Residue "G ARG 42": "NH1" <-> "NH2" Residue "G ARG 71": "NH1" <-> "NH2" Residue "G ARG 77": "NH1" <-> "NH2" Residue "G ARG 81": "NH1" <-> "NH2" Residue "G ARG 88": "NH1" <-> "NH2" Residue "G ARG 99": "NH1" <-> "NH2" Residue "H ARG 33": "NH1" <-> "NH2" Residue "H ARG 72": "NH1" <-> "NH2" Residue "H ARG 79": "NH1" <-> "NH2" Residue "H ARG 86": "NH1" <-> "NH2" Residue "H ARG 92": "NH1" <-> "NH2" Residue "H ARG 99": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 11953 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 844 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Time building chain proxies: 7.26, per 1000 atoms: 0.61 Number of scatterers: 11953 At special positions: 0 Unit cell: (75.26, 120.84, 116.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 289 15.00 O 2798 8.00 N 2246 7.00 C 6606 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 - 3.50 Amino acid : False - 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: 6.17 Conformation dependent library (CDL) restraints added in 1.1 seconds 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1412 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 73.4% alpha, 2.9% beta 144 base pairs and 276 stacking pairs defined. Time for finding SS restraints: 5.84 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.709A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.772A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 124 removed outlier: 3.653A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.752A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.558A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.501A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.575A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.897A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.945A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.551A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.907A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.095A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 414 hydrogen bonds defined for protein. 1215 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 368 hydrogen bonds 736 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 276 stacking parallelities Total time for adding SS restraints: 4.74 Time building geometry restraints manager: 6.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1548 1.32 - 1.44: 4687 1.44 - 1.57: 5915 1.57 - 1.69: 579 1.69 - 1.81: 24 Bond restraints: 12753 Sorted by residual: bond pdb=" CZ ARG A 129 " pdb=" NH2 ARG A 129 " ideal model delta sigma weight residual 1.330 1.285 0.045 1.30e-02 5.92e+03 1.20e+01 bond pdb=" CA ALA C 103 " pdb=" CB ALA C 103 " ideal model delta sigma weight residual 1.529 1.471 0.058 1.69e-02 3.50e+03 1.18e+01 bond pdb=" ND1 HIS H 82 " pdb=" CE1 HIS H 82 " ideal model delta sigma weight residual 1.321 1.354 -0.033 1.00e-02 1.00e+04 1.11e+01 bond pdb=" CZ ARG A 134 " pdb=" NH2 ARG A 134 " ideal model delta sigma weight residual 1.330 1.287 0.043 1.30e-02 5.92e+03 1.09e+01 bond pdb=" CZ ARG E 131 " pdb=" NH2 ARG E 131 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 9.91e+00 ... (remaining 12748 not shown) Histogram of bond angle deviations from ideal: 97.35 - 104.54: 1073 104.54 - 111.73: 6675 111.73 - 118.91: 3866 118.91 - 126.10: 5928 126.10 - 133.29: 922 Bond angle restraints: 18464 Sorted by residual: angle pdb=" C5' DC I 7 " pdb=" C4' DC I 7 " pdb=" O4' DC I 7 " ideal model delta sigma weight residual 109.40 115.29 -5.89 1.50e+00 4.44e-01 1.54e+01 angle pdb=" C PRO H 50 " pdb=" N ASP H 51 " pdb=" CA ASP H 51 " ideal model delta sigma weight residual 120.72 127.14 -6.42 1.67e+00 3.59e-01 1.48e+01 angle pdb=" CB HIS H 82 " pdb=" CG HIS H 82 " pdb=" CD2 HIS H 82 " ideal model delta sigma weight residual 131.20 126.26 4.94 1.30e+00 5.92e-01 1.44e+01 angle pdb=" O ASP G 72 " pdb=" C ASP G 72 " pdb=" N ASN G 73 " ideal model delta sigma weight residual 122.22 117.79 4.43 1.17e+00 7.31e-01 1.43e+01 angle pdb=" C GLY E 132 " pdb=" N GLU E 133 " pdb=" CA GLU E 133 " ideal model delta sigma weight residual 120.87 127.27 -6.40 1.69e+00 3.50e-01 1.43e+01 ... (remaining 18459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 4408 17.67 - 35.33: 1035 35.33 - 53.00: 1144 53.00 - 70.67: 319 70.67 - 88.33: 24 Dihedral angle restraints: 6930 sinusoidal: 4738 harmonic: 2192 Sorted by residual: dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual 180.00 151.86 28.14 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA LEU F 22 " pdb=" C LEU F 22 " pdb=" N ARG F 23 " pdb=" CA ARG F 23 " ideal model delta harmonic sigma weight residual -180.00 -158.06 -21.94 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA PRO D 103 " pdb=" C PRO D 103 " pdb=" N GLY D 104 " pdb=" CA GLY D 104 " ideal model delta harmonic sigma weight residual 180.00 158.42 21.58 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 6927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1797 0.069 - 0.138: 256 0.138 - 0.207: 31 0.207 - 0.275: 12 0.275 - 0.344: 4 Chirality restraints: 2100 Sorted by residual: chirality pdb=" CA LYS G 74 " pdb=" N LYS G 74 " pdb=" C LYS G 74 " pdb=" CB LYS G 74 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" C4' DC I -70 " pdb=" C5' DC I -70 " pdb=" O4' DC I -70 " pdb=" C3' DC I -70 " both_signs ideal model delta sigma weight residual False -2.53 -2.18 -0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" CA ASN G 73 " pdb=" N ASN G 73 " pdb=" C ASN G 73 " pdb=" CB ASN G 73 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.32e+00 ... (remaining 2097 not shown) Planarity restraints: 1335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT J -24 " 0.050 2.00e-02 2.50e+03 6.62e-02 1.10e+02 pdb=" N1 DT J -24 " 0.046 2.00e-02 2.50e+03 pdb=" C2 DT J -24 " -0.018 2.00e-02 2.50e+03 pdb=" O2 DT J -24 " -0.117 2.00e-02 2.50e+03 pdb=" N3 DT J -24 " 0.013 2.00e-02 2.50e+03 pdb=" C4 DT J -24 " 0.027 2.00e-02 2.50e+03 pdb=" O4 DT J -24 " 0.080 2.00e-02 2.50e+03 pdb=" C5 DT J -24 " -0.005 2.00e-02 2.50e+03 pdb=" C7 DT J -24 " -0.125 2.00e-02 2.50e+03 pdb=" C6 DT J -24 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 55 " 0.095 2.00e-02 2.50e+03 6.04e-02 9.12e+01 pdb=" N1 DT I 55 " 0.038 2.00e-02 2.50e+03 pdb=" C2 DT I 55 " -0.020 2.00e-02 2.50e+03 pdb=" O2 DT I 55 " -0.093 2.00e-02 2.50e+03 pdb=" N3 DT I 55 " -0.015 2.00e-02 2.50e+03 pdb=" C4 DT I 55 " 0.021 2.00e-02 2.50e+03 pdb=" O4 DT I 55 " 0.100 2.00e-02 2.50e+03 pdb=" C5 DT I 55 " -0.033 2.00e-02 2.50e+03 pdb=" C7 DT I 55 " -0.063 2.00e-02 2.50e+03 pdb=" C6 DT I 55 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 5 " -0.101 2.00e-02 2.50e+03 6.31e-02 8.96e+01 pdb=" N1 DC I 5 " -0.023 2.00e-02 2.50e+03 pdb=" C2 DC I 5 " 0.008 2.00e-02 2.50e+03 pdb=" O2 DC I 5 " 0.067 2.00e-02 2.50e+03 pdb=" N3 DC I 5 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DC I 5 " 0.023 2.00e-02 2.50e+03 pdb=" N4 DC I 5 " -0.107 2.00e-02 2.50e+03 pdb=" C5 DC I 5 " 0.078 2.00e-02 2.50e+03 pdb=" C6 DC I 5 " 0.051 2.00e-02 2.50e+03 ... (remaining 1332 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 4264 2.93 - 3.43: 10430 3.43 - 3.92: 24382 3.92 - 4.41: 27712 4.41 - 4.90: 36602 Nonbonded interactions: 103390 Sorted by model distance: nonbonded pdb=" N ASP D 51 " pdb=" OD1 ASP D 51 " model vdw 2.443 3.120 nonbonded pdb=" OG SER G 18 " pdb=" O PHE G 25 " model vdw 2.467 3.040 nonbonded pdb=" OD2 ASP D 68 " pdb=" OH TYR F 98 " model vdw 2.486 3.040 nonbonded pdb=" OG SER C 40 " pdb=" O ARG C 42 " model vdw 2.504 3.040 nonbonded pdb=" NH2 ARG G 32 " pdb=" OE1 GLU H 35 " model vdw 2.521 3.120 ... (remaining 103385 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 'E' and resid 40 through 135) } ncs_group { reference = (chain 'B' and resid 22 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 11 through 118) selection = (chain 'G' and resid 11 through 118) } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.880 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: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 40.030 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:12.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 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 0.058 12753 Z= 0.416 Angle : 0.961 8.220 18464 Z= 0.616 Chirality : 0.054 0.344 2100 Planarity : 0.012 0.112 1335 Dihedral : 28.235 88.333 5518 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % 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: 2.32 (0.29), residues: 742 helix: 2.20 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -0.20 (0.36), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS G 82 PHE 0.008 0.002 PHE E 67 TYR 0.036 0.003 TYR G 39 ARG 0.013 0.001 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8516 (ttt180) cc_final: 0.8312 (tpt90) REVERT: C 15 LYS cc_start: 0.7916 (mtpt) cc_final: 0.7683 (mtmt) REVERT: C 95 LYS cc_start: 0.8930 (ttmt) cc_final: 0.8498 (tttp) REVERT: E 97 GLU cc_start: 0.9069 (mt-10) cc_final: 0.8852 (mt-10) REVERT: G 95 LYS cc_start: 0.8499 (ttmt) cc_final: 0.7913 (tttt) REVERT: H 93 GLU cc_start: 0.8887 (mp0) cc_final: 0.8483 (mp0) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 2.1881 time to fit residues: 343.5772 Evaluate side-chains 137 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN B 25 ASN D 84 ASN E 68 GLN F 25 ASN H 84 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 12753 Z= 0.196 Angle : 0.555 5.498 18464 Z= 0.343 Chirality : 0.034 0.127 2100 Planarity : 0.004 0.034 1335 Dihedral : 30.426 96.089 4021 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 1.59 % Allowed : 12.44 % Favored : 85.96 % 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: 3.00 (0.30), residues: 742 helix: 2.76 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.24 (0.38), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 49 PHE 0.008 0.001 PHE E 67 TYR 0.011 0.001 TYR F 51 ARG 0.005 0.000 ARG D 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 147 time to evaluate : 0.944 Fit side-chains revert: symmetry clash REVERT: C 15 LYS cc_start: 0.7824 (mtpt) cc_final: 0.7609 (mtmt) REVERT: C 36 LYS cc_start: 0.8542 (mppt) cc_final: 0.8207 (mmtp) REVERT: E 97 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8722 (mt-10) REVERT: G 95 LYS cc_start: 0.8485 (ttmt) cc_final: 0.7893 (tttt) outliers start: 10 outliers final: 3 residues processed: 148 average time/residue: 2.1382 time to fit residues: 332.2711 Evaluate side-chains 146 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 143 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 61 optimal weight: 0.0980 chunk 25 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 12753 Z= 0.300 Angle : 0.602 5.583 18464 Z= 0.366 Chirality : 0.038 0.133 2100 Planarity : 0.005 0.038 1335 Dihedral : 30.740 92.128 4021 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.23 % Allowed : 12.28 % Favored : 85.49 % 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: 2.63 (0.30), residues: 742 helix: 2.50 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.42 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.008 0.002 PHE E 67 TYR 0.014 0.002 TYR F 51 ARG 0.006 0.001 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 139 time to evaluate : 0.883 Fit side-chains revert: symmetry clash REVERT: C 15 LYS cc_start: 0.8008 (mtpt) cc_final: 0.7691 (mtmt) REVERT: D 68 ASP cc_start: 0.9358 (t0) cc_final: 0.9051 (t0) REVERT: E 97 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8857 (mt-10) REVERT: G 64 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8057 (tt0) REVERT: G 95 LYS cc_start: 0.8516 (ttmt) cc_final: 0.7903 (tttt) REVERT: H 93 GLU cc_start: 0.8858 (mp0) cc_final: 0.8558 (mp0) outliers start: 14 outliers final: 5 residues processed: 144 average time/residue: 2.0583 time to fit residues: 310.8476 Evaluate side-chains 143 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 137 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 6.9990 chunk 47 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 20.0000 chunk 26 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12753 Z= 0.200 Angle : 0.574 7.606 18464 Z= 0.352 Chirality : 0.034 0.128 2100 Planarity : 0.005 0.069 1335 Dihedral : 30.708 92.616 4021 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 2.07 % Allowed : 12.92 % Favored : 85.01 % 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: 2.76 (0.30), residues: 742 helix: 2.62 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.44 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 49 PHE 0.009 0.001 PHE E 67 TYR 0.012 0.001 TYR F 51 ARG 0.005 0.000 ARG H 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 139 time to evaluate : 0.910 Fit side-chains revert: symmetry clash REVERT: C 15 LYS cc_start: 0.7992 (mtpt) cc_final: 0.7689 (mtmt) REVERT: D 71 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8100 (mt-10) REVERT: E 97 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8831 (mt-10) REVERT: G 64 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8054 (tt0) REVERT: G 95 LYS cc_start: 0.8520 (ttmt) cc_final: 0.7887 (tttt) REVERT: H 93 GLU cc_start: 0.8851 (mp0) cc_final: 0.8539 (mp0) outliers start: 13 outliers final: 9 residues processed: 141 average time/residue: 2.1370 time to fit residues: 315.9058 Evaluate side-chains 148 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 137 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 86 optimal weight: 20.0000 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12753 Z= 0.212 Angle : 0.564 5.060 18464 Z= 0.347 Chirality : 0.035 0.128 2100 Planarity : 0.004 0.057 1335 Dihedral : 30.622 94.057 4021 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 1.59 % Allowed : 13.40 % Favored : 85.01 % 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: 2.81 (0.30), residues: 742 helix: 2.65 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.40 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 49 PHE 0.009 0.001 PHE E 67 TYR 0.012 0.002 TYR F 51 ARG 0.004 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 139 time to evaluate : 0.921 Fit side-chains revert: symmetry clash REVERT: C 15 LYS cc_start: 0.7961 (mtpt) cc_final: 0.7673 (mtmt) REVERT: D 71 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8120 (mt-10) REVERT: E 97 GLU cc_start: 0.9071 (mt-10) cc_final: 0.8837 (mt-10) REVERT: G 64 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8042 (tt0) REVERT: G 95 LYS cc_start: 0.8510 (ttmt) cc_final: 0.7875 (tttt) REVERT: H 93 GLU cc_start: 0.8845 (mp0) cc_final: 0.8491 (mp0) outliers start: 10 outliers final: 7 residues processed: 142 average time/residue: 2.1001 time to fit residues: 312.7775 Evaluate side-chains 146 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 137 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.1980 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 8 optimal weight: 0.4980 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12753 Z= 0.183 Angle : 0.553 5.122 18464 Z= 0.341 Chirality : 0.034 0.126 2100 Planarity : 0.004 0.081 1335 Dihedral : 30.592 94.163 4021 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 2.39 % Allowed : 12.44 % Favored : 85.17 % 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: 2.86 (0.30), residues: 742 helix: 2.69 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.38 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 49 PHE 0.008 0.001 PHE E 67 TYR 0.011 0.001 TYR F 51 ARG 0.003 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 139 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 15 LYS cc_start: 0.7972 (mtpt) cc_final: 0.7691 (mtmt) REVERT: D 71 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8102 (mt-10) REVERT: E 97 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8835 (mt-10) REVERT: G 64 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8055 (tt0) REVERT: G 95 LYS cc_start: 0.8508 (ttmt) cc_final: 0.7872 (tttt) REVERT: H 93 GLU cc_start: 0.8846 (mp0) cc_final: 0.8493 (mp0) outliers start: 15 outliers final: 10 residues processed: 144 average time/residue: 2.1465 time to fit residues: 324.3325 Evaluate side-chains 152 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 140 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12753 Z= 0.192 Angle : 0.550 5.067 18464 Z= 0.340 Chirality : 0.034 0.125 2100 Planarity : 0.004 0.045 1335 Dihedral : 30.531 94.838 4021 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 1.75 % Allowed : 12.76 % Favored : 85.49 % 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: 2.89 (0.30), residues: 742 helix: 2.70 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.34 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 49 PHE 0.009 0.001 PHE E 67 TYR 0.013 0.001 TYR B 88 ARG 0.004 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 140 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 15 LYS cc_start: 0.7970 (mtpt) cc_final: 0.7683 (mtmt) REVERT: D 71 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8084 (mt-10) REVERT: D 113 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8550 (mm-30) REVERT: G 64 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8044 (tt0) REVERT: G 95 LYS cc_start: 0.8520 (ttmt) cc_final: 0.7890 (tttt) outliers start: 11 outliers final: 8 residues processed: 143 average time/residue: 2.1089 time to fit residues: 316.3102 Evaluate side-chains 149 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 139 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 12753 Z= 0.279 Angle : 0.586 5.154 18464 Z= 0.357 Chirality : 0.037 0.132 2100 Planarity : 0.005 0.049 1335 Dihedral : 30.584 92.731 4021 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 2.07 % Allowed : 12.44 % Favored : 85.49 % 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: 2.68 (0.30), residues: 742 helix: 2.55 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.44 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.009 0.002 PHE E 67 TYR 0.019 0.002 TYR B 88 ARG 0.010 0.001 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 139 time to evaluate : 0.977 Fit side-chains revert: symmetry clash REVERT: C 15 LYS cc_start: 0.8030 (mtpt) cc_final: 0.7716 (mtmt) REVERT: C 104 GLN cc_start: 0.8631 (mt0) cc_final: 0.8428 (mt0) REVERT: D 68 ASP cc_start: 0.9347 (t0) cc_final: 0.9039 (t0) REVERT: D 71 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8103 (mt-10) REVERT: E 97 GLU cc_start: 0.9112 (mt-10) cc_final: 0.8895 (mt-10) REVERT: G 64 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8048 (tt0) REVERT: G 95 LYS cc_start: 0.8481 (ttmt) cc_final: 0.7850 (tttt) REVERT: H 93 GLU cc_start: 0.8829 (mp0) cc_final: 0.8525 (mp0) outliers start: 13 outliers final: 8 residues processed: 142 average time/residue: 2.1413 time to fit residues: 319.2147 Evaluate side-chains 148 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 138 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 39 optimal weight: 0.0020 chunk 70 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12753 Z= 0.228 Angle : 0.578 7.857 18464 Z= 0.353 Chirality : 0.035 0.127 2100 Planarity : 0.005 0.055 1335 Dihedral : 30.581 92.841 4021 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 1.91 % Allowed : 12.76 % Favored : 85.33 % 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: 2.73 (0.30), residues: 742 helix: 2.59 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.43 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.008 0.001 PHE E 67 TYR 0.017 0.002 TYR B 88 ARG 0.004 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 138 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7767 (ttp80) cc_final: 0.7479 (ttt-90) REVERT: C 15 LYS cc_start: 0.8021 (mtpt) cc_final: 0.7706 (mtmt) REVERT: D 68 ASP cc_start: 0.9338 (t0) cc_final: 0.9019 (t0) REVERT: D 71 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8109 (mt-10) REVERT: E 97 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8876 (mt-10) REVERT: G 64 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8042 (tt0) REVERT: G 95 LYS cc_start: 0.8475 (ttmt) cc_final: 0.7845 (tttt) REVERT: H 93 GLU cc_start: 0.8828 (mp0) cc_final: 0.8525 (mp0) outliers start: 12 outliers final: 8 residues processed: 141 average time/residue: 2.1506 time to fit residues: 317.8589 Evaluate side-chains 147 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 137 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 99 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN G 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 12753 Z= 0.256 Angle : 0.580 6.849 18464 Z= 0.353 Chirality : 0.036 0.131 2100 Planarity : 0.005 0.067 1335 Dihedral : 30.560 93.122 4021 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 2.07 % Allowed : 13.08 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.67 (0.30), residues: 742 helix: 2.55 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.45 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.009 0.001 PHE E 67 TYR 0.027 0.002 TYR B 88 ARG 0.005 0.001 ARG A 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 137 time to evaluate : 0.887 Fit side-chains revert: symmetry clash REVERT: C 15 LYS cc_start: 0.8028 (mtpt) cc_final: 0.7711 (mtmt) REVERT: D 71 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8111 (mt-10) REVERT: E 97 GLU cc_start: 0.9108 (mt-10) cc_final: 0.8886 (mt-10) REVERT: G 64 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8045 (tt0) REVERT: G 95 LYS cc_start: 0.8478 (ttmt) cc_final: 0.7846 (tttt) REVERT: H 93 GLU cc_start: 0.8830 (mp0) cc_final: 0.8482 (mp0) outliers start: 13 outliers final: 8 residues processed: 140 average time/residue: 2.0463 time to fit residues: 301.0304 Evaluate side-chains 147 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 137 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 7.9990 chunk 11 optimal weight: 0.0970 chunk 22 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 4 optimal weight: 0.0570 chunk 57 optimal weight: 0.9990 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN G 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.164178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.115548 restraints weight = 10963.305| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.13 r_work: 0.3064 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12753 Z= 0.204 Angle : 0.573 9.099 18464 Z= 0.350 Chirality : 0.034 0.129 2100 Planarity : 0.005 0.107 1335 Dihedral : 30.553 93.100 4021 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 2.07 % Allowed : 12.92 % Favored : 85.01 % 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: 2.74 (0.30), residues: 742 helix: 2.59 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.41 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 49 PHE 0.009 0.001 PHE E 67 TYR 0.021 0.002 TYR B 88 ARG 0.008 0.000 ARG A 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4948.81 seconds wall clock time: 88 minutes 27.35 seconds (5307.35 seconds total)