Starting phenix.real_space_refine on Fri Jul 3 09:48:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ea5_31039/07_2026/7ea5_31039.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ea5_31039/07_2026/7ea5_31039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ea5_31039/07_2026/7ea5_31039.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ea5_31039/07_2026/7ea5_31039.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ea5_31039/07_2026/7ea5_31039.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ea5_31039/07_2026/7ea5_31039.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ea5_31039/07_2026/7ea5_31039.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ea5_31039/07_2026/7ea5_31039.map" } resolution = 3.3 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 290 5.49 5 S 33 5.16 5 C 7743 2.51 5 N 2547 2.21 5 O 3154 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 13770 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 830 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "B" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 730 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 800 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 714 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 1866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1866 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 4, 'TRANS': 223} Chain: "K" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' ZN': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12277 SG CYS K 82 65.116 67.711 47.853 1.00 53.52 S ATOM 12395 SG CYS K 97 60.815 66.338 50.205 1.00 41.97 S ATOM 12450 SG CYS K 105 64.400 68.875 51.580 1.00 57.96 S ATOM 12168 SG CYS K 68 65.754 65.298 51.958 1.00 49.16 S ATOM 12182 SG CYS K 70 68.099 67.624 50.381 1.00 61.08 S ATOM 12277 SG CYS K 82 65.116 67.711 47.853 1.00 53.52 S ATOM 13648 SG CYS K 248 53.165 52.723 14.294 1.00 68.97 S ATOM 13705 SG CYS K 255 56.658 49.593 12.841 1.00 58.18 S Time building chain proxies: 2.79, per 1000 atoms: 0.20 Number of scatterers: 13770 At special positions: 0 Unit cell: (154.78, 91.56, 130.8, 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 3 29.99 S 33 16.00 P 290 15.00 O 3154 8.00 N 2547 7.00 C 7743 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 315.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 82 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 105 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 97 " pdb=" ZN K 302 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 68 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 82 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 70 " pdb=" ZN K 303 " pdb="ZN ZN K 303 " - pdb=" SG CYS K 255 " pdb="ZN ZN K 303 " - pdb=" SG CYS K 248 " 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1832 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 14 sheets defined 59.0% alpha, 3.9% beta 143 base pairs and 240 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.522A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 114 removed outlier: 3.638A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.668A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.500A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.534A pdb=" N ARG B 36 " --> pdb=" O PRO B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.290A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.776A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.755A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.922A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.584A pdb=" N ASN C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.563A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.696A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.830A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 4.191A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.753A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.580A pdb=" N ILE F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.352A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.721A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 72 Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 36 through 46 removed outlier: 3.598A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.764A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 120 removed outlier: 3.761A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 44 removed outlier: 3.908A pdb=" N GLU K 38 " --> pdb=" O PRO K 34 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR K 42 " --> pdb=" O GLU K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 93 Processing helix chain 'K' and resid 156 through 169 removed outlier: 4.152A pdb=" N ASP K 161 " --> pdb=" O MET K 157 " (cutoff:3.500A) Processing helix chain 'K' and resid 192 through 196 removed outlier: 3.987A pdb=" N ARG K 195 " --> pdb=" O SER K 192 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE K 196 " --> pdb=" O LEU K 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 192 through 196' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.193A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.179A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.627A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.986A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.130A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.550A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.203A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 45 through 46 removed outlier: 6.334A pdb=" N GLU K 45 " --> pdb=" O GLY K 191 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'K' and resid 122 through 124 removed outlier: 4.030A pdb=" N ALA K 123 " --> pdb=" O ARG K 135 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 152 through 155 Processing sheet with id=AB5, first strand: chain 'K' and resid 210 through 211 405 hydrogen bonds defined for protein. 1200 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 367 hydrogen bonds 734 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 240 stacking parallelities Total time for adding SS restraints: 2.20 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3042 1.34 - 1.46: 4521 1.46 - 1.58: 6418 1.58 - 1.70: 578 1.70 - 1.82: 51 Bond restraints: 14610 Sorted by residual: bond pdb=" C3' DG J 95 " pdb=" C2' DG J 95 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 bond pdb=" C3' DA J 19 " pdb=" O3' DA J 19 " ideal model delta sigma weight residual 1.435 1.479 -0.044 1.30e-02 5.92e+03 1.14e+01 bond pdb=" C5' DA I 69 " pdb=" C4' DA I 69 " ideal model delta sigma weight residual 1.512 1.535 -0.023 7.00e-03 2.04e+04 1.11e+01 bond pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " ideal model delta sigma weight residual 1.435 1.478 -0.043 1.30e-02 5.92e+03 1.11e+01 bond pdb=" C3' DT J 87 " pdb=" C2' DT J 87 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 ... (remaining 14605 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 19717 1.73 - 3.45: 1178 3.45 - 5.18: 54 5.18 - 6.90: 12 6.90 - 8.63: 6 Bond angle restraints: 20967 Sorted by residual: angle pdb=" N3 DT J 83 " pdb=" C4 DT J 83 " pdb=" O4 DT J 83 " ideal model delta sigma weight residual 119.90 122.74 -2.84 6.00e-01 2.78e+00 2.24e+01 angle pdb=" O4' DG I 121 " pdb=" C4' DG I 121 " pdb=" C3' DG I 121 " ideal model delta sigma weight residual 106.00 103.28 2.72 6.00e-01 2.78e+00 2.06e+01 angle pdb=" N3 DT J 50 " pdb=" C4 DT J 50 " pdb=" O4 DT J 50 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" N3 DT J 51 " pdb=" C4 DT J 51 " pdb=" O4 DT J 51 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT J 105 " pdb=" C4 DT J 105 " pdb=" O4 DT J 105 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 ... (remaining 20962 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.35: 6753 35.35 - 70.70: 1249 70.70 - 106.05: 16 106.05 - 141.41: 3 141.41 - 176.76: 1 Dihedral angle restraints: 8022 sinusoidal: 5182 harmonic: 2840 Sorted by residual: dihedral pdb=" C4' DA J 19 " pdb=" C3' DA J 19 " pdb=" O3' DA J 19 " pdb=" P DC J 20 " ideal model delta sinusoidal sigma weight residual -140.00 36.76 -176.76 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J 94 " pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " pdb=" P DG J 95 " ideal model delta sinusoidal sigma weight residual 220.00 81.82 138.18 1 3.50e+01 8.16e-04 1.37e+01 dihedral pdb=" C4' DC J 126 " pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " pdb=" P DC J 127 " ideal model delta sinusoidal sigma weight residual 220.00 82.01 137.99 1 3.50e+01 8.16e-04 1.37e+01 ... (remaining 8019 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1582 0.044 - 0.089: 627 0.089 - 0.133: 129 0.133 - 0.177: 16 0.177 - 0.222: 4 Chirality restraints: 2358 Sorted by residual: chirality pdb=" SD SAM K 304 " pdb=" CG SAM K 304 " pdb=" CE SAM K 304 " pdb=" C5' SAM K 304 " both_signs ideal model delta sigma weight residual False 5.50 5.28 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" C3' DC J 126 " pdb=" C4' DC J 126 " pdb=" O3' DC J 126 " pdb=" C2' DC J 126 " both_signs ideal model delta sigma weight residual False -2.73 -2.52 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" C1' SAM K 304 " pdb=" C2' SAM K 304 " pdb=" N9 SAM K 304 " pdb=" O4' SAM K 304 " both_signs ideal model delta sigma weight residual False 2.30 2.48 -0.19 2.00e-01 2.50e+01 8.57e-01 ... (remaining 2355 not shown) Planarity restraints: 1663 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU K 252 " -0.039 5.00e-02 4.00e+02 5.88e-02 5.52e+00 pdb=" N PRO K 253 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO K 253 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO K 253 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.034 5.00e-02 4.00e+02 5.06e-02 4.10e+00 pdb=" N PRO C 80 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO G 80 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.027 5.00e-02 4.00e+02 ... (remaining 1660 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 3573 2.84 - 3.35: 10795 3.35 - 3.87: 25371 3.87 - 4.38: 28991 4.38 - 4.90: 42183 Nonbonded interactions: 110913 Sorted by model distance: nonbonded pdb=" O ILE K 89 " pdb=" OG1 THR K 93 " model vdw 2.319 3.040 nonbonded pdb=" O CYS K 197 " pdb=" OH TYR K 236 " model vdw 2.320 3.040 nonbonded pdb=" OG1 THR D 29 " pdb=" OP1 DT I 104 " model vdw 2.339 3.040 nonbonded pdb=" NH1 ARG C 42 " pdb=" OG1 THR D 85 " model vdw 2.377 3.120 nonbonded pdb=" OG1 THR A 118 " pdb=" NH1 ARG B 45 " model vdw 2.402 3.120 ... (remaining 110908 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 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 14 through 117) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 30 through 120) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.440 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 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 : 0.012 0.588 14620 Z= 0.617 Angle : 0.818 8.630 20967 Z= 0.686 Chirality : 0.047 0.222 2358 Planarity : 0.005 0.059 1663 Dihedral : 24.939 176.756 6190 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % 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: -3.00 (0.21), residues: 957 helix: -1.43 (0.17), residues: 568 sheet: -2.01 (1.11), residues: 28 loop : -2.78 (0.27), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 42 TYR 0.013 0.001 TYR F 98 PHE 0.019 0.002 PHE G 25 TRP 0.022 0.005 TRP K 210 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.51 (14610) covalent geometry : angle 0.81844 / 0.69 (20967) hydrogen bonds : bond 0.10338 / 6.80 ( 772) hydrogen bonds : angle 4.42462 / 3.03 ( 1934) metal coordination : bond 0.44504 / 31.43 ( 8) Misc. bond : bond 0.00156 / 0.09 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8625 (mttt) cc_final: 0.8311 (mtpp) REVERT: C 101 THR cc_start: 0.8310 (m) cc_final: 0.8042 (m) REVERT: F 31 LYS cc_start: 0.8787 (tttt) cc_final: 0.8463 (tttm) REVERT: K 85 ASP cc_start: 0.6343 (m-30) cc_final: 0.6074 (t0) REVERT: K 233 THR cc_start: 0.6394 (p) cc_final: 0.6042 (p) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.1824 time to fit residues: 65.5573 Evaluate side-chains 159 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 30.0000 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 117 optimal weight: 10.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS A 68 GLN A 113 HIS A 125 GLN C 68 ASN C 84 GLN D 106 HIS E 39 HIS E 68 GLN F 25 ASN G 38 ASN G 84 GLN H 46 HIS ** K 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 144 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.187292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.140632 restraints weight = 17884.906| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.60 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14620 Z= 0.148 Angle : 0.579 6.172 20967 Z= 0.351 Chirality : 0.043 0.220 2358 Planarity : 0.004 0.043 1663 Dihedral : 29.567 175.584 4248 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.21 % Allowed : 7.26 % Favored : 91.53 % 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: -0.78 (0.26), residues: 957 helix: 0.75 (0.21), residues: 570 sheet: -2.12 (0.95), residues: 38 loop : -2.53 (0.28), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 83 TYR 0.009 0.001 TYR K 52 PHE 0.011 0.001 PHE K 65 TRP 0.005 0.002 TRP K 210 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.15 (14610) covalent geometry : angle 0.57869 / 0.35 (20967) hydrogen bonds : bond 0.04847 / 3.27 ( 772) hydrogen bonds : angle 2.85352 / 1.99 ( 1934) metal coordination : bond 0.01380 / 0.89 ( 8) Misc. bond : bond 0.00147 / 0.08 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 169 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8475 (mttt) cc_final: 0.8262 (mtpp) REVERT: C 41 GLU cc_start: 0.7419 (tt0) cc_final: 0.7208 (tt0) REVERT: C 101 THR cc_start: 0.8186 (m) cc_final: 0.7961 (m) REVERT: E 39 HIS cc_start: 0.7661 (OUTLIER) cc_final: 0.7206 (t-170) REVERT: F 68 ASP cc_start: 0.7483 (m-30) cc_final: 0.7262 (m-30) REVERT: G 36 LYS cc_start: 0.8076 (ttpt) cc_final: 0.7738 (tttp) REVERT: K 85 ASP cc_start: 0.6407 (m-30) cc_final: 0.6058 (t0) REVERT: K 178 MET cc_start: 0.7293 (tpp) cc_final: 0.6595 (tpp) REVERT: K 233 THR cc_start: 0.6313 (p) cc_final: 0.6109 (m) outliers start: 10 outliers final: 7 residues processed: 173 average time/residue: 0.1415 time to fit residues: 33.5688 Evaluate side-chains 158 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 150 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 212 VAL Chi-restraints excluded: chain K residue 259 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 95 optimal weight: 10.9990 chunk 76 optimal weight: 20.0000 chunk 60 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 80 optimal weight: 20.0000 chunk 115 optimal weight: 5.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN G 73 ASN ** K 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 144 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.179860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.130315 restraints weight = 17579.549| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.55 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14620 Z= 0.201 Angle : 0.619 6.475 20967 Z= 0.363 Chirality : 0.044 0.228 2358 Planarity : 0.005 0.046 1663 Dihedral : 29.857 177.079 4248 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.06 % Allowed : 9.93 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.11 (0.27), residues: 957 helix: 1.36 (0.22), residues: 570 sheet: -1.12 (1.23), residues: 28 loop : -2.47 (0.27), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG K 162 TYR 0.021 0.002 TYR K 71 PHE 0.028 0.003 PHE K 65 TRP 0.010 0.003 TRP K 210 HIS 0.026 0.002 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.20 (14610) covalent geometry : angle 0.61866 / 0.36 (20967) hydrogen bonds : bond 0.06082 / 4.09 ( 772) hydrogen bonds : angle 2.87427 / 2.01 ( 1934) metal coordination : bond 0.00593 / 0.43 ( 8) Misc. bond : bond 0.00254 / 0.14 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: C 89 ASN cc_start: 0.8648 (m-40) cc_final: 0.8432 (m110) REVERT: D 61 SER cc_start: 0.8919 (t) cc_final: 0.8664 (m) REVERT: D 76 ARG cc_start: 0.7779 (mtm-85) cc_final: 0.7533 (mtm-85) REVERT: E 115 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8366 (mtmm) REVERT: K 85 ASP cc_start: 0.6588 (m-30) cc_final: 0.6238 (t0) REVERT: K 178 MET cc_start: 0.7484 (tpp) cc_final: 0.6765 (tpp) REVERT: K 241 TYR cc_start: 0.6010 (OUTLIER) cc_final: 0.5535 (p90) outliers start: 17 outliers final: 11 residues processed: 179 average time/residue: 0.1522 time to fit residues: 36.4615 Evaluate side-chains 170 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 212 VAL Chi-restraints excluded: chain K residue 241 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 78 optimal weight: 20.0000 chunk 86 optimal weight: 50.0000 chunk 85 optimal weight: 50.0000 chunk 48 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 39 HIS F 25 ASN K 144 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.181289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.131363 restraints weight = 17539.655| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.36 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14620 Z= 0.133 Angle : 0.546 6.265 20967 Z= 0.327 Chirality : 0.041 0.232 2358 Planarity : 0.004 0.040 1663 Dihedral : 29.882 175.551 4248 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.82 % Allowed : 11.62 % Favored : 86.56 % 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: 0.49 (0.28), residues: 957 helix: 1.89 (0.23), residues: 570 sheet: -0.98 (1.25), residues: 28 loop : -2.29 (0.28), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 83 TYR 0.009 0.001 TYR F 51 PHE 0.023 0.002 PHE K 65 TRP 0.002 0.001 TRP K 210 HIS 0.009 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.13 (14610) covalent geometry : angle 0.54622 / 0.33 (20967) hydrogen bonds : bond 0.04835 / 3.25 ( 772) hydrogen bonds : angle 2.70323 / 1.89 ( 1934) metal coordination : bond 0.00325 / 0.24 ( 8) Misc. bond : bond 0.00143 / 0.08 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: C 89 ASN cc_start: 0.8642 (m-40) cc_final: 0.8432 (m110) REVERT: K 85 ASP cc_start: 0.6609 (m-30) cc_final: 0.6239 (t0) REVERT: K 178 MET cc_start: 0.7381 (tpp) cc_final: 0.6614 (tpp) REVERT: K 241 TYR cc_start: 0.5882 (OUTLIER) cc_final: 0.5316 (p90) outliers start: 15 outliers final: 12 residues processed: 162 average time/residue: 0.1483 time to fit residues: 32.2903 Evaluate side-chains 162 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 241 TYR Chi-restraints excluded: chain K residue 259 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 15 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 91 optimal weight: 20.0000 chunk 69 optimal weight: 4.9990 chunk 87 optimal weight: 30.0000 chunk 1 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.180504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.130176 restraints weight = 17615.779| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.44 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14620 Z= 0.140 Angle : 0.541 6.618 20967 Z= 0.324 Chirality : 0.041 0.232 2358 Planarity : 0.004 0.044 1663 Dihedral : 29.907 175.050 4248 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.94 % Allowed : 12.23 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.28), residues: 957 helix: 2.03 (0.22), residues: 570 sheet: -0.90 (1.25), residues: 28 loop : -2.23 (0.28), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 83 TYR 0.009 0.001 TYR D 37 PHE 0.022 0.002 PHE K 65 TRP 0.002 0.001 TRP K 210 HIS 0.003 0.001 HIS K 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.14 (14610) covalent geometry : angle 0.54101 / 0.32 (20967) hydrogen bonds : bond 0.04878 / 3.28 ( 772) hydrogen bonds : angle 2.65731 / 1.86 ( 1934) metal coordination : bond 0.00181 / 0.14 ( 8) Misc. bond : bond 0.00134 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: C 89 ASN cc_start: 0.8662 (m-40) cc_final: 0.8448 (m110) REVERT: K 85 ASP cc_start: 0.6589 (m-30) cc_final: 0.6223 (t0) REVERT: K 233 THR cc_start: 0.6834 (p) cc_final: 0.6602 (m) REVERT: K 241 TYR cc_start: 0.5829 (OUTLIER) cc_final: 0.5093 (p90) outliers start: 16 outliers final: 14 residues processed: 157 average time/residue: 0.1328 time to fit residues: 28.3705 Evaluate side-chains 160 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 198 ASN Chi-restraints excluded: chain K residue 212 VAL Chi-restraints excluded: chain K residue 241 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 15 optimal weight: 0.1980 chunk 97 optimal weight: 30.0000 chunk 93 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 chunk 87 optimal weight: 30.0000 chunk 105 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 43 optimal weight: 0.6980 chunk 96 optimal weight: 10.0000 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN C 31 HIS G 31 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.174935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.124312 restraints weight = 17348.395| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.55 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 14620 Z= 0.227 Angle : 0.662 7.130 20967 Z= 0.371 Chirality : 0.047 0.221 2358 Planarity : 0.006 0.064 1663 Dihedral : 30.168 176.530 4248 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.27 % Allowed : 11.99 % Favored : 84.75 % 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: 0.20 (0.27), residues: 957 helix: 1.54 (0.22), residues: 574 sheet: -1.06 (1.21), residues: 28 loop : -2.24 (0.28), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 83 TYR 0.015 0.002 TYR D 37 PHE 0.038 0.003 PHE G 25 TRP 0.007 0.002 TRP K 210 HIS 0.008 0.002 HIS K 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.23 (14610) covalent geometry : angle 0.66176 / 0.37 (20967) hydrogen bonds : bond 0.07033 / 4.72 ( 772) hydrogen bonds : angle 2.97393 / 2.09 ( 1934) metal coordination : bond 0.00185 / 0.13 ( 8) Misc. bond : bond 0.00145 / 0.08 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.7472 (mtp85) REVERT: E 115 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8193 (mtmm) REVERT: H 56 MET cc_start: 0.7949 (tpp) cc_final: 0.7588 (tpt) REVERT: K 241 TYR cc_start: 0.5911 (OUTLIER) cc_final: 0.5111 (p90) outliers start: 27 outliers final: 22 residues processed: 166 average time/residue: 0.1446 time to fit residues: 32.4874 Evaluate side-chains 165 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 198 ASN Chi-restraints excluded: chain K residue 212 VAL Chi-restraints excluded: chain K residue 241 TYR Chi-restraints excluded: chain K residue 259 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 53 optimal weight: 0.9980 chunk 84 optimal weight: 50.0000 chunk 111 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 85 optimal weight: 50.0000 chunk 95 optimal weight: 9.9990 chunk 114 optimal weight: 9.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.177142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.127738 restraints weight = 17378.871| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.73 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14620 Z= 0.141 Angle : 0.575 6.757 20967 Z= 0.335 Chirality : 0.043 0.231 2358 Planarity : 0.004 0.046 1663 Dihedral : 30.122 175.533 4248 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.66 % Allowed : 12.47 % Favored : 84.87 % 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: 0.61 (0.28), residues: 957 helix: 1.90 (0.22), residues: 573 sheet: -1.07 (1.20), residues: 28 loop : -2.12 (0.28), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 83 TYR 0.011 0.001 TYR F 51 PHE 0.020 0.002 PHE K 65 TRP 0.002 0.001 TRP K 210 HIS 0.004 0.001 HIS K 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.14 (14610) covalent geometry : angle 0.57522 / 0.33 (20967) hydrogen bonds : bond 0.05377 / 3.61 ( 772) hydrogen bonds : angle 2.76783 / 1.95 ( 1934) metal coordination : bond 0.00114 / 0.08 ( 8) Misc. bond : bond 0.00122 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: C 89 ASN cc_start: 0.8722 (m-40) cc_final: 0.8429 (m110) REVERT: E 115 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8068 (mtmm) REVERT: H 56 MET cc_start: 0.7905 (tpp) cc_final: 0.7599 (tpt) REVERT: K 241 TYR cc_start: 0.5862 (OUTLIER) cc_final: 0.4987 (p90) outliers start: 22 outliers final: 18 residues processed: 157 average time/residue: 0.1418 time to fit residues: 29.8664 Evaluate side-chains 162 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 157 MET Chi-restraints excluded: chain K residue 198 ASN Chi-restraints excluded: chain K residue 212 VAL Chi-restraints excluded: chain K residue 241 TYR Chi-restraints excluded: chain K residue 259 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 113 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 105 optimal weight: 20.0000 chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 chunk 57 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.175329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.125595 restraints weight = 17287.122| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.60 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14620 Z= 0.190 Angle : 0.612 8.212 20967 Z= 0.349 Chirality : 0.044 0.226 2358 Planarity : 0.005 0.050 1663 Dihedral : 30.137 175.911 4248 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.75 % Allowed : 11.86 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.28), residues: 957 helix: 1.79 (0.22), residues: 573 sheet: -1.14 (1.20), residues: 28 loop : -2.04 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 83 TYR 0.016 0.001 TYR K 236 PHE 0.024 0.002 PHE G 25 TRP 0.004 0.001 TRP K 210 HIS 0.005 0.001 HIS K 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 (14610) covalent geometry : angle 0.61184 / 0.35 (20967) hydrogen bonds : bond 0.06038 / 4.04 ( 772) hydrogen bonds : angle 2.86236 / 2.01 ( 1934) metal coordination : bond 0.00141 / 0.10 ( 8) Misc. bond : bond 0.00120 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.7203 (mtp85) REVERT: E 115 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8131 (mtmm) REVERT: H 43 LYS cc_start: 0.8198 (mmmt) cc_final: 0.7958 (mmtm) REVERT: H 90 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7329 (mm-30) REVERT: K 241 TYR cc_start: 0.5930 (OUTLIER) cc_final: 0.5077 (p90) outliers start: 31 outliers final: 25 residues processed: 159 average time/residue: 0.1576 time to fit residues: 33.4555 Evaluate side-chains 169 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 157 MET Chi-restraints excluded: chain K residue 198 ASN Chi-restraints excluded: chain K residue 212 VAL Chi-restraints excluded: chain K residue 223 GLN Chi-restraints excluded: chain K residue 238 VAL Chi-restraints excluded: chain K residue 241 TYR Chi-restraints excluded: chain K residue 259 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 15 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 113 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 59 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.176147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.126311 restraints weight = 17403.062| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.61 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14620 Z= 0.152 Angle : 0.591 7.988 20967 Z= 0.339 Chirality : 0.043 0.226 2358 Planarity : 0.004 0.045 1663 Dihedral : 30.122 176.011 4248 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.39 % Allowed : 12.23 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.28), residues: 957 helix: 1.93 (0.22), residues: 570 sheet: -1.36 (1.03), residues: 33 loop : -1.99 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 83 TYR 0.016 0.001 TYR K 236 PHE 0.020 0.002 PHE K 65 TRP 0.003 0.001 TRP K 210 HIS 0.004 0.001 HIS K 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 (14610) covalent geometry : angle 0.59052 / 0.34 (20967) hydrogen bonds : bond 0.05581 / 3.74 ( 772) hydrogen bonds : angle 2.81835 / 1.98 ( 1934) metal coordination : bond 0.00117 / 0.08 ( 8) Misc. bond : bond 0.00112 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 0.339 Fit side-chains REVERT: A 131 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.7175 (mtp85) REVERT: C 89 ASN cc_start: 0.8737 (m-40) cc_final: 0.8458 (m110) REVERT: E 115 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8112 (mtmm) REVERT: H 43 LYS cc_start: 0.8204 (mmmt) cc_final: 0.7993 (mmtm) REVERT: H 90 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7383 (mm-30) REVERT: K 241 TYR cc_start: 0.5858 (OUTLIER) cc_final: 0.4930 (p90) outliers start: 28 outliers final: 23 residues processed: 157 average time/residue: 0.1484 time to fit residues: 31.2774 Evaluate side-chains 166 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 157 MET Chi-restraints excluded: chain K residue 198 ASN Chi-restraints excluded: chain K residue 212 VAL Chi-restraints excluded: chain K residue 223 GLN Chi-restraints excluded: chain K residue 241 TYR Chi-restraints excluded: chain K residue 259 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 95 optimal weight: 20.0000 chunk 32 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 93 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 20 optimal weight: 0.0040 chunk 16 optimal weight: 0.9980 chunk 86 optimal weight: 50.0000 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 75 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.177710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.127518 restraints weight = 17418.326| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.48 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14620 Z= 0.126 Angle : 0.568 9.484 20967 Z= 0.330 Chirality : 0.042 0.238 2358 Planarity : 0.004 0.056 1663 Dihedral : 30.072 175.448 4248 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.42 % Allowed : 13.56 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.28), residues: 957 helix: 2.11 (0.22), residues: 570 sheet: -1.16 (1.05), residues: 33 loop : -1.94 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 99 TYR 0.017 0.001 TYR K 236 PHE 0.019 0.001 PHE K 65 TRP 0.005 0.001 TRP K 210 HIS 0.002 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.13 (14610) covalent geometry : angle 0.56846 / 0.33 (20967) hydrogen bonds : bond 0.04889 / 3.28 ( 772) hydrogen bonds : angle 2.71640 / 1.91 ( 1934) metal coordination : bond 0.00089 / 0.07 ( 8) Misc. bond : bond 0.00093 / 0.05 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.7185 (mtp85) REVERT: C 89 ASN cc_start: 0.8766 (m-40) cc_final: 0.8465 (m110) REVERT: E 115 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8187 (mtmm) REVERT: H 56 MET cc_start: 0.7786 (tpp) cc_final: 0.7092 (tpt) REVERT: K 241 TYR cc_start: 0.5854 (OUTLIER) cc_final: 0.4944 (p90) outliers start: 20 outliers final: 15 residues processed: 155 average time/residue: 0.1571 time to fit residues: 32.9525 Evaluate side-chains 162 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 157 MET Chi-restraints excluded: chain K residue 198 ASN Chi-restraints excluded: chain K residue 212 VAL Chi-restraints excluded: chain K residue 241 TYR Chi-restraints excluded: chain K residue 259 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 33 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 4 optimal weight: 0.0770 chunk 6 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 80 optimal weight: 20.0000 chunk 113 optimal weight: 5.9990 chunk 40 optimal weight: 0.0770 chunk 90 optimal weight: 20.0000 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.179590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.129953 restraints weight = 17434.905| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.33 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 14620 Z= 0.120 Angle : 0.539 9.492 20967 Z= 0.318 Chirality : 0.040 0.245 2358 Planarity : 0.004 0.044 1663 Dihedral : 29.964 174.855 4248 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.69 % Allowed : 14.29 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.28), residues: 957 helix: 2.31 (0.22), residues: 571 sheet: 0.09 (1.48), residues: 18 loop : -1.89 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 83 TYR 0.014 0.001 TYR K 236 PHE 0.012 0.001 PHE K 65 TRP 0.003 0.001 TRP K 210 HIS 0.002 0.000 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00189 / 0.12 (14610) covalent geometry : angle 0.53899 / 0.32 (20967) hydrogen bonds : bond 0.04301 / 2.89 ( 772) hydrogen bonds : angle 2.59831 / 1.82 ( 1934) metal coordination : bond 0.00069 / 0.05 ( 8) Misc. bond : bond 0.00091 / 0.05 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2100.63 seconds wall clock time: 36 minutes 49.61 seconds (2209.61 seconds total)