Starting phenix.real_space_refine on Thu Aug 6 14:19:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8jhf_36264/08_2026/8jhf_36264.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jhf_36264/08_2026/8jhf_36264.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jhf_36264/08_2026/8jhf_36264.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jhf_36264/08_2026/8jhf_36264.map" model { file = "/net/cci-nas-00/data/ceres_data/8jhf_36264/08_2026/8jhf_36264.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jhf_36264/08_2026/8jhf_36264.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8jhf_36264/08_2026/8jhf_36264.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8jhf_36264/08_2026/8jhf_36264.cif" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1772 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 320 5.49 5 S 35 5.16 5 C 8219 2.51 5 N 2739 2.21 5 O 3389 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14703 Number of models: 1 Model: "" Number of chains: 12 Chain: "K" Number of atoms: 2014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2014 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain breaks: 2 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'TRP:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "A" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 776 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 672 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "C" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 850 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain: "D" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 693 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "G" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 825 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "H" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 740 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 3253 Classifications: {'DNA': 160} Link IDs: {'rna3p': 159} Chain: "J" Number of atoms: 3307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 3307 Classifications: {'DNA': 160} Link IDs: {'rna3p': 159} Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1726 SG CYS K 319 83.531 34.352 85.709 1.00145.38 S ATOM 1741 SG CYS K 321 84.756 36.893 84.198 1.00141.85 S ATOM 1766 SG CYS K 324 86.241 36.603 85.599 1.00143.31 S Time building chain proxies: 3.21, per 1000 atoms: 0.22 Number of scatterers: 14703 At special positions: 0 Unit cell: (110.4, 125.12, 142.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 35 16.00 P 320 15.00 O 3389 8.00 N 2739 7.00 C 8219 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: 1.27 Conformation dependent library (CDL) restraints added in 469.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 401 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 319 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 324 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 321 " 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1916 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 8 sheets defined 61.1% alpha, 2.3% beta 141 base pairs and 245 stacking pairs defined. Time for finding SS restraints: 2.13 Creating SS restraints... Processing helix chain 'K' and resid 77 through 94 removed outlier: 3.560A pdb=" N ASP K 90 " --> pdb=" O SER K 86 " (cutoff:3.500A) Proline residue: K 91 - end of helix Processing helix chain 'K' and resid 149 through 159 Processing helix chain 'K' and resid 160 through 170 Processing helix chain 'K' and resid 174 through 191 removed outlier: 3.689A pdb=" N PHE K 189 " --> pdb=" O TYR K 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 266 through 270 removed outlier: 3.583A pdb=" N PHE K 270 " --> pdb=" O PRO K 267 " (cutoff:3.500A) Processing helix chain 'K' and resid 321 through 327 Processing helix chain 'K' and resid 354 through 360 Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.511A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.790A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 113 removed outlier: 4.037A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.679A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.109A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 18 through 23 removed outlier: 3.705A pdb=" N ALA C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 38 Processing helix chain 'C' and resid 49 through 71 removed outlier: 3.793A pdb=" N ASN C 71 " --> pdb=" O GLU C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 77 Processing helix chain 'C' and resid 82 through 93 removed outlier: 3.709A pdb=" N ASP C 93 " --> pdb=" O ALA C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 100 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 53 through 81 removed outlier: 3.558A pdb=" N GLY D 57 " --> pdb=" O SER D 53 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.602A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 120 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.597A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.653A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.667A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 29 removed outlier: 4.061A pdb=" N ILE F 26 " --> pdb=" O ARG F 23 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.053A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL F 57 " --> pdb=" O GLU F 53 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 18 through 23 Processing helix chain 'G' and resid 28 through 37 removed outlier: 3.540A pdb=" N ILE G 32 " --> pdb=" O PRO G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 76 Processing helix chain 'G' and resid 82 through 93 removed outlier: 3.984A pdb=" N ASP G 93 " --> pdb=" O ALA G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 100 Processing helix chain 'G' and resid 114 through 119 removed outlier: 3.919A pdb=" N ILE G 118 " --> pdb=" O HIS G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 124 removed outlier: 3.837A pdb=" N GLN G 124 " --> pdb=" O LYS G 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 53 through 81 removed outlier: 3.678A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 98 Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.563A pdb=" N THR H 119 " --> pdb=" O VAL H 115 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 230 through 234 removed outlier: 4.324A pdb=" N ALA K 261 " --> pdb=" O LEU K 234 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 281 through 282 Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.904A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.590A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 45 through 46 removed outlier: 6.556A pdb=" N ARG C 45 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.129A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 45 through 46 removed outlier: 7.060A pdb=" N ARG G 45 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 80 through 81 431 hydrogen bonds defined for protein. 1263 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 365 hydrogen bonds 730 hydrogen bond angles 0 basepair planarities 141 basepair parallelities 245 stacking parallelities Total time for adding SS restraints: 3.09 Time building geometry restraints manager: 1.72 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: 3082 1.33 - 1.45: 4823 1.45 - 1.57: 7022 1.57 - 1.69: 638 1.69 - 1.81: 55 Bond restraints: 15620 Sorted by residual: bond pdb=" C3' DC I 82 " pdb=" C2' DC I 82 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.21e+01 bond pdb=" C3' DG J 148 " pdb=" C2' DG J 148 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.17e+01 bond pdb=" C3' DA I 75 " pdb=" C2' DA I 75 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.17e+01 bond pdb=" C3' DT I 99 " pdb=" C2' DT I 99 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 bond pdb=" C3' DG J 113 " pdb=" C2' DG J 113 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 ... (remaining 15615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 21943 2.27 - 4.55: 473 4.55 - 6.82: 24 6.82 - 9.10: 3 9.10 - 11.37: 1 Bond angle restraints: 22444 Sorted by residual: angle pdb=" O4' DG I 110 " pdb=" C4' DG I 110 " pdb=" C3' DG I 110 " ideal model delta sigma weight residual 106.00 102.86 3.14 6.00e-01 2.78e+00 2.74e+01 angle pdb=" O4' DG I 104 " pdb=" C4' DG I 104 " pdb=" C3' DG I 104 " ideal model delta sigma weight residual 106.00 103.19 2.81 6.00e-01 2.78e+00 2.19e+01 angle pdb=" N3 DT I 99 " pdb=" C4 DT I 99 " pdb=" O4 DT I 99 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.02e+01 angle pdb=" N LEU G 96 " pdb=" CA LEU G 96 " pdb=" C LEU G 96 " ideal model delta sigma weight residual 111.82 106.63 5.19 1.16e+00 7.43e-01 2.00e+01 angle pdb=" N3 DT J 93 " pdb=" C4 DT J 93 " pdb=" O4 DT J 93 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 ... (remaining 22439 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 7070 35.97 - 71.94: 1437 71.94 - 107.90: 24 107.90 - 143.87: 1 143.87 - 179.84: 5 Dihedral angle restraints: 8537 sinusoidal: 5566 harmonic: 2971 Sorted by residual: dihedral pdb=" C4' DT J 138 " pdb=" C3' DT J 138 " pdb=" O3' DT J 138 " pdb=" P DC J 139 " ideal model delta sinusoidal sigma weight residual -140.00 39.84 -179.84 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DA I 145 " pdb=" C3' DA I 145 " pdb=" O3' DA I 145 " pdb=" P DT I 146 " ideal model delta sinusoidal sigma weight residual 220.00 45.07 174.93 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT I 99 " pdb=" C3' DT I 99 " pdb=" O3' DT I 99 " pdb=" P DA I 100 " ideal model delta sinusoidal sigma weight residual 220.00 64.06 155.94 1 3.50e+01 8.16e-04 1.50e+01 ... (remaining 8534 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1544 0.035 - 0.069: 704 0.069 - 0.104: 225 0.104 - 0.138: 50 0.138 - 0.173: 10 Chirality restraints: 2533 Sorted by residual: chirality pdb=" C2' SAM K 402 " pdb=" C1' SAM K 402 " pdb=" C3' SAM K 402 " pdb=" O2' SAM K 402 " both_signs ideal model delta sigma weight residual False -2.76 -2.58 -0.17 2.00e-01 2.50e+01 7.48e-01 chirality pdb=" CA ASP D 48 " pdb=" N ASP D 48 " pdb=" C ASP D 48 " pdb=" CB ASP D 48 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.36e-01 chirality pdb=" CA ASP E 81 " pdb=" N ASP E 81 " pdb=" C ASP E 81 " pdb=" CB ASP E 81 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.11e-01 ... (remaining 2530 not shown) Planarity restraints: 1733 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE K 231 " 0.012 2.00e-02 2.50e+03 2.32e-02 5.40e+00 pdb=" C ILE K 231 " -0.040 2.00e-02 2.50e+03 pdb=" O ILE K 231 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA K 232 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 264 " 0.013 2.00e-02 2.50e+03 1.45e-02 5.28e+00 pdb=" CG TRP K 264 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP K 264 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP K 264 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP K 264 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP K 264 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP K 264 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 264 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 264 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP K 264 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS F 31 " -0.030 5.00e-02 4.00e+02 4.53e-02 3.28e+00 pdb=" N PRO F 32 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO F 32 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 32 " -0.025 5.00e-02 4.00e+02 ... (remaining 1730 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 422 2.67 - 3.23: 12731 3.23 - 3.78: 25247 3.78 - 4.34: 31782 4.34 - 4.90: 46876 Nonbonded interactions: 117058 Sorted by model distance: nonbonded pdb=" O THR K 284 " pdb=" OG1 THR K 288 " model vdw 2.111 3.040 nonbonded pdb=" O MET K 188 " pdb=" OG SER K 193 " model vdw 2.169 3.040 nonbonded pdb=" O2 DT I 157 " pdb=" N6 DA J 11 " model vdw 2.210 3.120 nonbonded pdb=" OG1 THR K 97 " pdb=" OD1 ASN K 208 " model vdw 2.224 3.040 nonbonded pdb=" OG1 THR K 97 " pdb=" O ASN K 208 " model vdw 2.231 3.040 ... (remaining 117053 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 41 through 134) selection = (chain 'E' and (resid 41 through 60 or (resid 61 and (name N or name CA or name \ C or name O or name CB )) or resid 62 through 134)) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 19 through 102) } ncs_group { reference = (chain 'C' and resid 16 through 124) selection = chain 'G' } ncs_group { reference = (chain 'D' and (resid 28 through 72 or (resid 73 through 74 and (name N or name \ CA or name C or name O or name CB )) or resid 75 through 122)) 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.040 Find NCS groups from input model: 0.150 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 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 0.058 15623 Z= 0.500 Angle : 0.763 11.372 22444 Z= 0.648 Chirality : 0.044 0.173 2533 Planarity : 0.004 0.045 1733 Dihedral : 27.171 179.840 6621 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.70 % Allowed : 0.35 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.59 (0.27), residues: 1007 helix: 1.90 (0.22), residues: 598 sheet: -0.18 (0.84), residues: 22 loop : -2.15 (0.27), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 83 TYR 0.025 0.001 TYR F 88 PHE 0.010 0.001 PHE K 281 TRP 0.037 0.004 TRP K 264 HIS 0.004 0.001 HIS K 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.50 (15620) covalent geometry : angle 0.76299 / 0.65 (22444) hydrogen bonds : bond 0.12945 / 8.82 ( 796) hydrogen bonds : angle 5.07210 / 3.54 ( 1993) metal coordination : bond 0.00281 / 0.14 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 157 time to evaluate : 0.395 Fit side-chains REVERT: K 100 MET cc_start: 0.7208 (pmm) cc_final: 0.6878 (pmm) REVERT: E 76 GLN cc_start: 0.8591 (tm-30) cc_final: 0.8325 (tm-30) REVERT: G 95 GLU cc_start: 0.7085 (mm-30) cc_final: 0.6652 (mm-30) REVERT: G 115 LYS cc_start: 0.7753 (ttmm) cc_final: 0.7519 (tptp) outliers start: 6 outliers final: 0 residues processed: 161 average time/residue: 0.1458 time to fit residues: 33.0577 Evaluate side-chains 134 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 50.0000 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 124 optimal weight: 40.0000 chunk 103 optimal weight: 30.0000 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 40.0000 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 0.0060 chunk 129 optimal weight: 50.0000 overall best weight: 2.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 181 HIS ** K 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 273 HIS ** K 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS E 108 ASN G 114 HIS ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.136794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.090429 restraints weight = 34089.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.090303 restraints weight = 19809.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.091127 restraints weight = 14314.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.091234 restraints weight = 13514.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.091209 restraints weight = 12167.169| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.0816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15623 Z= 0.176 Angle : 0.642 7.871 22444 Z= 0.380 Chirality : 0.046 0.287 2533 Planarity : 0.004 0.043 1733 Dihedral : 30.189 179.936 4626 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.41 % Allowed : 10.19 % Favored : 88.41 % 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: 0.87 (0.27), residues: 1007 helix: 2.12 (0.22), residues: 606 sheet: 0.18 (0.84), residues: 24 loop : -2.16 (0.28), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 76 TYR 0.021 0.002 TYR F 88 PHE 0.011 0.001 PHE K 178 TRP 0.009 0.002 TRP K 264 HIS 0.005 0.001 HIS G 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.18 (15620) covalent geometry : angle 0.64163 / 0.38 (22444) hydrogen bonds : bond 0.07081 / 4.57 ( 796) hydrogen bonds : angle 3.60993 / 2.53 ( 1993) metal coordination : bond 0.00251 / 0.13 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.408 Fit side-chains REVERT: K 100 MET cc_start: 0.7040 (pmm) cc_final: 0.6565 (pmm) REVERT: E 76 GLN cc_start: 0.8695 (tm-30) cc_final: 0.8442 (tm-30) REVERT: G 115 LYS cc_start: 0.7797 (ttmm) cc_final: 0.7554 (tptp) outliers start: 12 outliers final: 9 residues processed: 149 average time/residue: 0.1436 time to fit residues: 30.2321 Evaluate side-chains 137 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 253 MET Chi-restraints excluded: chain K residue 291 VAL Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 118 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 14 optimal weight: 8.9990 chunk 99 optimal weight: 50.0000 chunk 54 optimal weight: 5.9990 chunk 104 optimal weight: 40.0000 chunk 107 optimal weight: 30.0000 chunk 5 optimal weight: 6.9990 chunk 125 optimal weight: 40.0000 chunk 56 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 262 GLN ** K 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.134372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.086874 restraints weight = 34366.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.086794 restraints weight = 20145.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.087666 restraints weight = 14576.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.087609 restraints weight = 13905.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.087670 restraints weight = 12662.615| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15623 Z= 0.209 Angle : 0.658 7.407 22444 Z= 0.383 Chirality : 0.047 0.267 2533 Planarity : 0.004 0.044 1733 Dihedral : 30.405 179.959 4626 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.76 % Allowed : 14.87 % Favored : 83.37 % 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: 0.77 (0.27), residues: 1007 helix: 2.09 (0.22), residues: 606 sheet: 0.18 (0.89), residues: 22 loop : -2.27 (0.28), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 83 TYR 0.021 0.002 TYR F 88 PHE 0.011 0.001 PHE K 195 TRP 0.014 0.002 TRP K 264 HIS 0.006 0.001 HIS K 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.21 (15620) covalent geometry : angle 0.65811 / 0.38 (22444) hydrogen bonds : bond 0.07281 / 4.73 ( 796) hydrogen bonds : angle 3.59759 / 2.54 ( 1993) metal coordination : bond 0.00393 / 0.20 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.408 Fit side-chains REVERT: K 100 MET cc_start: 0.6986 (pmm) cc_final: 0.6499 (pmm) REVERT: K 188 MET cc_start: 0.7522 (tmm) cc_final: 0.7246 (tmm) REVERT: K 241 MET cc_start: 0.7517 (tmm) cc_final: 0.6894 (tmm) REVERT: E 76 GLN cc_start: 0.8755 (tm-30) cc_final: 0.8490 (tm-30) REVERT: G 115 LYS cc_start: 0.7828 (ttmm) cc_final: 0.7540 (tptp) outliers start: 15 outliers final: 10 residues processed: 152 average time/residue: 0.1449 time to fit residues: 31.0094 Evaluate side-chains 144 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 291 VAL Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 118 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 48 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 117 optimal weight: 40.0000 chunk 77 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 100 optimal weight: 50.0000 chunk 21 optimal weight: 8.9990 chunk 84 optimal weight: 3.9990 chunk 98 optimal weight: 50.0000 chunk 59 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 181 HIS K 316 ASN E 108 ASN ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.137054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.090559 restraints weight = 34447.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.090865 restraints weight = 20603.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.091776 restraints weight = 14191.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.091790 restraints weight = 13016.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.091844 restraints weight = 11938.295| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15623 Z= 0.147 Angle : 0.590 7.894 22444 Z= 0.352 Chirality : 0.043 0.279 2533 Planarity : 0.004 0.047 1733 Dihedral : 30.376 179.277 4626 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.11 % Allowed : 15.57 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.05 (0.27), residues: 1007 helix: 2.33 (0.22), residues: 606 sheet: -0.02 (0.86), residues: 24 loop : -2.17 (0.28), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 220 TYR 0.020 0.001 TYR H 80 PHE 0.012 0.001 PHE K 195 TRP 0.004 0.001 TRP K 264 HIS 0.004 0.001 HIS K 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.15 (15620) covalent geometry : angle 0.58976 / 0.35 (22444) hydrogen bonds : bond 0.05856 / 3.78 ( 796) hydrogen bonds : angle 3.22383 / 2.26 ( 1993) metal coordination : bond 0.00145 / 0.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.399 Fit side-chains REVERT: K 100 MET cc_start: 0.7050 (pmm) cc_final: 0.6372 (mmp) REVERT: K 188 MET cc_start: 0.7641 (tmm) cc_final: 0.7329 (tmm) REVERT: K 241 MET cc_start: 0.7491 (tmm) cc_final: 0.6830 (tmm) REVERT: A 73 GLU cc_start: 0.7798 (tt0) cc_final: 0.7446 (tt0) REVERT: E 76 GLN cc_start: 0.8694 (tm-30) cc_final: 0.8461 (tm-30) outliers start: 18 outliers final: 10 residues processed: 157 average time/residue: 0.1367 time to fit residues: 31.0581 Evaluate side-chains 148 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 138 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 291 VAL Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 118 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 129 optimal weight: 50.0000 chunk 0 optimal weight: 40.0000 chunk 121 optimal weight: 30.0000 chunk 114 optimal weight: 50.0000 chunk 74 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 120 optimal weight: 30.0000 chunk 2 optimal weight: 20.0000 chunk 71 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 108 ASN ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.134943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.087676 restraints weight = 33972.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.087806 restraints weight = 22792.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.088504 restraints weight = 16207.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.088691 restraints weight = 13765.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.088745 restraints weight = 12695.008| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15623 Z= 0.216 Angle : 0.655 7.471 22444 Z= 0.377 Chirality : 0.046 0.281 2533 Planarity : 0.004 0.044 1733 Dihedral : 30.473 178.714 4626 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.58 % Allowed : 16.39 % Favored : 81.03 % 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: 0.84 (0.27), residues: 1007 helix: 2.18 (0.22), residues: 604 sheet: -0.45 (0.81), residues: 24 loop : -2.24 (0.28), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 40 TYR 0.016 0.002 TYR F 88 PHE 0.010 0.001 PHE D 62 TRP 0.011 0.002 TRP K 264 HIS 0.006 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.22 (15620) covalent geometry : angle 0.65465 / 0.38 (22444) hydrogen bonds : bond 0.06936 / 4.51 ( 796) hydrogen bonds : angle 3.46159 / 2.45 ( 1993) metal coordination : bond 0.00417 / 0.21 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.410 Fit side-chains REVERT: K 100 MET cc_start: 0.7115 (pmm) cc_final: 0.6674 (pmm) REVERT: K 188 MET cc_start: 0.7682 (tmm) cc_final: 0.7340 (tmm) REVERT: K 241 MET cc_start: 0.7502 (tmm) cc_final: 0.6815 (tmm) REVERT: E 76 GLN cc_start: 0.8772 (tm-30) cc_final: 0.8479 (tm-30) outliers start: 22 outliers final: 15 residues processed: 155 average time/residue: 0.1356 time to fit residues: 30.3219 Evaluate side-chains 150 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 228 VAL Chi-restraints excluded: chain K residue 282 VAL Chi-restraints excluded: chain K residue 291 VAL Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 118 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 117 optimal weight: 40.0000 chunk 41 optimal weight: 0.9980 chunk 2 optimal weight: 20.0000 chunk 48 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 125 optimal weight: 40.0000 chunk 47 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 181 HIS D 46 HIS E 108 ASN ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.137477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.091067 restraints weight = 34219.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.091377 restraints weight = 25513.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.091509 restraints weight = 17177.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.091889 restraints weight = 16319.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.091889 restraints weight = 15315.278| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15623 Z= 0.139 Angle : 0.579 7.928 22444 Z= 0.346 Chirality : 0.042 0.286 2533 Planarity : 0.004 0.049 1733 Dihedral : 30.438 178.313 4626 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.99 % Allowed : 17.45 % Favored : 80.56 % 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: 1.11 (0.27), residues: 1007 helix: 2.43 (0.22), residues: 604 sheet: -0.48 (0.84), residues: 24 loop : -2.19 (0.28), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 40 TYR 0.016 0.001 TYR H 80 PHE 0.007 0.001 PHE B 61 TRP 0.006 0.001 TRP K 264 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.14 (15620) covalent geometry : angle 0.57914 / 0.35 (22444) hydrogen bonds : bond 0.05560 / 3.59 ( 796) hydrogen bonds : angle 3.09429 / 2.18 ( 1993) metal coordination : bond 0.00088 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.398 Fit side-chains REVERT: K 100 MET cc_start: 0.7123 (pmm) cc_final: 0.6444 (mmp) REVERT: K 188 MET cc_start: 0.7774 (tmm) cc_final: 0.7471 (tmm) REVERT: K 241 MET cc_start: 0.7467 (tmm) cc_final: 0.6795 (tmm) REVERT: E 76 GLN cc_start: 0.8702 (tm-30) cc_final: 0.8430 (tm-30) outliers start: 17 outliers final: 13 residues processed: 154 average time/residue: 0.1409 time to fit residues: 31.0701 Evaluate side-chains 150 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 228 VAL Chi-restraints excluded: chain K residue 291 VAL Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 118 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 124 optimal weight: 40.0000 chunk 60 optimal weight: 0.7980 chunk 58 optimal weight: 10.0000 chunk 97 optimal weight: 0.7980 chunk 15 optimal weight: 20.0000 chunk 128 optimal weight: 50.0000 chunk 30 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 119 optimal weight: 30.0000 overall best weight: 4.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 108 ASN ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.135023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.087816 restraints weight = 33600.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.088036 restraints weight = 21784.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.088630 restraints weight = 15922.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.088686 restraints weight = 13772.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.088767 restraints weight = 12756.408| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15623 Z= 0.216 Angle : 0.658 7.640 22444 Z= 0.377 Chirality : 0.046 0.287 2533 Planarity : 0.004 0.043 1733 Dihedral : 30.539 177.966 4626 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.11 % Allowed : 18.15 % Favored : 79.74 % 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: 0.81 (0.27), residues: 1007 helix: 2.13 (0.22), residues: 610 sheet: -0.41 (0.94), residues: 22 loop : -2.28 (0.28), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 83 TYR 0.027 0.002 TYR F 88 PHE 0.011 0.001 PHE D 62 TRP 0.012 0.002 TRP K 264 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.22 (15620) covalent geometry : angle 0.65780 / 0.38 (22444) hydrogen bonds : bond 0.07013 / 4.55 ( 796) hydrogen bonds : angle 3.43333 / 2.44 ( 1993) metal coordination : bond 0.00469 / 0.24 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.460 Fit side-chains REVERT: K 100 MET cc_start: 0.7113 (pmm) cc_final: 0.6672 (pmm) REVERT: K 178 PHE cc_start: 0.6268 (m-10) cc_final: 0.6015 (m-10) REVERT: K 241 MET cc_start: 0.7481 (tmm) cc_final: 0.6809 (tmm) REVERT: E 76 GLN cc_start: 0.8765 (tm-30) cc_final: 0.8446 (tm-30) outliers start: 18 outliers final: 15 residues processed: 152 average time/residue: 0.1373 time to fit residues: 30.1820 Evaluate side-chains 149 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 228 VAL Chi-restraints excluded: chain K residue 291 VAL Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 118 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 120 optimal weight: 30.0000 chunk 108 optimal weight: 30.0000 chunk 28 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 125 optimal weight: 40.0000 chunk 110 optimal weight: 40.0000 chunk 97 optimal weight: 2.9990 chunk 104 optimal weight: 40.0000 chunk 63 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 181 HIS D 46 HIS E 108 ASN ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.136157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.089267 restraints weight = 33987.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.089548 restraints weight = 22730.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.090149 restraints weight = 15598.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.090439 restraints weight = 13498.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.090423 restraints weight = 12498.408| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15623 Z= 0.158 Angle : 0.601 8.152 22444 Z= 0.354 Chirality : 0.043 0.293 2533 Planarity : 0.004 0.045 1733 Dihedral : 30.504 177.678 4626 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.58 % Allowed : 17.68 % Favored : 79.74 % 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: 0.95 (0.27), residues: 1007 helix: 2.32 (0.22), residues: 604 sheet: -0.65 (0.87), residues: 24 loop : -2.28 (0.28), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 40 TYR 0.014 0.001 TYR H 80 PHE 0.008 0.001 PHE H 62 TRP 0.012 0.002 TRP K 264 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.16 (15620) covalent geometry : angle 0.60109 / 0.35 (22444) hydrogen bonds : bond 0.06107 / 3.95 ( 796) hydrogen bonds : angle 3.21491 / 2.28 ( 1993) metal coordination : bond 0.00236 / 0.12 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.385 Fit side-chains REVERT: K 100 MET cc_start: 0.7146 (pmm) cc_final: 0.6692 (pmm) REVERT: K 178 PHE cc_start: 0.6247 (m-10) cc_final: 0.5969 (m-10) REVERT: K 188 MET cc_start: 0.7677 (tmm) cc_final: 0.7448 (tmm) REVERT: K 241 MET cc_start: 0.7501 (tmm) cc_final: 0.6805 (tmm) REVERT: K 271 ILE cc_start: 0.6627 (tp) cc_final: 0.6421 (mm) REVERT: E 76 GLN cc_start: 0.8724 (tm-30) cc_final: 0.8438 (tm-30) outliers start: 22 outliers final: 15 residues processed: 157 average time/residue: 0.1351 time to fit residues: 30.6376 Evaluate side-chains 152 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 228 VAL Chi-restraints excluded: chain K residue 282 VAL Chi-restraints excluded: chain K residue 291 VAL Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 118 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 74 optimal weight: 2.9990 chunk 99 optimal weight: 50.0000 chunk 6 optimal weight: 6.9990 chunk 125 optimal weight: 40.0000 chunk 75 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 98 optimal weight: 50.0000 chunk 72 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 181 HIS D 46 HIS E 108 ASN F 75 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.134783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.086980 restraints weight = 35617.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.088449 restraints weight = 19930.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.088985 restraints weight = 13544.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.089316 restraints weight = 11350.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.089366 restraints weight = 10804.165| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15623 Z= 0.142 Angle : 0.589 8.362 22444 Z= 0.347 Chirality : 0.042 0.290 2533 Planarity : 0.004 0.051 1733 Dihedral : 30.513 177.222 4626 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.11 % Allowed : 18.74 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.08 (0.27), residues: 1007 helix: 2.42 (0.22), residues: 604 sheet: -0.53 (0.92), residues: 24 loop : -2.24 (0.28), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 40 TYR 0.034 0.001 TYR F 88 PHE 0.007 0.001 PHE H 62 TRP 0.007 0.001 TRP K 264 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.14 (15620) covalent geometry : angle 0.58870 / 0.35 (22444) hydrogen bonds : bond 0.05519 / 3.56 ( 796) hydrogen bonds : angle 3.08415 / 2.18 ( 1993) metal coordination : bond 0.00143 / 0.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.392 Fit side-chains REVERT: K 100 MET cc_start: 0.6985 (pmm) cc_final: 0.6485 (pmm) REVERT: K 178 PHE cc_start: 0.6505 (m-10) cc_final: 0.6177 (m-10) REVERT: K 188 MET cc_start: 0.7588 (tmm) cc_final: 0.7327 (tmm) REVERT: K 241 MET cc_start: 0.7479 (tmm) cc_final: 0.6819 (tmm) REVERT: K 271 ILE cc_start: 0.6730 (tp) cc_final: 0.6459 (mm) REVERT: E 76 GLN cc_start: 0.8729 (tm-30) cc_final: 0.8433 (tm-30) REVERT: F 84 MET cc_start: 0.8251 (mmt) cc_final: 0.8009 (mmt) REVERT: G 95 GLU cc_start: 0.7564 (mp0) cc_final: 0.7022 (mp0) REVERT: H 102 GLU cc_start: 0.6935 (pm20) cc_final: 0.6375 (pm20) outliers start: 18 outliers final: 15 residues processed: 157 average time/residue: 0.1360 time to fit residues: 30.6194 Evaluate side-chains 155 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 228 VAL Chi-restraints excluded: chain K residue 291 VAL Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 118 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 26 optimal weight: 7.9990 chunk 27 optimal weight: 0.2980 chunk 45 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 99 optimal weight: 50.0000 chunk 44 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 4 optimal weight: 8.9990 chunk 107 optimal weight: 30.0000 chunk 116 optimal weight: 50.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 169 ASN K 181 HIS D 46 HIS E 108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.135717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.088330 restraints weight = 35682.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.089175 restraints weight = 19967.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.090625 restraints weight = 14192.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.090478 restraints weight = 10882.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.090588 restraints weight = 11255.464| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15623 Z= 0.134 Angle : 0.570 6.650 22444 Z= 0.338 Chirality : 0.041 0.289 2533 Planarity : 0.004 0.053 1733 Dihedral : 30.533 178.263 4626 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.87 % Allowed : 18.97 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.22 (0.27), residues: 1007 helix: 2.52 (0.21), residues: 606 sheet: -0.44 (0.93), residues: 24 loop : -2.16 (0.28), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 40 TYR 0.013 0.001 TYR F 88 PHE 0.006 0.001 PHE H 62 TRP 0.006 0.001 TRP K 264 HIS 0.004 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.13 (15620) covalent geometry : angle 0.56955 / 0.34 (22444) hydrogen bonds : bond 0.05032 / 3.23 ( 796) hydrogen bonds : angle 2.96813 / 2.09 ( 1993) metal coordination : bond 0.00090 / 0.05 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.408 Fit side-chains REVERT: K 100 MET cc_start: 0.6975 (pmm) cc_final: 0.6457 (pmm) REVERT: K 178 PHE cc_start: 0.6515 (m-10) cc_final: 0.6179 (m-10) REVERT: K 188 MET cc_start: 0.7669 (tmm) cc_final: 0.7415 (tmm) REVERT: K 241 MET cc_start: 0.7514 (tmm) cc_final: 0.7150 (tmm) REVERT: C 77 LYS cc_start: 0.8429 (mmtt) cc_final: 0.8200 (mmtm) REVERT: E 76 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8430 (tm-30) REVERT: G 95 GLU cc_start: 0.7621 (mp0) cc_final: 0.7093 (mp0) REVERT: H 102 GLU cc_start: 0.6868 (pm20) cc_final: 0.6279 (pm20) outliers start: 16 outliers final: 13 residues processed: 161 average time/residue: 0.1318 time to fit residues: 30.4084 Evaluate side-chains 163 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 228 VAL Chi-restraints excluded: chain K residue 291 VAL Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 118 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 97 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 17 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 125 optimal weight: 40.0000 chunk 72 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 121 optimal weight: 30.0000 chunk 23 optimal weight: 0.8980 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 181 HIS D 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.133173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.086243 restraints weight = 35691.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.085177 restraints weight = 20946.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.086252 restraints weight = 16613.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.086299 restraints weight = 13362.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.086335 restraints weight = 13452.592| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15623 Z= 0.195 Angle : 0.634 7.133 22444 Z= 0.366 Chirality : 0.044 0.292 2533 Planarity : 0.004 0.047 1733 Dihedral : 30.607 178.512 4626 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.11 % Allowed : 19.20 % Favored : 78.69 % 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: 0.98 (0.27), residues: 1007 helix: 2.26 (0.21), residues: 612 sheet: -0.23 (1.00), residues: 22 loop : -2.22 (0.28), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 40 TYR 0.031 0.002 TYR F 88 PHE 0.010 0.001 PHE H 62 TRP 0.010 0.001 TRP K 264 HIS 0.005 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.20 (15620) covalent geometry : angle 0.63420 / 0.37 (22444) hydrogen bonds : bond 0.06573 / 4.26 ( 796) hydrogen bonds : angle 3.29253 / 2.33 ( 1993) metal coordination : bond 0.00359 / 0.18 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2257.63 seconds wall clock time: 39 minutes 48.07 seconds (2388.07 seconds total)