Starting phenix.real_space_refine on Fri Jul 3 18:58:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8jhf_36264/07_2026/8jhf_36264.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jhf_36264/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8jhf_36264/07_2026/8jhf_36264.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8jhf_36264/07_2026/8jhf_36264.cif" model { file = "/net/cci-nas-00/data/ceres_data/8jhf_36264/07_2026/8jhf_36264.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jhf_36264/07_2026/8jhf_36264.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jhf_36264/07_2026/8jhf_36264.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jhf_36264/07_2026/8jhf_36264.map" } 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-dev-6108/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: 2.53, per 1000 atoms: 0.17 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: 1.01 Conformation dependent library (CDL) restraints added in 356.0 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: 1.98 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: 2.39 Time building geometry restraints manager: 1.32 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: 21946 2.27 - 4.55: 470 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: 0.870 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: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.040 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.580 ------------------------------------------------------------------------------- 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 : 0.757 11.372 22444 Z= 0.642 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 0.75729 / 0.64 (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 : 0.313 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: 0.1230 time to fit residues: 27.8181 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 : 0.334 ------------------------------------------------------------------------------- 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: 30.0000 chunk 103 optimal weight: 30.0000 chunk 77 optimal weight: 5.9990 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: 3.3602 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.136125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.090060 restraints weight = 34272.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.089391 restraints weight = 21545.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.090255 restraints weight = 16227.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.090378 restraints weight = 13690.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.090429 restraints weight = 12942.051| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.0850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15623 Z= 0.183 Angle : 0.641 7.665 22444 Z= 0.379 Chirality : 0.046 0.284 2533 Planarity : 0.004 0.043 1733 Dihedral : 30.248 179.977 4626 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.41 % Allowed : 10.42 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.82 (0.27), residues: 1007 helix: 2.09 (0.22), residues: 605 sheet: 0.13 (0.84), residues: 24 loop : -2.16 (0.28), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 83 TYR 0.020 0.001 TYR F 88 PHE 0.011 0.001 PHE K 195 TRP 0.009 0.001 TRP K 264 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.18 (15620) covalent geometry : angle 0.64137 / 0.38 (22444) hydrogen bonds : bond 0.07174 / 4.63 ( 796) hydrogen bonds : angle 3.63156 / 2.55 ( 1993) metal coordination : bond 0.00300 / 0.15 ( 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 153 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.378 Fit side-chains REVERT: K 100 MET cc_start: 0.7086 (pmm) cc_final: 0.6630 (pmm) REVERT: K 241 MET cc_start: 0.7603 (tmm) cc_final: 0.6994 (tmm) REVERT: E 76 GLN cc_start: 0.8709 (tm-30) cc_final: 0.8452 (tm-30) REVERT: G 115 LYS cc_start: 0.7795 (ttmm) cc_final: 0.7567 (tptp) outliers start: 12 outliers final: 8 residues processed: 148 average time/residue: 0.1219 time to fit residues: 25.3860 Evaluate side-chains 138 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 99 optimal weight: 50.0000 chunk 54 optimal weight: 3.9990 chunk 104 optimal weight: 40.0000 chunk 107 optimal weight: 30.0000 chunk 5 optimal weight: 7.9990 chunk 125 optimal weight: 40.0000 chunk 56 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 181 HIS K 262 GLN ** K 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.135508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.088430 restraints weight = 34599.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.088270 restraints weight = 21787.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.089012 restraints weight = 15363.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.089082 restraints weight = 14364.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.089138 restraints weight = 13101.072| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15623 Z= 0.177 Angle : 0.609 7.363 22444 Z= 0.363 Chirality : 0.044 0.238 2533 Planarity : 0.004 0.042 1733 Dihedral : 30.377 179.556 4626 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.52 % Allowed : 14.17 % Favored : 84.31 % 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: 0.92 (0.27), residues: 1007 helix: 2.20 (0.22), residues: 607 sheet: 0.19 (0.89), residues: 24 loop : -2.21 (0.28), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 83 TYR 0.019 0.001 TYR F 88 PHE 0.013 0.001 PHE K 195 TRP 0.011 0.001 TRP K 264 HIS 0.005 0.001 HIS K 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.18 (15620) covalent geometry : angle 0.60930 / 0.36 (22444) hydrogen bonds : bond 0.06637 / 4.30 ( 796) hydrogen bonds : angle 3.46153 / 2.43 ( 1993) metal coordination : bond 0.00240 / 0.12 ( 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: 13 poor density : 145 time to evaluate : 0.278 Fit side-chains REVERT: K 100 MET cc_start: 0.7061 (pmm) cc_final: 0.6379 (mmp) REVERT: K 188 MET cc_start: 0.7594 (tmm) cc_final: 0.7332 (tmm) REVERT: K 220 ARG cc_start: 0.5595 (OUTLIER) cc_final: 0.5218 (mmp80) REVERT: K 241 MET cc_start: 0.7519 (tmm) cc_final: 0.6882 (tmm) REVERT: E 76 GLN cc_start: 0.8723 (tm-30) cc_final: 0.8463 (tm-30) REVERT: G 115 LYS cc_start: 0.7834 (ttmm) cc_final: 0.7614 (tptp) outliers start: 13 outliers final: 9 residues processed: 153 average time/residue: 0.1236 time to fit residues: 26.6089 Evaluate side-chains 145 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 220 ARG 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 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: 8.9990 chunk 73 optimal weight: 7.9990 chunk 117 optimal weight: 40.0000 chunk 77 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 100 optimal weight: 50.0000 chunk 21 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 98 optimal weight: 50.0000 chunk 59 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 316 ASN 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 = 0.3977 r_free = 0.3977 target = 0.134037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.087767 restraints weight = 34112.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.087083 restraints weight = 26173.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.087550 restraints weight = 19296.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.087788 restraints weight = 17344.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.087800 restraints weight = 16567.763| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15623 Z= 0.230 Angle : 0.668 7.828 22444 Z= 0.387 Chirality : 0.047 0.257 2533 Planarity : 0.004 0.044 1733 Dihedral : 30.509 178.818 4626 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.16 % Allowed : 16.39 % Favored : 80.44 % 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: 0.68 (0.27), residues: 1007 helix: 2.04 (0.22), residues: 603 sheet: -0.21 (0.81), residues: 24 loop : -2.29 (0.28), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 39 TYR 0.015 0.002 TYR K 203 PHE 0.011 0.002 PHE K 281 TRP 0.012 0.002 TRP K 264 HIS 0.006 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.23 (15620) covalent geometry : angle 0.66828 / 0.39 (22444) hydrogen bonds : bond 0.07528 / 4.90 ( 796) hydrogen bonds : angle 3.61090 / 2.56 ( 1993) metal coordination : bond 0.00497 / 0.25 ( 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 163 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 0.402 Fit side-chains REVERT: K 100 MET cc_start: 0.7186 (pmm) cc_final: 0.6773 (pmm) REVERT: K 188 MET cc_start: 0.7627 (tmm) cc_final: 0.7306 (tmm) REVERT: K 241 MET cc_start: 0.7477 (tmm) cc_final: 0.6799 (tmm) REVERT: E 76 GLN cc_start: 0.8783 (tm-30) cc_final: 0.8512 (tm-30) REVERT: G 115 LYS cc_start: 0.7860 (ttmm) cc_final: 0.7651 (tptp) outliers start: 27 outliers final: 15 residues processed: 155 average time/residue: 0.1218 time to fit residues: 27.0452 Evaluate side-chains 143 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 226 LEU 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 Chi-restraints excluded: chain H residue 115 VAL 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: 0.7980 chunk 73 optimal weight: 0.9990 chunk 120 optimal weight: 30.0000 chunk 2 optimal weight: 20.0000 chunk 71 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 46 HIS 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 = 0.3973 r_free = 0.3973 target = 0.133746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.086018 restraints weight = 34138.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.086010 restraints weight = 21237.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.086991 restraints weight = 14859.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.086966 restraints weight = 13411.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.087052 restraints weight = 12354.612| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15623 Z= 0.225 Angle : 0.660 7.752 22444 Z= 0.383 Chirality : 0.046 0.265 2533 Planarity : 0.004 0.045 1733 Dihedral : 30.546 178.130 4626 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.81 % Allowed : 17.21 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.27), residues: 1007 helix: 2.02 (0.22), residues: 602 sheet: -0.41 (0.81), residues: 24 loop : -2.34 (0.28), residues: 381 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 0.010 0.001 PHE H 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 0.00477 / 0.22 (15620) covalent geometry : angle 0.65975 / 0.38 (22444) hydrogen bonds : bond 0.07331 / 4.77 ( 796) hydrogen bonds : angle 3.55901 / 2.52 ( 1993) metal coordination : bond 0.00443 / 0.22 ( 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 163 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 0.267 Fit side-chains REVERT: K 100 MET cc_start: 0.7053 (pmm) cc_final: 0.6589 (pmm) REVERT: K 188 MET cc_start: 0.7683 (tmm) cc_final: 0.7355 (tmm) REVERT: K 241 MET cc_start: 0.7529 (tmm) cc_final: 0.6845 (tmm) REVERT: E 76 GLN cc_start: 0.8765 (tm-30) cc_final: 0.8467 (tm-30) REVERT: G 115 LYS cc_start: 0.7772 (ttmm) cc_final: 0.7520 (tptp) outliers start: 24 outliers final: 17 residues processed: 156 average time/residue: 0.1064 time to fit residues: 24.2710 Evaluate side-chains 152 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 226 LEU 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 C residue 81 ILE 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 F residue 73 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain H residue 115 VAL 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: 2.9990 chunk 2 optimal weight: 9.9990 chunk 48 optimal weight: 7.9990 chunk 85 optimal weight: 0.2980 chunk 90 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 125 optimal weight: 40.0000 chunk 47 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 181 HIS 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 = 0.4022 r_free = 0.4022 target = 0.137041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.090925 restraints weight = 34181.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.091656 restraints weight = 24959.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.091857 restraints weight = 16673.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.092122 restraints weight = 16112.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.092132 restraints weight = 14768.419| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1598 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= 0.141 Angle : 0.583 7.998 22444 Z= 0.349 Chirality : 0.042 0.266 2533 Planarity : 0.004 0.050 1733 Dihedral : 30.501 177.733 4626 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.87 % Allowed : 18.85 % Favored : 79.27 % 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: 2.34 (0.22), residues: 603 sheet: -0.56 (0.87), residues: 24 loop : -2.24 (0.28), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 40 TYR 0.024 0.001 TYR H 80 PHE 0.007 0.001 PHE K 195 TRP 0.008 0.001 TRP K 264 HIS 0.004 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.14 (15620) covalent geometry : angle 0.58274 / 0.35 (22444) hydrogen bonds : bond 0.05729 / 3.71 ( 796) hydrogen bonds : angle 3.14426 / 2.21 ( 1993) metal coordination : bond 0.00067 / 0.03 ( 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 163 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.445 Fit side-chains REVERT: K 100 MET cc_start: 0.7067 (pmm) cc_final: 0.6440 (mmp) REVERT: K 178 PHE cc_start: 0.6037 (m-10) cc_final: 0.5812 (m-10) REVERT: K 188 MET cc_start: 0.7801 (tmm) cc_final: 0.7575 (tmm) REVERT: K 241 MET cc_start: 0.7439 (tmm) cc_final: 0.6742 (tmm) REVERT: E 76 GLN cc_start: 0.8665 (tm-30) cc_final: 0.8402 (tm-30) REVERT: G 95 GLU cc_start: 0.7479 (mp0) cc_final: 0.7262 (mp0) outliers start: 16 outliers final: 10 residues processed: 158 average time/residue: 0.1136 time to fit residues: 25.8538 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 : 0.327 ------------------------------------------------------------------------------- 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 C residue 20 SER Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 81 ILE 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: 3.9990 chunk 18 optimal weight: 9.9990 chunk 124 optimal weight: 40.0000 chunk 60 optimal weight: 0.0770 chunk 58 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 128 optimal weight: 50.0000 chunk 30 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 119 optimal weight: 30.0000 overall best weight: 2.8146 ------------------------------------------------------------------------------- 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 = 0.4007 r_free = 0.4007 target = 0.136064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.089302 restraints weight = 33868.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.089721 restraints weight = 22143.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.090230 restraints weight = 15043.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.090544 restraints weight = 13621.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.090567 restraints weight = 12296.468| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15623 Z= 0.161 Angle : 0.600 8.186 22444 Z= 0.354 Chirality : 0.043 0.265 2533 Planarity : 0.004 0.048 1733 Dihedral : 30.558 177.405 4626 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.34 % Allowed : 18.74 % Favored : 78.92 % 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: 0.96 (0.27), residues: 1007 helix: 2.26 (0.22), residues: 610 sheet: -0.49 (1.00), residues: 22 loop : -2.23 (0.28), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 40 TYR 0.030 0.001 TYR F 88 PHE 0.008 0.001 PHE H 62 TRP 0.010 0.001 TRP K 264 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.16 (15620) covalent geometry : angle 0.60010 / 0.35 (22444) hydrogen bonds : bond 0.06032 / 3.91 ( 796) hydrogen bonds : angle 3.22800 / 2.27 ( 1993) metal coordination : bond 0.00249 / 0.13 ( 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 160 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.295 Fit side-chains REVERT: K 100 MET cc_start: 0.7120 (pmm) cc_final: 0.6399 (mmp) REVERT: K 178 PHE cc_start: 0.6303 (m-10) cc_final: 0.6026 (m-10) REVERT: K 241 MET cc_start: 0.7488 (tmm) cc_final: 0.6803 (tmm) REVERT: C 39 ARG cc_start: 0.7757 (tpp80) cc_final: 0.7548 (tpp80) REVERT: E 76 GLN cc_start: 0.8714 (tm-30) cc_final: 0.8433 (tm-30) REVERT: G 95 GLU cc_start: 0.7713 (mp0) cc_final: 0.7477 (mp0) outliers start: 20 outliers final: 14 residues processed: 152 average time/residue: 0.1215 time to fit residues: 26.4228 Evaluate side-chains 152 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 53 GLU 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=2.00 ------------------------------------------------------------------------------- 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: 0.9990 chunk 90 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 125 optimal weight: 30.0000 chunk 110 optimal weight: 40.0000 chunk 97 optimal weight: 9.9990 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.136205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.090293 restraints weight = 34246.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.089946 restraints weight = 23950.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.090231 restraints weight = 17661.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.090585 restraints weight = 16123.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.090561 restraints weight = 15608.283| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15623 Z= 0.159 Angle : 0.594 8.010 22444 Z= 0.352 Chirality : 0.043 0.270 2533 Planarity : 0.004 0.048 1733 Dihedral : 30.572 177.051 4626 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.22 % Allowed : 19.20 % Favored : 78.57 % 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: 2.27 (0.22), residues: 610 sheet: -0.46 (0.98), residues: 22 loop : -2.26 (0.28), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 83 TYR 0.013 0.001 TYR F 88 PHE 0.008 0.001 PHE H 62 TRP 0.013 0.002 TRP K 264 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.16 (15620) covalent geometry : angle 0.59449 / 0.35 (22444) hydrogen bonds : bond 0.05983 / 3.87 ( 796) hydrogen bonds : angle 3.19528 / 2.25 ( 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 161 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.374 Fit side-chains REVERT: K 100 MET cc_start: 0.7148 (pmm) cc_final: 0.6419 (mmp) REVERT: K 178 PHE cc_start: 0.6218 (m-10) cc_final: 0.6005 (m-10) REVERT: K 188 MET cc_start: 0.7737 (tmm) cc_final: 0.7514 (tmm) REVERT: K 241 MET cc_start: 0.7474 (tmm) cc_final: 0.6760 (tmm) REVERT: E 76 GLN cc_start: 0.8706 (tm-30) cc_final: 0.8420 (tm-30) outliers start: 19 outliers final: 14 residues processed: 155 average time/residue: 0.1211 time to fit residues: 26.7884 Evaluate side-chains 157 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 74 optimal weight: 4.9990 chunk 99 optimal weight: 50.0000 chunk 6 optimal weight: 10.0000 chunk 125 optimal weight: 40.0000 chunk 75 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 98 optimal weight: 50.0000 chunk 72 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.3998 r_free = 0.3998 target = 0.135353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.089216 restraints weight = 36180.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.088920 restraints weight = 24982.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.089548 restraints weight = 16979.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.089744 restraints weight = 15684.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.089744 restraints weight = 14782.802| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1865 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= 0.135 Angle : 0.573 8.673 22444 Z= 0.342 Chirality : 0.041 0.268 2533 Planarity : 0.004 0.053 1733 Dihedral : 30.563 176.552 4626 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.34 % Allowed : 19.32 % Favored : 78.34 % 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: 2.36 (0.22), residues: 612 sheet: -0.27 (1.00), residues: 22 loop : -2.22 (0.28), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 39 TYR 0.020 0.001 TYR H 80 PHE 0.007 0.001 PHE H 62 TRP 0.010 0.001 TRP K 264 HIS 0.005 0.001 HIS K 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.14 (15620) covalent geometry : angle 0.57293 / 0.34 (22444) hydrogen bonds : bond 0.05202 / 3.36 ( 796) hydrogen bonds : angle 3.00483 / 2.11 ( 1993) metal coordination : bond 0.00119 / 0.06 ( 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 169 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.305 Fit side-chains REVERT: K 100 MET cc_start: 0.7043 (pmm) cc_final: 0.6564 (pmm) REVERT: K 178 PHE cc_start: 0.6402 (m-10) cc_final: 0.6148 (m-10) REVERT: K 188 MET cc_start: 0.7669 (tmm) cc_final: 0.7407 (tmm) REVERT: K 241 MET cc_start: 0.7542 (tmm) cc_final: 0.6833 (tmm) REVERT: C 77 LYS cc_start: 0.8404 (mmtt) cc_final: 0.8170 (mmtm) REVERT: E 76 GLN cc_start: 0.8666 (tm-30) cc_final: 0.8402 (tm-30) REVERT: G 95 GLU cc_start: 0.7483 (mp0) cc_final: 0.6898 (mp0) REVERT: H 102 GLU cc_start: 0.6757 (pm20) cc_final: 0.6344 (pm20) outliers start: 20 outliers final: 16 residues processed: 163 average time/residue: 0.1073 time to fit residues: 25.4511 Evaluate side-chains 159 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 291 VAL Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 53 GLU 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 F residue 82 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: 9.9990 chunk 76 optimal weight: 5.9990 chunk 99 optimal weight: 50.0000 chunk 44 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 107 optimal weight: 30.0000 chunk 116 optimal weight: 50.0000 overall best weight: 4.4588 ------------------------------------------------------------------------------- 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 = 0.3961 r_free = 0.3961 target = 0.132956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.085043 restraints weight = 35445.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.085520 restraints weight = 21434.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.086294 restraints weight = 14929.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.086289 restraints weight = 12952.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.086275 restraints weight = 12060.812| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15623 Z= 0.202 Angle : 0.635 7.400 22444 Z= 0.368 Chirality : 0.044 0.271 2533 Planarity : 0.004 0.046 1733 Dihedral : 30.652 176.922 4626 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.22 % Allowed : 19.91 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.27), residues: 1007 helix: 2.19 (0.22), residues: 610 sheet: -0.27 (0.99), residues: 22 loop : -2.28 (0.28), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 39 TYR 0.029 0.002 TYR H 80 PHE 0.010 0.001 PHE H 62 TRP 0.014 0.002 TRP K 264 HIS 0.005 0.001 HIS K 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.20 (15620) covalent geometry : angle 0.63511 / 0.37 (22444) hydrogen bonds : bond 0.06660 / 4.33 ( 796) hydrogen bonds : angle 3.32371 / 2.35 ( 1993) metal coordination : bond 0.00403 / 0.20 ( 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 155 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.266 Fit side-chains REVERT: K 178 PHE cc_start: 0.6597 (m-10) cc_final: 0.6297 (m-10) REVERT: K 188 MET cc_start: 0.7614 (tmm) cc_final: 0.7352 (tmm) REVERT: K 241 MET cc_start: 0.7491 (tmm) cc_final: 0.6855 (tmm) REVERT: E 76 GLN cc_start: 0.8781 (tm-30) cc_final: 0.8446 (tm-30) REVERT: G 95 GLU cc_start: 0.7690 (mp0) cc_final: 0.7230 (mp0) outliers start: 19 outliers final: 16 residues processed: 149 average time/residue: 0.1170 time to fit residues: 25.0295 Evaluate side-chains 150 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 291 VAL Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 53 GLU 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 F residue 82 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 97 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 125 optimal weight: 40.0000 chunk 72 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 43 optimal weight: 0.0980 chunk 121 optimal weight: 30.0000 chunk 23 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 169 ASN K 181 HIS D 46 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.134857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.087026 restraints weight = 35664.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.087983 restraints weight = 20189.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.089385 restraints weight = 14265.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.089236 restraints weight = 11047.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.089308 restraints weight = 11490.421| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15623 Z= 0.139 Angle : 0.578 7.100 22444 Z= 0.344 Chirality : 0.041 0.274 2533 Planarity : 0.004 0.052 1733 Dihedral : 30.600 176.866 4626 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.22 % Allowed : 19.56 % Favored : 78.22 % 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: 1.04 (0.27), residues: 1007 helix: 2.34 (0.21), residues: 612 sheet: -0.37 (1.00), residues: 22 loop : -2.25 (0.28), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 40 TYR 0.019 0.001 TYR H 80 PHE 0.007 0.001 PHE B 61 TRP 0.010 0.001 TRP K 264 HIS 0.005 0.001 HIS K 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.14 (15620) covalent geometry : angle 0.57816 / 0.34 (22444) hydrogen bonds : bond 0.05451 / 3.52 ( 796) hydrogen bonds : angle 3.04147 / 2.14 ( 1993) metal coordination : bond 0.00114 / 0.06 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1882.10 seconds wall clock time: 33 minutes 10.48 seconds (1990.48 seconds total)