Starting phenix.real_space_refine on Wed Mar 4 12:02:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ea5_31039/03_2026/7ea5_31039.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ea5_31039/03_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_31039/03_2026/7ea5_31039.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ea5_31039/03_2026/7ea5_31039.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ea5_31039/03_2026/7ea5_31039.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ea5_31039/03_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-5986/lib/python3.9/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: 2.78, 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: 1.01 Conformation dependent library (CDL) restraints added in 401.0 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: 2.05 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: 2.49 Time building geometry restraints manager: 1.42 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=" C2 SAM K 304 " pdb=" N3 SAM K 304 " ideal model delta sigma weight residual 1.322 1.382 -0.060 2.00e-02 2.50e+03 8.89e+00 bond pdb=" C8 SAM K 304 " pdb=" N7 SAM K 304 " ideal model delta sigma weight residual 1.298 1.351 -0.053 2.00e-02 2.50e+03 7.08e+00 bond pdb=" C2 SAM K 304 " pdb=" N1 SAM K 304 " ideal model delta sigma weight residual 1.329 1.381 -0.052 2.00e-02 2.50e+03 6.67e+00 bond pdb=" C6 SAM K 304 " pdb=" N1 SAM K 304 " ideal model delta sigma weight residual 1.337 1.379 -0.042 2.00e-02 2.50e+03 4.44e+00 bond pdb=" C3' DA J 19 " pdb=" O3' DA J 19 " ideal model delta sigma weight residual 1.422 1.479 -0.057 3.00e-02 1.11e+03 3.60e+00 ... (remaining 14605 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 20317 1.73 - 3.45: 588 3.45 - 5.18: 45 5.18 - 6.90: 11 6.90 - 8.63: 6 Bond angle restraints: 20967 Sorted by residual: angle pdb=" C3' DA J 19 " pdb=" O3' DA J 19 " pdb=" P DC J 20 " ideal model delta sigma weight residual 120.20 124.75 -4.55 1.50e+00 4.44e-01 9.20e+00 angle pdb=" N SER D 84 " pdb=" CA SER D 84 " pdb=" C SER D 84 " ideal model delta sigma weight residual 114.56 110.74 3.82 1.27e+00 6.20e-01 9.07e+00 angle pdb=" C GLY C 46 " pdb=" N ALA C 47 " pdb=" CA ALA C 47 " ideal model delta sigma weight residual 119.78 123.45 -3.67 1.24e+00 6.50e-01 8.74e+00 angle pdb=" CA LYS B 31 " pdb=" C LYS B 31 " pdb=" N PRO B 32 " ideal model delta sigma weight residual 118.44 123.01 -4.57 1.59e+00 3.96e-01 8.28e+00 angle pdb=" O SAM K 304 " pdb=" C SAM K 304 " pdb=" OXT SAM K 304 " ideal model delta sigma weight residual 126.77 118.14 8.63 3.00e+00 1.11e-01 8.28e+00 ... (remaining 20962 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.35: 6773 35.35 - 70.70: 1261 70.70 - 106.05: 16 106.05 - 141.41: 3 141.41 - 176.76: 1 Dihedral angle restraints: 8054 sinusoidal: 5214 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 8051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1846 0.044 - 0.089: 398 0.089 - 0.133: 97 0.133 - 0.177: 14 0.177 - 0.222: 3 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=" 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 chirality pdb=" C2' SAM K 304 " pdb=" C1' SAM K 304 " pdb=" C3' SAM K 304 " pdb=" O2' SAM K 304 " both_signs ideal model delta sigma weight residual False -2.76 -2.57 -0.18 2.00e-01 2.50e+01 8.25e-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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.750 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 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 : 0.011 0.588 14620 Z= 0.396 Angle : 0.682 8.630 20967 Z= 0.410 Chirality : 0.041 0.222 2358 Planarity : 0.005 0.059 1663 Dihedral : 24.985 176.756 6222 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 covalent geometry : bond 0.00373 (14610) covalent geometry : angle 0.68180 (20967) hydrogen bonds : bond 0.10338 ( 772) hydrogen bonds : angle 4.42462 ( 1934) metal coordination : bond 0.44504 ( 8) Misc. bond : bond 0.00156 ( 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 : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8625 (mttt) cc_final: 0.8310 (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 233 THR cc_start: 0.6394 (p) cc_final: 0.6043 (p) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.1829 time to fit residues: 64.8041 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 : 0.371 ------------------------------------------------------------------------------- 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: 0.8980 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 68 GLN A 125 GLN C 68 ASN D 106 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** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.182594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.133913 restraints weight = 17654.000| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.34 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14620 Z= 0.158 Angle : 0.532 6.587 20967 Z= 0.314 Chirality : 0.034 0.155 2358 Planarity : 0.004 0.044 1663 Dihedral : 29.231 179.748 4280 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.09 % Allowed : 7.87 % Favored : 91.04 % 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: -0.54 (0.26), residues: 957 helix: 0.96 (0.22), residues: 570 sheet: -1.55 (1.15), residues: 28 loop : -2.53 (0.27), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 83 TYR 0.012 0.002 TYR G 50 PHE 0.014 0.002 PHE G 25 TRP 0.009 0.002 TRP K 210 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00347 (14610) covalent geometry : angle 0.53201 (20967) hydrogen bonds : bond 0.04495 ( 772) hydrogen bonds : angle 2.69636 ( 1934) metal coordination : bond 0.00646 ( 8) Misc. bond : bond 0.00128 ( 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 188 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 179 time to evaluate : 0.375 Fit side-chains REVERT: B 24 ASP cc_start: 0.7118 (p0) cc_final: 0.6873 (p0) REVERT: B 79 LYS cc_start: 0.8477 (mttt) cc_final: 0.8267 (mtpp) REVERT: C 89 ASN cc_start: 0.8592 (m-40) cc_final: 0.8360 (m110) REVERT: F 59 LYS cc_start: 0.8356 (tttt) cc_final: 0.7910 (tttp) REVERT: F 63 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7057 (mt-10) REVERT: G 36 LYS cc_start: 0.8058 (ttpt) cc_final: 0.7737 (tttp) REVERT: K 85 ASP cc_start: 0.6578 (m-30) cc_final: 0.6273 (t0) REVERT: K 178 MET cc_start: 0.7302 (tpp) cc_final: 0.6527 (tpp) REVERT: K 241 TYR cc_start: 0.5818 (OUTLIER) cc_final: 0.5420 (p90) outliers start: 9 outliers final: 6 residues processed: 185 average time/residue: 0.1470 time to fit residues: 36.4382 Evaluate side-chains 160 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 153 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 109 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 95 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 115 optimal weight: 0.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN E 39 HIS G 31 HIS G 73 ASN ** K 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.177464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.128181 restraints weight = 17587.623| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.54 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14620 Z= 0.191 Angle : 0.568 6.508 20967 Z= 0.332 Chirality : 0.036 0.139 2358 Planarity : 0.004 0.043 1663 Dihedral : 29.465 178.617 4280 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.66 % Allowed : 9.93 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.27), residues: 957 helix: 1.52 (0.22), residues: 572 sheet: -1.17 (1.19), residues: 28 loop : -2.38 (0.28), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 83 TYR 0.013 0.002 TYR D 37 PHE 0.023 0.002 PHE G 25 TRP 0.009 0.003 TRP K 210 HIS 0.006 0.001 HIS K 199 Details of bonding type rmsd covalent geometry : bond 0.00440 (14610) covalent geometry : angle 0.56808 (20967) hydrogen bonds : bond 0.05479 ( 772) hydrogen bonds : angle 2.73934 ( 1934) metal coordination : bond 0.00218 ( 8) Misc. bond : bond 0.00177 ( 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: 22 poor density : 161 time to evaluate : 0.345 Fit side-chains REVERT: B 24 ASP cc_start: 0.6828 (p0) cc_final: 0.6579 (p0) REVERT: B 79 LYS cc_start: 0.8452 (mttt) cc_final: 0.8246 (mtpp) REVERT: C 89 ASN cc_start: 0.8796 (m-40) cc_final: 0.8513 (m110) REVERT: D 76 ARG cc_start: 0.7805 (mtm-85) cc_final: 0.7556 (mtm-85) REVERT: E 39 HIS cc_start: 0.7775 (OUTLIER) cc_final: 0.7265 (t-170) REVERT: E 115 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8189 (mtmm) REVERT: G 77 ARG cc_start: 0.8105 (mtp85) cc_final: 0.7892 (mtm180) REVERT: K 233 THR cc_start: 0.6643 (p) cc_final: 0.6349 (m) REVERT: K 241 TYR cc_start: 0.5800 (OUTLIER) cc_final: 0.4638 (p90) outliers start: 22 outliers final: 15 residues processed: 174 average time/residue: 0.1621 time to fit residues: 36.9442 Evaluate side-chains 172 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 36 ILE 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 39 HIS 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 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 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: 6.9990 chunk 86 optimal weight: 20.0000 chunk 85 optimal weight: 30.0000 chunk 48 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN F 25 ASN ** K 112 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 = 0.4021 r_free = 0.4021 target = 0.177653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.127844 restraints weight = 17460.860| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.50 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14620 Z= 0.168 Angle : 0.530 6.508 20967 Z= 0.314 Chirality : 0.034 0.145 2358 Planarity : 0.004 0.042 1663 Dihedral : 29.414 178.428 4280 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.18 % Allowed : 11.02 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.50 (0.28), residues: 957 helix: 1.82 (0.22), residues: 572 sheet: -0.96 (1.21), residues: 28 loop : -2.17 (0.28), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 83 TYR 0.010 0.001 TYR D 37 PHE 0.028 0.002 PHE K 159 TRP 0.004 0.001 TRP K 210 HIS 0.016 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00380 (14610) covalent geometry : angle 0.53039 (20967) hydrogen bonds : bond 0.04740 ( 772) hydrogen bonds : angle 2.60826 ( 1934) metal coordination : bond 0.00122 ( 8) Misc. bond : bond 0.00116 ( 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 170 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8515 (mttt) cc_final: 0.8307 (mtpp) REVERT: C 89 ASN cc_start: 0.8795 (m-40) cc_final: 0.8509 (m110) REVERT: D 76 ARG cc_start: 0.7823 (mtm-85) cc_final: 0.7610 (mtm-85) REVERT: E 115 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8147 (mtmm) REVERT: H 56 MET cc_start: 0.7813 (tpp) cc_final: 0.7501 (tpt) REVERT: K 233 THR cc_start: 0.6609 (p) cc_final: 0.6345 (m) REVERT: K 241 TYR cc_start: 0.5792 (OUTLIER) cc_final: 0.4397 (p90) outliers start: 18 outliers final: 13 residues processed: 161 average time/residue: 0.1567 time to fit residues: 33.4208 Evaluate side-chains 157 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 115 LYS 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 E residue 115 LYS Chi-restraints excluded: chain F residue 25 ASN 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 212 VAL Chi-restraints excluded: chain K residue 241 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 15 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 45 optimal weight: 0.0270 chunk 55 optimal weight: 1.9990 overall best weight: 1.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 HIS F 25 ASN K 90 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.177687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.127264 restraints weight = 17513.690| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.42 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14620 Z= 0.159 Angle : 0.525 6.288 20967 Z= 0.311 Chirality : 0.034 0.144 2358 Planarity : 0.004 0.041 1663 Dihedral : 29.351 178.675 4280 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.18 % Allowed : 11.86 % Favored : 85.96 % 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: 0.72 (0.28), residues: 957 helix: 1.97 (0.22), residues: 572 sheet: -1.10 (0.96), residues: 38 loop : -2.02 (0.29), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 83 TYR 0.010 0.001 TYR D 37 PHE 0.029 0.002 PHE K 159 TRP 0.002 0.001 TRP K 210 HIS 0.003 0.001 HIS K 199 Details of bonding type rmsd covalent geometry : bond 0.00355 (14610) covalent geometry : angle 0.52487 (20967) hydrogen bonds : bond 0.04552 ( 772) hydrogen bonds : angle 2.54408 ( 1934) metal coordination : bond 0.00112 ( 8) Misc. bond : bond 0.00137 ( 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 166 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8557 (mttt) cc_final: 0.8336 (mtpp) REVERT: C 89 ASN cc_start: 0.8747 (m-40) cc_final: 0.8463 (m110) REVERT: D 76 ARG cc_start: 0.7762 (mtm-85) cc_final: 0.7523 (mtm-85) REVERT: E 115 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8163 (mtmm) REVERT: H 56 MET cc_start: 0.7745 (tpp) cc_final: 0.7098 (tpt) REVERT: K 233 THR cc_start: 0.6603 (p) cc_final: 0.6385 (m) REVERT: K 241 TYR cc_start: 0.5708 (OUTLIER) cc_final: 0.4238 (p90) outliers start: 18 outliers final: 13 residues processed: 157 average time/residue: 0.1545 time to fit residues: 32.0013 Evaluate side-chains 153 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU 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 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 86 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL 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: 3.9990 chunk 97 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 114 optimal weight: 0.7980 chunk 87 optimal weight: 10.0000 chunk 105 optimal weight: 20.0000 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN ** K 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.172346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.120735 restraints weight = 17322.201| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.36 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 14620 Z= 0.260 Angle : 0.614 7.708 20967 Z= 0.355 Chirality : 0.039 0.140 2358 Planarity : 0.005 0.046 1663 Dihedral : 29.621 179.042 4280 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.63 % Allowed : 11.02 % Favored : 85.35 % 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: 0.29 (0.27), residues: 957 helix: 1.54 (0.22), residues: 574 sheet: -1.25 (0.95), residues: 38 loop : -2.05 (0.29), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 83 TYR 0.014 0.002 TYR F 51 PHE 0.026 0.003 PHE K 159 TRP 0.005 0.001 TRP K 210 HIS 0.005 0.001 HIS K 199 Details of bonding type rmsd covalent geometry : bond 0.00618 (14610) covalent geometry : angle 0.61446 (20967) hydrogen bonds : bond 0.06558 ( 772) hydrogen bonds : angle 2.84911 ( 1934) metal coordination : bond 0.00275 ( 8) Misc. bond : bond 0.00152 ( 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 178 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: D 56 MET cc_start: 0.8504 (tpp) cc_final: 0.8182 (mmm) REVERT: E 115 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8272 (mtmm) REVERT: K 241 TYR cc_start: 0.5942 (OUTLIER) cc_final: 0.4848 (p90) outliers start: 30 outliers final: 22 residues processed: 167 average time/residue: 0.1573 time to fit residues: 34.7488 Evaluate side-chains 158 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU 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 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 115 LYS 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 85 ASP Chi-restraints excluded: chain K residue 115 GLN Chi-restraints excluded: chain K residue 122 ILE Chi-restraints excluded: chain K residue 164 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 53 optimal weight: 0.9990 chunk 84 optimal weight: 20.0000 chunk 111 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 12 optimal weight: 0.0870 chunk 63 optimal weight: 0.9980 chunk 85 optimal weight: 30.0000 chunk 95 optimal weight: 6.9990 chunk 114 optimal weight: 8.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN ** K 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.178026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.126844 restraints weight = 17385.112| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.26 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14620 Z= 0.139 Angle : 0.522 6.234 20967 Z= 0.311 Chirality : 0.033 0.161 2358 Planarity : 0.004 0.042 1663 Dihedral : 29.275 176.987 4280 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.57 % Allowed : 13.08 % Favored : 85.35 % 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: 0.94 (0.28), residues: 957 helix: 2.18 (0.22), residues: 566 sheet: -0.92 (0.98), residues: 38 loop : -1.93 (0.29), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 83 TYR 0.010 0.001 TYR K 236 PHE 0.045 0.001 PHE K 159 TRP 0.005 0.001 TRP K 210 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00297 (14610) covalent geometry : angle 0.52162 (20967) hydrogen bonds : bond 0.03933 ( 772) hydrogen bonds : angle 2.47934 ( 1934) metal coordination : bond 0.00049 ( 8) Misc. bond : bond 0.00125 ( 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 162 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: C 89 ASN cc_start: 0.8758 (m-40) cc_final: 0.8455 (m110) REVERT: H 56 MET cc_start: 0.7784 (tpp) cc_final: 0.7456 (mmm) REVERT: K 241 TYR cc_start: 0.5729 (OUTLIER) cc_final: 0.4383 (p90) outliers start: 13 outliers final: 9 residues processed: 156 average time/residue: 0.1486 time to fit residues: 30.8284 Evaluate side-chains 150 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 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 109 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 K residue 241 TYR 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: 1.9990 chunk 116 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 90 optimal weight: 8.9990 chunk 57 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.177537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.126507 restraints weight = 17296.445| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.26 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14620 Z= 0.149 Angle : 0.532 8.953 20967 Z= 0.314 Chirality : 0.034 0.154 2358 Planarity : 0.004 0.043 1663 Dihedral : 29.251 178.768 4280 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.33 % Allowed : 13.92 % 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: 1.03 (0.28), residues: 957 helix: 2.22 (0.22), residues: 572 sheet: -0.90 (0.99), residues: 38 loop : -1.90 (0.29), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 83 TYR 0.014 0.001 TYR K 236 PHE 0.041 0.002 PHE K 159 TRP 0.002 0.001 TRP K 210 HIS 0.002 0.001 HIS K 199 Details of bonding type rmsd covalent geometry : bond 0.00329 (14610) covalent geometry : angle 0.53183 (20967) hydrogen bonds : bond 0.04291 ( 772) hydrogen bonds : angle 2.50373 ( 1934) metal coordination : bond 0.00070 ( 8) Misc. bond : bond 0.00124 ( 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 154 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: C 89 ASN cc_start: 0.8734 (m-40) cc_final: 0.8442 (m110) REVERT: H 90 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7353 (mm-30) REVERT: K 157 MET cc_start: 0.6169 (ptp) cc_final: 0.5945 (ptp) REVERT: K 241 TYR cc_start: 0.5730 (OUTLIER) cc_final: 0.4475 (p90) outliers start: 11 outliers final: 9 residues processed: 148 average time/residue: 0.1521 time to fit residues: 30.1452 Evaluate side-chains 151 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 140 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 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 109 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 241 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 15 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN K 115 GLN ** K 198 ASN ** 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 = 0.3981 r_free = 0.3981 target = 0.174230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.123754 restraints weight = 17337.667| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.41 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14620 Z= 0.209 Angle : 0.588 10.164 20967 Z= 0.340 Chirality : 0.036 0.146 2358 Planarity : 0.004 0.044 1663 Dihedral : 29.406 179.697 4280 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.94 % Allowed : 13.68 % 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: 0.76 (0.28), residues: 957 helix: 1.93 (0.22), residues: 573 sheet: -1.01 (0.95), residues: 38 loop : -1.88 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 83 TYR 0.012 0.001 TYR F 51 PHE 0.039 0.002 PHE K 159 TRP 0.003 0.001 TRP K 210 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00488 (14610) covalent geometry : angle 0.58777 (20967) hydrogen bonds : bond 0.05685 ( 772) hydrogen bonds : angle 2.73302 ( 1934) metal coordination : bond 0.00169 ( 8) Misc. bond : bond 0.00143 ( 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 157 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8675 (tptm) cc_final: 0.8377 (tttt) REVERT: D 56 MET cc_start: 0.8358 (tpp) cc_final: 0.8156 (mmm) REVERT: H 90 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7319 (mm-30) REVERT: K 241 TYR cc_start: 0.5808 (OUTLIER) cc_final: 0.4695 (p90) outliers start: 16 outliers final: 12 residues processed: 149 average time/residue: 0.1559 time to fit residues: 31.1333 Evaluate side-chains 152 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 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 109 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 62 ILE Chi-restraints excluded: chain G residue 114 VAL 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 241 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 95 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 86 optimal weight: 20.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.177728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.128163 restraints weight = 17362.039| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.38 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.4016 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= 0.145 Angle : 0.541 10.808 20967 Z= 0.318 Chirality : 0.033 0.159 2358 Planarity : 0.004 0.042 1663 Dihedral : 29.198 177.585 4280 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.45 % Allowed : 14.77 % Favored : 83.78 % 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: 1.09 (0.28), residues: 957 helix: 2.24 (0.22), residues: 570 sheet: -0.94 (0.97), residues: 38 loop : -1.80 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 83 TYR 0.008 0.001 TYR D 37 PHE 0.040 0.002 PHE K 159 TRP 0.004 0.001 TRP K 210 HIS 0.002 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00316 (14610) covalent geometry : angle 0.54056 (20967) hydrogen bonds : bond 0.04087 ( 772) hydrogen bonds : angle 2.52500 ( 1934) metal coordination : bond 0.00092 ( 8) Misc. bond : bond 0.00112 ( 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 153 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8541 (tptm) cc_final: 0.8278 (tttt) REVERT: C 89 ASN cc_start: 0.8680 (m-40) cc_final: 0.8387 (m110) REVERT: H 56 MET cc_start: 0.7774 (tpp) cc_final: 0.7394 (mmm) REVERT: H 90 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7281 (mm-30) REVERT: K 241 TYR cc_start: 0.5658 (OUTLIER) cc_final: 0.4400 (p90) outliers start: 12 outliers final: 9 residues processed: 147 average time/residue: 0.1489 time to fit residues: 29.4514 Evaluate side-chains 149 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 109 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 241 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 33 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 27 optimal weight: 0.3980 chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN ** K 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.178844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.128735 restraints weight = 17364.396| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.28 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14620 Z= 0.139 Angle : 0.538 10.565 20967 Z= 0.316 Chirality : 0.033 0.164 2358 Planarity : 0.004 0.043 1663 Dihedral : 29.151 178.342 4280 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.45 % Allowed : 14.89 % Favored : 83.66 % 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: 1.26 (0.28), residues: 957 helix: 2.41 (0.22), residues: 567 sheet: -1.55 (0.77), residues: 53 loop : -1.64 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 83 TYR 0.008 0.001 TYR D 37 PHE 0.037 0.001 PHE K 159 TRP 0.002 0.001 TRP K 210 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00299 (14610) covalent geometry : angle 0.53766 (20967) hydrogen bonds : bond 0.03900 ( 772) hydrogen bonds : angle 2.50673 ( 1934) metal coordination : bond 0.00080 ( 8) Misc. bond : bond 0.00108 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2055.76 seconds wall clock time: 35 minutes 59.43 seconds (2159.43 seconds total)