Starting phenix.real_space_refine on Thu Feb 13 07:17:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m4g_30077/02_2025/6m4g_30077.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m4g_30077/02_2025/6m4g_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_30077/02_2025/6m4g_30077.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m4g_30077/02_2025/6m4g_30077.map" model { file = "/net/cci-nas-00/data/ceres_data/6m4g_30077/02_2025/6m4g_30077.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m4g_30077/02_2025/6m4g_30077.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.80, per 1000 atoms: 0.64 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: 2.51 Conformation dependent library (CDL) restraints added in 671.4 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: 3.87 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: 2.89 Time building geometry restraints manager: 2.79 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 25.620 Find NCS groups from input model: 0.190 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:12.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 40.340 ------------------------------------------------------------------------------- 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= 0.362 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 (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: -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 HIS 0.011 0.002 HIS B 75 PHE 0.021 0.002 PHE A 67 TYR 0.026 0.003 TYR B 51 ARG 0.005 0.001 ARG B 78 *********************** 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 : 0.785 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: 1.3268 time to fit residues: 236.2232 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 : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 20 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4098 r_free = 0.4098 target = 0.185285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.160934 restraints weight = 11298.525| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 1.07 r_work: 0.3729 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2556 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= 0.215 Angle : 0.629 5.373 13685 Z= 0.366 Chirality : 0.038 0.153 1586 Planarity : 0.006 0.048 1080 Dihedral : 30.888 172.209 2754 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.56 % Allowed : 12.81 % 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 (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: -2.49 (0.27), residues: 640 helix: -1.24 (0.20), residues: 478 sheet: None (None), residues: 0 loop : -2.46 (0.37), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.011 0.002 PHE A 67 TYR 0.015 0.001 TYR F 51 ARG 0.006 0.001 ARG A 72 *********************** 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: 20 poor density : 128 time to evaluate : 0.703 Fit side-chains REVERT: A 73 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.6671 (tp30) REVERT: B 84 MET cc_start: 0.8091 (mmm) cc_final: 0.7874 (tpp) REVERT: D 37 TYR cc_start: 0.8488 (m-80) cc_final: 0.8280 (m-80) REVERT: D 46 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7530 (tptp) REVERT: E 73 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.6715 (tp30) outliers start: 20 outliers final: 7 residues processed: 135 average time/residue: 1.1930 time to fit residues: 172.1212 Evaluate side-chains 133 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain D residue 38 SER 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 32 optimal weight: 0.8980 chunk 69 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 H 63 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.168027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.144346 restraints weight = 11252.048| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 1.05 r_work: 0.3544 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 9539 Z= 0.331 Angle : 0.675 5.776 13685 Z= 0.388 Chirality : 0.042 0.179 1586 Planarity : 0.005 0.045 1080 Dihedral : 31.076 164.731 2754 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 4.09 % Allowed : 15.66 % 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 (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: -0.80 (0.31), residues: 640 helix: 0.04 (0.22), residues: 484 sheet: None (None), residues: 0 loop : -2.08 (0.39), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.018 0.002 PHE G 29 TYR 0.017 0.002 TYR B 51 ARG 0.005 0.001 ARG A 72 *********************** 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 163 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.833 Fit side-chains REVERT: A 73 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.6806 (tp30) REVERT: B 84 MET cc_start: 0.8252 (mmm) cc_final: 0.8014 (tpp) REVERT: D 38 SER cc_start: 0.9028 (OUTLIER) cc_final: 0.8803 (m) REVERT: D 42 TYR cc_start: 0.7805 (t80) cc_final: 0.7261 (t80) REVERT: E 73 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.6729 (tp30) REVERT: C 89 MET cc_start: 0.8105 (ptm) cc_final: 0.7166 (tpt) REVERT: G 89 MET cc_start: 0.8230 (ptm) cc_final: 0.7209 (tpt) outliers start: 23 outliers final: 7 residues processed: 146 average time/residue: 1.3810 time to fit residues: 213.2836 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 : 0.721 ------------------------------------------------------------------------------- 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 38 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 22 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 chunk 56 optimal weight: 0.2980 chunk 14 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3946 r_free = 0.3946 target = 0.170998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.147230 restraints weight = 11025.416| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 1.03 r_work: 0.3578 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9539 Z= 0.196 Angle : 0.609 5.462 13685 Z= 0.356 Chirality : 0.038 0.193 1586 Planarity : 0.005 0.041 1080 Dihedral : 31.111 165.677 2754 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.91 % Allowed : 19.93 % Favored : 76.16 % 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: 0.00 (0.31), residues: 640 helix: 0.60 (0.23), residues: 484 sheet: None (None), residues: 0 loop : -1.73 (0.41), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 82 PHE 0.015 0.002 PHE G 29 TYR 0.013 0.001 TYR F 51 ARG 0.005 0.001 ARG C 80 *********************** 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 156 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.746 Fit side-chains REVERT: A 73 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.6757 (tp30) REVERT: B 84 MET cc_start: 0.8173 (mmm) cc_final: 0.7952 (tpp) REVERT: E 73 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.6668 (tp30) REVERT: C 89 MET cc_start: 0.8003 (ptm) cc_final: 0.7072 (tpt) REVERT: G 89 MET cc_start: 0.8126 (ptm) cc_final: 0.7113 (tpt) outliers start: 22 outliers final: 7 residues processed: 140 average time/residue: 1.3195 time to fit residues: 195.9562 Evaluate side-chains 137 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 120 MET 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 64 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.162264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.138836 restraints weight = 10968.561| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.08 r_work: 0.3476 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.5143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 9539 Z= 0.419 Angle : 0.708 6.313 13685 Z= 0.405 Chirality : 0.045 0.204 1586 Planarity : 0.006 0.049 1080 Dihedral : 31.348 166.105 2754 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 4.27 % Allowed : 19.22 % Favored : 76.51 % 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: 0.12 (0.31), residues: 640 helix: 0.65 (0.23), residues: 498 sheet: None (None), residues: 0 loop : -1.74 (0.43), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.025 0.002 PHE C 29 TYR 0.018 0.002 TYR B 51 ARG 0.005 0.001 ARG G 80 *********************** 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 160 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.687 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.6784 (tp30) REVERT: A 77 ASP cc_start: 0.8344 (t70) cc_final: 0.8111 (t70) REVERT: D 42 TYR cc_start: 0.7908 (t80) cc_final: 0.7303 (t80) REVERT: E 73 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.6683 (tp30) REVERT: E 77 ASP cc_start: 0.8317 (t70) cc_final: 0.8019 (t70) outliers start: 24 outliers final: 11 residues processed: 142 average time/residue: 1.3170 time to fit residues: 198.1483 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 : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 101 LEU 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 39 ILE 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 68 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.165057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.141722 restraints weight = 10975.497| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.03 r_work: 0.3520 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.5162 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= 0.230 Angle : 0.635 6.570 13685 Z= 0.371 Chirality : 0.039 0.187 1586 Planarity : 0.005 0.063 1080 Dihedral : 31.378 168.046 2754 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.56 % Allowed : 19.93 % Favored : 76.51 % 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: 0.46 (0.32), residues: 640 helix: 0.92 (0.23), residues: 498 sheet: None (None), residues: 0 loop : -1.75 (0.42), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 92 PHE 0.015 0.002 PHE G 29 TYR 0.013 0.001 TYR F 51 ARG 0.006 0.001 ARG A 72 *********************** 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 161 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.6810 (tp30) REVERT: E 73 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.6716 (tp30) REVERT: E 77 ASP cc_start: 0.8372 (t70) cc_final: 0.8090 (t70) REVERT: G 24 ARG cc_start: 0.5861 (OUTLIER) cc_final: 0.5094 (ttt-90) outliers start: 20 outliers final: 9 residues processed: 148 average time/residue: 1.3402 time to fit residues: 210.0677 Evaluate side-chains 151 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 118 THR 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 24 ARG 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 0 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.164479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.141232 restraints weight = 11111.738| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.04 r_work: 0.3489 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.5407 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= 0.299 Angle : 0.631 5.625 13685 Z= 0.366 Chirality : 0.040 0.184 1586 Planarity : 0.005 0.046 1080 Dihedral : 31.218 173.858 2754 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.85 % Allowed : 21.00 % Favored : 76.16 % 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: 0.66 (0.32), residues: 640 helix: 1.09 (0.23), residues: 498 sheet: None (None), residues: 0 loop : -1.82 (0.41), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 113 PHE 0.012 0.002 PHE E 78 TYR 0.015 0.001 TYR F 51 ARG 0.005 0.001 ARG A 72 *********************** 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 157 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 ARG cc_start: 0.8609 (mtt-85) cc_final: 0.8242 (mtt-85) REVERT: A 73 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.6784 (tp30) REVERT: A 77 ASP cc_start: 0.8282 (t70) cc_final: 0.8072 (t70) REVERT: D 86 ARG cc_start: 0.7757 (mtp85) cc_final: 0.7450 (mtt90) REVERT: E 77 ASP cc_start: 0.8306 (t70) cc_final: 0.8007 (t70) REVERT: G 24 ARG cc_start: 0.5888 (OUTLIER) cc_final: 0.5094 (ttt-90) outliers start: 16 outliers final: 8 residues processed: 147 average time/residue: 1.3387 time to fit residues: 208.7020 Evaluate side-chains 150 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 118 THR 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 24 ARG 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 5 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 78 optimal weight: 0.0370 chunk 47 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.166184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.142826 restraints weight = 11236.590| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 1.05 r_work: 0.3536 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.5424 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= 0.202 Angle : 0.624 8.829 13685 Z= 0.360 Chirality : 0.038 0.209 1586 Planarity : 0.005 0.042 1080 Dihedral : 31.236 174.621 2754 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.67 % Allowed : 21.53 % Favored : 75.80 % 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: 0.83 (0.32), residues: 640 helix: 1.21 (0.23), residues: 498 sheet: None (None), residues: 0 loop : -1.77 (0.42), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.014 0.001 PHE G 29 TYR 0.013 0.001 TYR D 40 ARG 0.005 0.001 ARG A 72 *********************** 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 153 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 ARG cc_start: 0.8543 (mtt-85) cc_final: 0.8190 (mtt-85) REVERT: A 73 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.6758 (tp30) REVERT: A 77 ASP cc_start: 0.8270 (t70) cc_final: 0.8060 (t70) REVERT: D 86 ARG cc_start: 0.7716 (mtp85) cc_final: 0.7444 (mtt90) REVERT: E 77 ASP cc_start: 0.8389 (t70) cc_final: 0.8097 (t70) REVERT: G 24 ARG cc_start: 0.5855 (OUTLIER) cc_final: 0.5068 (ttt-90) outliers start: 15 outliers final: 9 residues processed: 146 average time/residue: 1.3184 time to fit residues: 204.2068 Evaluate side-chains 147 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 118 THR 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 24 ARG 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 78 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.166876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.143610 restraints weight = 10975.655| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.05 r_work: 0.3521 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.5424 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= 0.219 Angle : 0.611 8.636 13685 Z= 0.355 Chirality : 0.037 0.180 1586 Planarity : 0.005 0.043 1080 Dihedral : 31.211 175.448 2754 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.14 % Allowed : 22.24 % Favored : 75.62 % 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: 0.89 (0.32), residues: 640 helix: 1.26 (0.23), residues: 498 sheet: None (None), residues: 0 loop : -1.75 (0.41), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS G 92 PHE 0.009 0.001 PHE G 29 TYR 0.014 0.001 TYR H 40 ARG 0.004 0.000 ARG C 80 *********************** 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 150 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 ARG cc_start: 0.8546 (mtt-85) cc_final: 0.8238 (mtt-85) REVERT: A 73 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.6758 (tp30) REVERT: A 77 ASP cc_start: 0.8267 (t70) cc_final: 0.8057 (t70) REVERT: D 86 ARG cc_start: 0.7738 (mtp85) cc_final: 0.7452 (mtt90) REVERT: E 77 ASP cc_start: 0.8382 (t70) cc_final: 0.8088 (t70) REVERT: G 24 ARG cc_start: 0.5863 (OUTLIER) cc_final: 0.5092 (ttt-90) outliers start: 12 outliers final: 9 residues processed: 143 average time/residue: 1.3244 time to fit residues: 200.8045 Evaluate side-chains 149 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 118 THR 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 24 ARG 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 0 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.163155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.139678 restraints weight = 11279.673| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.05 r_work: 0.3484 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.5515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9539 Z= 0.281 Angle : 0.628 7.981 13685 Z= 0.361 Chirality : 0.039 0.184 1586 Planarity : 0.005 0.044 1080 Dihedral : 31.242 176.001 2754 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.96 % Allowed : 23.13 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.32), residues: 640 helix: 1.31 (0.23), residues: 496 sheet: None (None), residues: 0 loop : -1.77 (0.40), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 75 PHE 0.013 0.002 PHE C 29 TYR 0.013 0.001 TYR B 51 ARG 0.004 0.001 ARG C 80 ********************** 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 150 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 ARG cc_start: 0.8607 (mtt-85) cc_final: 0.8292 (mtt-85) REVERT: A 73 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.6864 (tp30) REVERT: A 77 ASP cc_start: 0.8312 (t70) cc_final: 0.8082 (t70) REVERT: D 86 ARG cc_start: 0.7786 (mtp85) cc_final: 0.7440 (mtt90) REVERT: E 68 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8322 (tt0) REVERT: E 77 ASP cc_start: 0.8351 (t70) cc_final: 0.8069 (t70) REVERT: G 24 ARG cc_start: 0.5957 (OUTLIER) cc_final: 0.5244 (ttt-90) outliers start: 11 outliers final: 7 residues processed: 144 average time/residue: 1.3824 time to fit residues: 210.7177 Evaluate side-chains 149 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 139 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 68 GLN 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 24 ARG 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 6 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 61 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.162437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.139078 restraints weight = 11310.363| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.05 r_work: 0.3472 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.5618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9539 Z= 0.301 Angle : 0.632 6.852 13685 Z= 0.365 Chirality : 0.040 0.186 1586 Planarity : 0.005 0.043 1080 Dihedral : 31.292 176.217 2754 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.31 % Allowed : 22.78 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.32), residues: 640 helix: 1.31 (0.23), residues: 496 sheet: None (None), residues: 0 loop : -1.78 (0.40), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.014 0.002 PHE E 67 TYR 0.016 0.001 TYR C 61 ARG 0.005 0.001 ARG E 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6064.41 seconds wall clock time: 107 minutes 32.50 seconds (6452.50 seconds total)