Starting phenix.real_space_refine on Tue Mar 3 21:20:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m4g_30077/03_2026/6m4g_30077.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m4g_30077/03_2026/6m4g_30077.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6m4g_30077/03_2026/6m4g_30077.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m4g_30077/03_2026/6m4g_30077.map" model { file = "/net/cci-nas-00/data/ceres_data/6m4g_30077/03_2026/6m4g_30077.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m4g_30077/03_2026/6m4g_30077.cif" } resolution = 2.8 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= -0.002 sd= 1.046 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 186 5.49 5 S 16 5.16 5 C 5087 2.51 5 N 1657 2.21 5 O 2064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9010 Number of models: 1 Model: "" Number of chains: 6 Chain: "I" Number of atoms: 1924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1924 Classifications: {'DNA': 93} Link IDs: {'rna3p': 92} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 1888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1888 Classifications: {'DNA': 93} Link IDs: {'rna3p': 92} Chain: "A" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 599 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "B" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 610 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "D" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 685 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "C" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 705 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Restraints were copied for chains: E, F, G, H Time building chain proxies: 2.05, per 1000 atoms: 0.23 Number of scatterers: 9010 At special positions: 0 Unit cell: (80.08, 115.44, 115.44, 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 16 16.00 P 186 15.00 O 2064 8.00 N 1657 7.00 C 5087 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: 0.92 Conformation dependent library (CDL) restraints added in 204.9 milliseconds 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1244 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 6 sheets defined 75.9% alpha, 2.1% beta 66 base pairs and 163 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.584A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.532A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.628A pdb=" N GLY B 28 " --> pdb=" O ASN B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.634A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.648A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.703A pdb=" N TYR D 42 " --> pdb=" O SER D 38 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS D 43 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 84 removed outlier: 3.608A pdb=" N GLY D 60 " --> pdb=" O SER D 56 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.690A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 123 removed outlier: 4.028A pdb=" N LYS D 120 " --> pdb=" O LYS D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 75 Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.583A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.533A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.628A pdb=" N GLY F 28 " --> pdb=" O ASN F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.634A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.648A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.703A pdb=" N TYR H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS H 43 " --> pdb=" O ILE H 39 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 84 removed outlier: 3.607A pdb=" N GLY H 60 " --> pdb=" O SER H 56 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY H 75 " --> pdb=" O GLU H 71 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.689A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 123 removed outlier: 4.028A pdb=" N LYS H 120 " --> pdb=" O LYS H 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 25 Processing helix chain 'C' and resid 30 through 42 removed outlier: 3.538A pdb=" N VAL C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 78 removed outlier: 3.866A pdb=" N GLU C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 69 " --> pdb=" O LYS C 65 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN C 75 " --> pdb=" O GLY C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 93 removed outlier: 3.624A pdb=" N HIS C 92 " --> pdb=" O ASP C 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 25 Processing helix chain 'G' and resid 30 through 42 removed outlier: 3.538A pdb=" N VAL G 34 " --> pdb=" O SER G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 78 removed outlier: 3.865A pdb=" N GLU G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU G 69 " --> pdb=" O LYS G 65 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN G 75 " --> pdb=" O GLY G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 93 removed outlier: 3.624A pdb=" N HIS G 92 " --> pdb=" O ASP G 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.336A 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 97 through 98 Processing sheet with id=AA4, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.122A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA6, first strand: chain 'F' and resid 96 through 98 removed outlier: 6.674A pdb=" N THR F 96 " --> pdb=" O THR C 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 325 hydrogen bonds defined for protein. 969 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 169 hydrogen bonds 338 hydrogen bond angles 0 basepair planarities 66 basepair parallelities 163 stacking parallelities Total time for adding SS restraints: 1.62 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1683 1.33 - 1.45: 3039 1.45 - 1.57: 4417 1.57 - 1.68: 372 1.68 - 1.80: 28 Bond restraints: 9539 Sorted by residual: bond pdb=" CB GLU B 53 " pdb=" CG GLU B 53 " ideal model delta sigma weight residual 1.520 1.575 -0.055 3.00e-02 1.11e+03 3.38e+00 bond pdb=" CB GLU F 53 " pdb=" CG GLU F 53 " ideal model delta sigma weight residual 1.520 1.574 -0.054 3.00e-02 1.11e+03 3.30e+00 bond pdb=" C4' DC J 64 " pdb=" O4' DC J 64 " ideal model delta sigma weight residual 1.450 1.415 0.035 2.00e-02 2.50e+03 3.08e+00 bond pdb=" C3' DG I 38 " pdb=" C2' DG I 38 " ideal model delta sigma weight residual 1.525 1.559 -0.034 2.00e-02 2.50e+03 2.89e+00 bond pdb=" C4' DC I 85 " pdb=" O4' DC I 85 " ideal model delta sigma weight residual 1.450 1.417 0.033 2.00e-02 2.50e+03 2.70e+00 ... (remaining 9534 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 12268 1.47 - 2.94: 1217 2.94 - 4.40: 156 4.40 - 5.87: 32 5.87 - 7.34: 12 Bond angle restraints: 13685 Sorted by residual: angle pdb=" C2' DG I 53 " pdb=" C1' DG I 53 " pdb=" N9 DG I 53 " ideal model delta sigma weight residual 113.50 120.84 -7.34 1.50e+00 4.44e-01 2.39e+01 angle pdb=" C2' DG I 32 " pdb=" C1' DG I 32 " pdb=" N9 DG I 32 " ideal model delta sigma weight residual 113.50 120.34 -6.84 1.50e+00 4.44e-01 2.08e+01 angle pdb=" C2' DT I 57 " pdb=" C1' DT I 57 " pdb=" N1 DT I 57 " ideal model delta sigma weight residual 113.50 120.07 -6.57 1.50e+00 4.44e-01 1.92e+01 angle pdb=" CB GLU F 53 " pdb=" CG GLU F 53 " pdb=" CD GLU F 53 " ideal model delta sigma weight residual 112.60 119.76 -7.16 1.70e+00 3.46e-01 1.77e+01 angle pdb=" CB GLU B 53 " pdb=" CG GLU B 53 " pdb=" CD GLU B 53 " ideal model delta sigma weight residual 112.60 119.74 -7.14 1.70e+00 3.46e-01 1.76e+01 ... (remaining 13680 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.38: 4355 33.38 - 66.75: 879 66.75 - 100.13: 17 100.13 - 133.51: 1 133.51 - 166.88: 6 Dihedral angle restraints: 5258 sinusoidal: 3340 harmonic: 1918 Sorted by residual: dihedral pdb=" C4' DT J 32 " pdb=" C3' DT J 32 " pdb=" O3' DT J 32 " pdb=" P DG J 33 " ideal model delta sinusoidal sigma weight residual 220.00 53.12 166.88 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DT I 89 " pdb=" C3' DT I 89 " pdb=" O3' DT I 89 " pdb=" P DA I 90 " ideal model delta sinusoidal sigma weight residual 220.00 65.43 154.57 1 3.50e+01 8.16e-04 1.49e+01 dihedral pdb=" CA HIS C 92 " pdb=" C HIS C 92 " pdb=" N ASN C 93 " pdb=" CA ASN C 93 " ideal model delta harmonic sigma weight residual 180.00 160.72 19.28 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 5255 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1464 0.101 - 0.201: 117 0.201 - 0.302: 2 0.302 - 0.402: 1 0.402 - 0.503: 2 Chirality restraints: 1586 Sorted by residual: chirality pdb=" C1' DG I 53 " pdb=" O4' DG I 53 " pdb=" C2' DG I 53 " pdb=" N9 DG I 53 " both_signs ideal model delta sigma weight residual False 2.42 1.92 0.50 2.00e-01 2.50e+01 6.32e+00 chirality pdb=" C1' DT I 57 " pdb=" O4' DT I 57 " pdb=" C2' DT I 57 " pdb=" N1 DT I 57 " both_signs ideal model delta sigma weight residual False 2.47 1.99 0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" C1' DC J 28 " pdb=" O4' DC J 28 " pdb=" C2' DC J 28 " pdb=" N1 DC J 28 " both_signs ideal model delta sigma weight residual False 2.47 2.15 0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 1583 not shown) Planarity restraints: 1080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 117 " 0.021 2.00e-02 2.50e+03 4.80e-02 6.33e+01 pdb=" N9 DA I 117 " -0.122 2.00e-02 2.50e+03 pdb=" C8 DA I 117 " 0.095 2.00e-02 2.50e+03 pdb=" N7 DA I 117 " -0.014 2.00e-02 2.50e+03 pdb=" C5 DA I 117 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DA I 117 " -0.002 2.00e-02 2.50e+03 pdb=" N6 DA I 117 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DA I 117 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 117 " 0.020 2.00e-02 2.50e+03 pdb=" N3 DA I 117 " 0.017 2.00e-02 2.50e+03 pdb=" C4 DA I 117 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 116 " 0.038 2.00e-02 2.50e+03 3.97e-02 3.55e+01 pdb=" N1 DC J 116 " -0.095 2.00e-02 2.50e+03 pdb=" C2 DC J 116 " 0.057 2.00e-02 2.50e+03 pdb=" O2 DC J 116 " -0.014 2.00e-02 2.50e+03 pdb=" N3 DC J 116 " -0.008 2.00e-02 2.50e+03 pdb=" C4 DC J 116 " -0.001 2.00e-02 2.50e+03 pdb=" N4 DC J 116 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DC J 116 " 0.014 2.00e-02 2.50e+03 pdb=" C6 DC J 116 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 32 " -0.063 2.00e-02 2.50e+03 2.80e-02 2.36e+01 pdb=" N9 DG I 32 " 0.070 2.00e-02 2.50e+03 pdb=" C8 DG I 32 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DG I 32 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DG I 32 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DG I 32 " -0.007 2.00e-02 2.50e+03 pdb=" O6 DG I 32 " -0.016 2.00e-02 2.50e+03 pdb=" N1 DG I 32 " -0.007 2.00e-02 2.50e+03 pdb=" C2 DG I 32 " 0.003 2.00e-02 2.50e+03 pdb=" N2 DG I 32 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 32 " 0.008 2.00e-02 2.50e+03 pdb=" C4 DG I 32 " 0.006 2.00e-02 2.50e+03 ... (remaining 1077 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 831 2.72 - 3.26: 7789 3.26 - 3.81: 16217 3.81 - 4.35: 21301 4.35 - 4.90: 30325 Nonbonded interactions: 76463 Sorted by model distance: nonbonded pdb=" OE1 GLU D 76 " pdb=" NH2 ARG D 79 " model vdw 2.169 3.120 nonbonded pdb=" OE1 GLU H 76 " pdb=" NH2 ARG H 79 " model vdw 2.170 3.120 nonbonded pdb=" O HIS F 75 " pdb=" NH1 ARG H 92 " model vdw 2.248 3.120 nonbonded pdb=" N2 DG I 32 " pdb=" O2 DC J 116 " model vdw 2.254 3.120 nonbonded pdb=" OP2 DA J 91 " pdb=" NH2 ARG E 69 " model vdw 2.267 3.120 ... (remaining 76458 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' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } 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=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: 1.260 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.660 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 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 : 0.006 0.055 9539 Z= 0.300 Angle : 0.931 7.338 13685 Z= 0.578 Chirality : 0.058 0.503 1586 Planarity : 0.010 0.062 1080 Dihedral : 25.701 166.884 4014 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.14 % Allowed : 2.85 % Favored : 95.02 % 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 are not related in a simple way. whole: -6.14 (0.18), residues: 640 helix: -4.12 (0.10), residues: 458 sheet: None (None), residues: 0 loop : -3.19 (0.32), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 78 TYR 0.026 0.003 TYR B 51 PHE 0.021 0.002 PHE A 67 HIS 0.011 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00649 ( 9539) covalent geometry : angle 0.93099 (13685) hydrogen bonds : bond 0.14542 ( 494) hydrogen bonds : angle 6.10090 ( 1307) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 162 time to evaluate : 0.299 Fit side-chains REVERT: B 84 MET cc_start: 0.7144 (mmm) cc_final: 0.6922 (tpp) REVERT: C 89 MET cc_start: 0.7912 (ptt) cc_final: 0.7111 (tpt) REVERT: G 89 MET cc_start: 0.7988 (ptt) cc_final: 0.7159 (tpt) outliers start: 12 outliers final: 0 residues processed: 168 average time/residue: 0.6392 time to fit residues: 113.5048 Evaluate side-chains 134 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 84 ASN D 109 HIS E 68 GLN H 84 ASN H 109 HIS C 72 ASN G 72 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.185939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.161692 restraints weight = 11387.842| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 1.06 r_work: 0.3734 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3628 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9539 Z= 0.178 Angle : 0.630 5.406 13685 Z= 0.366 Chirality : 0.037 0.151 1586 Planarity : 0.006 0.048 1080 Dihedral : 30.822 172.917 2754 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.02 % Allowed : 13.35 % Favored : 83.63 % 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 are not related in a simple way. whole: -2.49 (0.27), residues: 640 helix: -1.24 (0.20), residues: 478 sheet: None (None), residues: 0 loop : -2.47 (0.37), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 72 TYR 0.014 0.001 TYR F 51 PHE 0.011 0.002 PHE A 78 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 9539) covalent geometry : angle 0.62996 (13685) hydrogen bonds : bond 0.04193 ( 494) hydrogen bonds : angle 3.47075 ( 1307) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.292 Fit side-chains REVERT: A 73 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.6671 (tp30) REVERT: B 84 MET cc_start: 0.8084 (mmm) cc_final: 0.7869 (tpp) REVERT: D 37 TYR cc_start: 0.8494 (m-80) cc_final: 0.8205 (m-80) REVERT: D 46 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7547 (tptp) REVERT: E 73 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.6712 (tp30) outliers start: 17 outliers final: 6 residues processed: 135 average time/residue: 0.5727 time to fit residues: 82.3383 Evaluate side-chains 134 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 99 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 45 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN D 63 ASN E 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.173247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.149500 restraints weight = 11237.067| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 1.04 r_work: 0.3600 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9539 Z= 0.205 Angle : 0.624 5.521 13685 Z= 0.362 Chirality : 0.039 0.161 1586 Planarity : 0.005 0.041 1080 Dihedral : 30.833 166.720 2754 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 4.98 % Allowed : 14.77 % Favored : 80.25 % 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 are not related in a simple way. whole: -0.71 (0.31), residues: 640 helix: 0.10 (0.23), residues: 484 sheet: None (None), residues: 0 loop : -2.05 (0.39), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 72 TYR 0.013 0.001 TYR B 51 PHE 0.017 0.002 PHE C 29 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 9539) covalent geometry : angle 0.62441 (13685) hydrogen bonds : bond 0.04229 ( 494) hydrogen bonds : angle 3.26327 ( 1307) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.246 Fit side-chains REVERT: B 84 MET cc_start: 0.8233 (mmm) cc_final: 0.8019 (tpp) REVERT: D 39 ILE cc_start: 0.8521 (tp) cc_final: 0.8202 (mp) REVERT: H 42 TYR cc_start: 0.7717 (t80) cc_final: 0.6886 (t80) REVERT: C 49 ARG cc_start: 0.7648 (tpt170) cc_final: 0.7445 (ttm170) REVERT: G 49 ARG cc_start: 0.7600 (tpt170) cc_final: 0.7359 (ttm170) outliers start: 28 outliers final: 9 residues processed: 149 average time/residue: 0.6118 time to fit residues: 96.3927 Evaluate side-chains 140 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 99 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 14 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.175081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.150932 restraints weight = 11211.576| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 1.03 r_work: 0.3621 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9539 Z= 0.165 Angle : 0.578 5.468 13685 Z= 0.338 Chirality : 0.036 0.154 1586 Planarity : 0.005 0.065 1080 Dihedral : 30.828 171.559 2754 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.74 % Allowed : 19.40 % Favored : 76.87 % 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 are not related in a simple way. whole: 0.23 (0.31), residues: 640 helix: 0.80 (0.23), residues: 484 sheet: None (None), residues: 0 loop : -1.77 (0.40), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 72 TYR 0.009 0.001 TYR G 61 PHE 0.007 0.001 PHE C 29 HIS 0.002 0.000 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 9539) covalent geometry : angle 0.57776 (13685) hydrogen bonds : bond 0.03634 ( 494) hydrogen bonds : angle 3.03423 ( 1307) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.237 Fit side-chains REVERT: A 73 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.6641 (tp30) REVERT: E 73 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6567 (tp30) REVERT: H 42 TYR cc_start: 0.7645 (t80) cc_final: 0.6866 (t80) REVERT: C 49 ARG cc_start: 0.7650 (tpt170) cc_final: 0.7442 (ttm170) REVERT: G 49 ARG cc_start: 0.7629 (tpt170) cc_final: 0.7376 (ttm170) outliers start: 21 outliers final: 11 residues processed: 137 average time/residue: 0.6909 time to fit residues: 99.8655 Evaluate side-chains 145 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 99 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 7 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 39 optimal weight: 9.9990 chunk 30 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.175386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.151390 restraints weight = 11088.644| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.03 r_work: 0.3629 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9539 Z= 0.160 Angle : 0.561 5.438 13685 Z= 0.329 Chirality : 0.035 0.150 1586 Planarity : 0.004 0.049 1080 Dihedral : 30.647 173.504 2754 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.74 % Allowed : 20.28 % Favored : 75.98 % 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 are not related in a simple way. whole: 0.99 (0.32), residues: 640 helix: 1.37 (0.23), residues: 484 sheet: None (None), residues: 0 loop : -1.58 (0.40), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 72 TYR 0.010 0.001 TYR F 51 PHE 0.010 0.001 PHE G 29 HIS 0.002 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 9539) covalent geometry : angle 0.56053 (13685) hydrogen bonds : bond 0.03591 ( 494) hydrogen bonds : angle 2.91001 ( 1307) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.230 Fit side-chains REVERT: D 63 ASN cc_start: 0.8109 (m110) cc_final: 0.7831 (m-40) REVERT: H 38 SER cc_start: 0.9211 (OUTLIER) cc_final: 0.8975 (m) outliers start: 21 outliers final: 9 residues processed: 141 average time/residue: 0.6775 time to fit residues: 100.8646 Evaluate side-chains 142 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 99 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 57 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 19 optimal weight: 0.3980 chunk 18 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3929 r_free = 0.3929 target = 0.169068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.145105 restraints weight = 10982.587| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.03 r_work: 0.3551 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9539 Z= 0.208 Angle : 0.603 5.652 13685 Z= 0.350 Chirality : 0.038 0.169 1586 Planarity : 0.005 0.043 1080 Dihedral : 30.929 172.495 2754 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.91 % Allowed : 21.71 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.32), residues: 640 helix: 1.34 (0.23), residues: 486 sheet: None (None), residues: 0 loop : -1.57 (0.41), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 86 TYR 0.014 0.001 TYR F 51 PHE 0.015 0.002 PHE C 29 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 9539) covalent geometry : angle 0.60317 (13685) hydrogen bonds : bond 0.03869 ( 494) hydrogen bonds : angle 3.07846 ( 1307) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6667 (tp30) REVERT: D 42 TYR cc_start: 0.7876 (t80) cc_final: 0.7297 (t80) REVERT: E 73 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.6678 (tp30) REVERT: H 38 SER cc_start: 0.9227 (OUTLIER) cc_final: 0.8986 (m) REVERT: H 86 ARG cc_start: 0.7327 (mtp85) cc_final: 0.7124 (mtt90) outliers start: 22 outliers final: 10 residues processed: 141 average time/residue: 0.6969 time to fit residues: 103.8074 Evaluate side-chains 149 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 99 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 20 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 62 optimal weight: 0.0170 chunk 44 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 25 optimal weight: 0.0870 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 = 0.3942 r_free = 0.3942 target = 0.170359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.146453 restraints weight = 11010.944| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 1.03 r_work: 0.3568 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9539 Z= 0.157 Angle : 0.597 6.445 13685 Z= 0.345 Chirality : 0.036 0.163 1586 Planarity : 0.004 0.040 1080 Dihedral : 30.933 173.260 2754 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.02 % Allowed : 22.78 % Favored : 74.20 % 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 are not related in a simple way. whole: 1.18 (0.32), residues: 640 helix: 1.49 (0.23), residues: 486 sheet: None (None), residues: 0 loop : -1.51 (0.41), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 86 TYR 0.012 0.001 TYR F 51 PHE 0.013 0.001 PHE G 29 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 9539) covalent geometry : angle 0.59686 (13685) hydrogen bonds : bond 0.03712 ( 494) hydrogen bonds : angle 3.06023 ( 1307) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6647 (tp30) REVERT: D 42 TYR cc_start: 0.7806 (t80) cc_final: 0.7206 (t80) REVERT: D 63 ASN cc_start: 0.8175 (m110) cc_final: 0.7882 (m-40) REVERT: E 73 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.6641 (tp30) REVERT: H 38 SER cc_start: 0.9235 (OUTLIER) cc_final: 0.8977 (m) REVERT: H 86 ARG cc_start: 0.7300 (mtp85) cc_final: 0.7063 (mtt90) REVERT: G 47 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8083 (mp) outliers start: 17 outliers final: 9 residues processed: 143 average time/residue: 0.6656 time to fit residues: 100.4455 Evaluate side-chains 148 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 99 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 50 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3942 r_free = 0.3942 target = 0.170405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.146495 restraints weight = 10939.869| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 1.02 r_work: 0.3570 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.5091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9539 Z= 0.170 Angle : 0.586 6.084 13685 Z= 0.340 Chirality : 0.037 0.170 1586 Planarity : 0.005 0.093 1080 Dihedral : 30.902 174.295 2754 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.67 % Allowed : 22.78 % Favored : 74.56 % 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 are not related in a simple way. whole: 1.29 (0.32), residues: 640 helix: 1.58 (0.23), residues: 486 sheet: None (None), residues: 0 loop : -1.49 (0.41), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 86 TYR 0.014 0.001 TYR D 40 PHE 0.012 0.001 PHE C 29 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 9539) covalent geometry : angle 0.58586 (13685) hydrogen bonds : bond 0.03636 ( 494) hydrogen bonds : angle 3.01297 ( 1307) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.6650 (tp30) REVERT: D 63 ASN cc_start: 0.8175 (m110) cc_final: 0.7873 (m-40) REVERT: E 73 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.6682 (tp30) REVERT: H 38 SER cc_start: 0.9229 (OUTLIER) cc_final: 0.8989 (m) REVERT: H 40 TYR cc_start: 0.8687 (m-80) cc_final: 0.8483 (m-80) REVERT: H 86 ARG cc_start: 0.7322 (mtp85) cc_final: 0.7078 (mtt90) REVERT: G 47 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8048 (mp) outliers start: 15 outliers final: 7 residues processed: 138 average time/residue: 0.6890 time to fit residues: 100.3015 Evaluate side-chains 145 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 99 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 0.0970 chunk 29 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3949 r_free = 0.3949 target = 0.170938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.147075 restraints weight = 10935.756| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 1.03 r_work: 0.3575 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.5097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9539 Z= 0.162 Angle : 0.582 5.871 13685 Z= 0.339 Chirality : 0.037 0.172 1586 Planarity : 0.005 0.041 1080 Dihedral : 30.892 174.910 2754 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.49 % Allowed : 23.13 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.32), residues: 640 helix: 1.62 (0.23), residues: 486 sheet: None (None), residues: 0 loop : -1.49 (0.41), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 86 TYR 0.010 0.001 TYR F 51 PHE 0.013 0.001 PHE C 29 HIS 0.002 0.000 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 9539) covalent geometry : angle 0.58177 (13685) hydrogen bonds : bond 0.03615 ( 494) hydrogen bonds : angle 3.02358 ( 1307) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 ARG cc_start: 0.8520 (mtt-85) cc_final: 0.8168 (mtt-85) REVERT: A 73 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.6641 (tp30) REVERT: D 63 ASN cc_start: 0.8198 (m110) cc_final: 0.7933 (m-40) REVERT: E 73 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.6667 (tp30) REVERT: H 38 SER cc_start: 0.9228 (OUTLIER) cc_final: 0.8994 (m) REVERT: G 47 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8434 (tp) outliers start: 14 outliers final: 9 residues processed: 138 average time/residue: 0.6564 time to fit residues: 95.5294 Evaluate side-chains 146 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 99 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 4 optimal weight: 3.9990 chunk 71 optimal weight: 0.0980 chunk 32 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- 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 = 0.3953 r_free = 0.3953 target = 0.171527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.147638 restraints weight = 10959.148| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.03 r_work: 0.3590 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.5115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9539 Z= 0.160 Angle : 0.582 6.390 13685 Z= 0.338 Chirality : 0.036 0.160 1586 Planarity : 0.005 0.041 1080 Dihedral : 30.880 175.447 2754 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.31 % Allowed : 23.67 % Favored : 74.02 % 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 are not related in a simple way. whole: 1.37 (0.32), residues: 640 helix: 1.64 (0.23), residues: 486 sheet: None (None), residues: 0 loop : -1.48 (0.41), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 86 TYR 0.013 0.001 TYR D 40 PHE 0.012 0.001 PHE C 29 HIS 0.002 0.000 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 9539) covalent geometry : angle 0.58150 (13685) hydrogen bonds : bond 0.03576 ( 494) hydrogen bonds : angle 3.01248 ( 1307) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 ARG cc_start: 0.8527 (mtt-85) cc_final: 0.8178 (mtt-85) REVERT: A 73 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.6630 (tp30) REVERT: D 63 ASN cc_start: 0.8194 (m110) cc_final: 0.7886 (m110) REVERT: E 73 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.6643 (tp30) REVERT: H 38 SER cc_start: 0.9223 (OUTLIER) cc_final: 0.8998 (m) REVERT: G 47 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8444 (tp) outliers start: 13 outliers final: 9 residues processed: 139 average time/residue: 0.6990 time to fit residues: 102.5118 Evaluate side-chains 147 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 99 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 37 optimal weight: 0.0470 chunk 78 optimal weight: 0.0570 chunk 73 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 = 0.3957 r_free = 0.3957 target = 0.171822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.148089 restraints weight = 10862.728| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 1.02 r_work: 0.3600 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9539 Z= 0.153 Angle : 0.580 6.180 13685 Z= 0.337 Chirality : 0.036 0.160 1586 Planarity : 0.005 0.040 1080 Dihedral : 30.872 175.956 2754 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.14 % Allowed : 24.02 % Favored : 73.84 % 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 are not related in a simple way. whole: 1.40 (0.32), residues: 640 helix: 1.66 (0.23), residues: 486 sheet: None (None), residues: 0 loop : -1.47 (0.41), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 86 TYR 0.012 0.001 TYR H 40 PHE 0.011 0.001 PHE C 29 HIS 0.002 0.000 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 9539) covalent geometry : angle 0.57956 (13685) hydrogen bonds : bond 0.03555 ( 494) hydrogen bonds : angle 3.00459 ( 1307) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3082.45 seconds wall clock time: 53 minutes 9.31 seconds (3189.31 seconds total)