Starting phenix.real_space_refine on Wed Aug 5 18:04:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8atv_15664/08_2026/8atv_15664.cif Found real_map, /net/cci-nas-00/data/ceres_data/8atv_15664/08_2026/8atv_15664.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8atv_15664/08_2026/8atv_15664.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8atv_15664/08_2026/8atv_15664.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8atv_15664/08_2026/8atv_15664.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8atv_15664/08_2026/8atv_15664.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8atv_15664/08_2026/8atv_15664.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8atv_15664/08_2026/8atv_15664.map" } resolution = 3.39 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= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 61 5.49 5 S 35 5.16 5 C 6950 2.51 5 N 1943 2.21 5 O 2172 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11161 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2733 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 314} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 7199 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 923, 7191 Classifications: {'peptide': 923} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 44, 'TRANS': 878} Chain breaks: 2 Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ASP:plan': 12, 'GLU:plan': 7, 'GLN:plan1': 1, 'ARG:plan': 3, 'PHE:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 95 Conformer: "B" Number of residues, atoms: 923, 7191 Classifications: {'peptide': 923} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 44, 'TRANS': 878} Chain breaks: 2 Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ASP:plan': 12, 'GLU:plan': 7, 'GLN:plan1': 1, 'ARG:plan': 3, 'PHE:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 95 bond proxies already assigned to first conformer: 7343 Chain: "N" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 560 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "T" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 548 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "C" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Classifications: {'RNAv2': 4} Modifications used: {'rna3p_pur': 4} Link IDs: {'rna3p': 3} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.89, per 1000 atoms: 0.35 Number of scatterers: 11161 At special positions: 0 Unit cell: (102.82, 117.37, 119.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 35 16.00 P 61 15.00 O 2172 8.00 N 1943 7.00 C 6950 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 559.6 milliseconds 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2380 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 11 sheets defined 58.3% alpha, 8.9% beta 21 base pairs and 40 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'B' and resid 7 through 12 Processing helix chain 'B' and resid 25 through 37 Processing helix chain 'B' and resid 37 through 42 removed outlier: 4.161A pdb=" N THR B 41 " --> pdb=" O ASP B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 47 Processing helix chain 'B' and resid 58 through 69 Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 104 through 113 removed outlier: 4.308A pdb=" N TYR B 108 " --> pdb=" O ASP B 104 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER B 109 " --> pdb=" O TRP B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 157 removed outlier: 3.782A pdb=" N ILE B 147 " --> pdb=" O SER B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 181 Processing helix chain 'B' and resid 190 through 199 Processing helix chain 'B' and resid 212 through 216 removed outlier: 3.504A pdb=" N GLY B 215 " --> pdb=" O GLU B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 Processing helix chain 'B' and resid 230 through 234 removed outlier: 3.663A pdb=" N GLU B 233 " --> pdb=" O SER B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 267 Processing helix chain 'B' and resid 273 through 282 removed outlier: 5.741A pdb=" N MET B 278 " --> pdb=" O ASN B 275 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ASP B 279 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY B 282 " --> pdb=" O ASP B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 293 Processing helix chain 'B' and resid 296 through 300 Processing helix chain 'B' and resid 307 through 321 Processing helix chain 'A' and resid 388 through 395 Processing helix chain 'A' and resid 397 through 412 Processing helix chain 'A' and resid 412 through 421 Processing helix chain 'A' and resid 422 through 441 Processing helix chain 'A' and resid 448 through 478 Proline residue: A 463 - end of helix removed outlier: 3.870A pdb=" N GLU A 478 " --> pdb=" O SER A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 497 removed outlier: 3.820A pdb=" N THR A 491 " --> pdb=" O ASN A 487 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN A 492 " --> pdb=" O LYS A 488 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY A 495 " --> pdb=" O THR A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 519 Processing helix chain 'A' and resid 531 through 555 removed outlier: 3.645A pdb=" N ILE A 536 " --> pdb=" O ALA A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 612 Processing helix chain 'A' and resid 652 through 660 removed outlier: 4.207A pdb=" N GLN A 658 " --> pdb=" O THR A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 668 Processing helix chain 'A' and resid 703 through 717 removed outlier: 3.864A pdb=" N VAL A 707 " --> pdb=" O SER A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 731 Processing helix chain 'A' and resid 737 through 751 removed outlier: 3.853A pdb=" N GLY A 751 " --> pdb=" O VAL A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 813 removed outlier: 3.500A pdb=" N THR A 803 " --> pdb=" O ASN A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 848 Processing helix chain 'A' and resid 860 through 873 Processing helix chain 'A' and resid 879 through 890 Processing helix chain 'A' and resid 890 through 900 Processing helix chain 'A' and resid 907 through 911 Processing helix chain 'A' and resid 913 through 929 Processing helix chain 'A' and resid 932 through 935 Processing helix chain 'A' and resid 948 through 959 Processing helix chain 'A' and resid 960 through 967 Processing helix chain 'A' and resid 977 through 994 Processing helix chain 'A' and resid 998 through 1004 removed outlier: 3.720A pdb=" N LEU A1004 " --> pdb=" O ASN A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1021 removed outlier: 4.145A pdb=" N VAL A1021 " --> pdb=" O VAL A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1038 removed outlier: 3.687A pdb=" N GLN A1036 " --> pdb=" O GLN A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1066 Processing helix chain 'A' and resid 1067 through 1085 Processing helix chain 'A' and resid 1090 through 1094 removed outlier: 3.545A pdb=" N GLU A1093 " --> pdb=" O ASP A1090 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYS A1094 " --> pdb=" O VAL A1091 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1090 through 1094' Processing helix chain 'A' and resid 1149 through 1180 Proline residue: A1158 - end of helix removed outlier: 3.629A pdb=" N ILE A1162 " --> pdb=" O PRO A1158 " (cutoff:3.500A) Processing helix chain 'A' and resid 1197 through 1213 Processing helix chain 'A' and resid 1216 through 1229 Processing helix chain 'A' and resid 1242 through 1260 removed outlier: 3.596A pdb=" N ILE A1248 " --> pdb=" O LEU A1244 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A1249 " --> pdb=" O ALA A1245 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1281 removed outlier: 3.581A pdb=" N LEU A1279 " --> pdb=" O ARG A1275 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1293 Processing helix chain 'A' and resid 1297 through 1301 Processing helix chain 'A' and resid 1339 through 1346 removed outlier: 3.506A pdb=" N LEU A1343 " --> pdb=" O VAL A1340 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN A1345 " --> pdb=" O VAL A1342 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.924A pdb=" N TYR B 73 " --> pdb=" O GLN B 96 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N LEU B 98 " --> pdb=" O TYR B 73 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU B 75 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LYS B 49 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N VAL B 135 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU B 51 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ASN B 137 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N LEU B 53 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LYS B 167 " --> pdb=" O PHE B 132 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N GLU B 246 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LEU B 204 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ASP B 248 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N THR B 202 " --> pdb=" O ASP B 248 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 528 through 530 Processing sheet with id=AA3, first strand: chain 'A' and resid 613 through 619 removed outlier: 3.637A pdb=" N GLY A 629 " --> pdb=" O VAL A 616 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 680 through 684 removed outlier: 4.485A pdb=" N TRP A 682 " --> pdb=" O SER A 687 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N SER A 687 " --> pdb=" O TRP A 682 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 698 through 699 Processing sheet with id=AA6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AA7, first strand: chain 'A' and resid 855 through 856 Processing sheet with id=AA8, first strand: chain 'A' and resid 942 through 945 Processing sheet with id=AA9, first strand: chain 'A' and resid 1087 through 1088 removed outlier: 3.546A pdb=" N LEU A1238 " --> pdb=" O MET A1321 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N MET A1321 " --> pdb=" O LEU A1238 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1109 through 1111 Processing sheet with id=AB2, first strand: chain 'A' and resid 1127 through 1131 removed outlier: 3.521A pdb=" N ILE A1139 " --> pdb=" O LYS A1128 " (cutoff:3.500A) 539 hydrogen bonds defined for protein. 1544 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 40 stacking parallelities Total time for adding SS restraints: 3.03 Time building geometry restraints manager: 0.94 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: 3129 1.34 - 1.45: 2167 1.45 - 1.57: 6081 1.57 - 1.69: 112 1.69 - 1.81: 59 Bond restraints: 11548 Sorted by residual: bond pdb=" O3' DT T 14 " pdb=" P DG T 15 " ideal model delta sigma weight residual 1.607 1.471 0.136 1.20e-02 6.94e+03 1.29e+02 bond pdb=" O3' DA T 13 " pdb=" P DT T 14 " ideal model delta sigma weight residual 1.607 1.494 0.113 1.20e-02 6.94e+03 8.85e+01 bond pdb=" O3' DC T 25 " pdb=" P DA T 26 " ideal model delta sigma weight residual 1.607 1.510 0.097 1.20e-02 6.94e+03 6.52e+01 bond pdb=" C3' DG N 108 " pdb=" C2' DG N 108 " ideal model delta sigma weight residual 1.516 1.457 0.059 8.00e-03 1.56e+04 5.53e+01 bond pdb=" O3' DT N 112 " pdb=" P DG N 113 " ideal model delta sigma weight residual 1.607 1.687 -0.080 1.20e-02 6.94e+03 4.48e+01 ... (remaining 11543 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 15719 2.63 - 5.26: 163 5.26 - 7.89: 20 7.89 - 10.52: 10 10.52 - 13.15: 2 Bond angle restraints: 15914 Sorted by residual: angle pdb=" O4' DT T 20 " pdb=" C4' DT T 20 " pdb=" C3' DT T 20 " ideal model delta sigma weight residual 106.00 101.62 4.38 6.00e-01 2.78e+00 5.32e+01 angle pdb=" C3' DT T 14 " pdb=" O3' DT T 14 " pdb=" P DG T 15 " ideal model delta sigma weight residual 119.70 127.00 -7.30 1.20e+00 6.94e-01 3.70e+01 angle pdb=" O4' DC T 21 " pdb=" C4' DC T 21 " pdb=" C3' DC T 21 " ideal model delta sigma weight residual 106.00 102.36 3.64 6.00e-01 2.78e+00 3.68e+01 angle pdb=" C3' DT N 112 " pdb=" O3' DT N 112 " pdb=" P DG N 113 " ideal model delta sigma weight residual 119.70 126.82 -7.12 1.20e+00 6.94e-01 3.52e+01 angle pdb=" O4' DC T 22 " pdb=" C4' DC T 22 " pdb=" C3' DC T 22 " ideal model delta sigma weight residual 106.00 102.99 3.01 6.00e-01 2.78e+00 2.51e+01 ... (remaining 15909 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.58: 6259 27.58 - 55.17: 490 55.17 - 82.75: 49 82.75 - 110.34: 6 110.34 - 137.92: 2 Dihedral angle restraints: 6806 sinusoidal: 3131 harmonic: 3675 Sorted by residual: dihedral pdb=" O3A GTP C 201 " pdb=" O3B GTP C 201 " pdb=" PB GTP C 201 " pdb=" PG GTP C 201 " ideal model delta sinusoidal sigma weight residual 303.79 165.87 137.92 1 2.00e+01 2.50e-03 4.18e+01 dihedral pdb=" C8 GTP C 201 " pdb=" C1' GTP C 201 " pdb=" N9 GTP C 201 " pdb=" O4' GTP C 201 " ideal model delta sinusoidal sigma weight residual 104.59 -12.68 117.28 1 2.00e+01 2.50e-03 3.50e+01 dihedral pdb=" O3B GTP C 201 " pdb=" O3A GTP C 201 " pdb=" PB GTP C 201 " pdb=" PA GTP C 201 " ideal model delta sinusoidal sigma weight residual -68.92 -166.09 97.17 1 2.00e+01 2.50e-03 2.70e+01 ... (remaining 6803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 1701 0.108 - 0.216: 53 0.216 - 0.324: 5 0.324 - 0.432: 2 0.432 - 0.540: 1 Chirality restraints: 1762 Sorted by residual: chirality pdb=" P DT N 127 " pdb=" OP1 DT N 127 " pdb=" OP2 DT N 127 " pdb=" O5' DT N 127 " both_signs ideal model delta sigma weight residual True 2.34 -2.88 -0.54 2.00e-01 2.50e+01 7.28e+00 chirality pdb=" C4' DA N 130 " pdb=" C5' DA N 130 " pdb=" O4' DA N 130 " pdb=" C3' DA N 130 " both_signs ideal model delta sigma weight residual False -2.53 -2.11 -0.42 2.00e-01 2.50e+01 4.50e+00 chirality pdb=" C3' DG N 108 " pdb=" C4' DG N 108 " pdb=" O3' DG N 108 " pdb=" C2' DG N 108 " both_signs ideal model delta sigma weight residual False -2.73 -2.32 -0.41 2.00e-01 2.50e+01 4.15e+00 ... (remaining 1759 not shown) Planarity restraints: 1828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 119 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.84e+00 pdb=" N PRO B 120 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 120 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 120 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 703 " -0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO A 704 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 704 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 704 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 775 " 0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO A 776 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 776 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 776 " 0.022 5.00e-02 4.00e+02 ... (remaining 1825 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 399 2.72 - 3.26: 10573 3.26 - 3.81: 18947 3.81 - 4.35: 23018 4.35 - 4.90: 38372 Nonbonded interactions: 91309 Sorted by model distance: nonbonded pdb=" O ASN A 487 " pdb=" OG1 THR A 491 " model vdw 2.173 3.040 nonbonded pdb=" OD1 ASP B 257 " pdb=" N ASN B 258 " model vdw 2.177 3.120 nonbonded pdb=" O PRO B 102 " pdb=" OH TYR B 108 " model vdw 2.214 3.040 nonbonded pdb=" NE2 GLN A 416 " pdb=" OE1 GLU A 420 " model vdw 2.261 3.120 nonbonded pdb=" O PHE B 90 " pdb=" OG SER B 93 " model vdw 2.264 3.040 ... (remaining 91304 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 14.500 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 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 : 0.004 0.136 11549 Z= 0.312 Angle : 0.689 13.149 15914 Z= 0.403 Chirality : 0.051 0.540 1762 Planarity : 0.004 0.042 1828 Dihedral : 18.000 137.923 4426 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: 1.00 (0.24), residues: 1250 helix: 1.67 (0.20), residues: 697 sheet: 0.70 (0.54), residues: 93 loop : -0.92 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1220 TYR 0.014 0.001 TYR B 161 PHE 0.012 0.001 PHE A 886 TRP 0.008 0.001 TRP A 864 HIS 0.007 0.001 HIS A1057 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.31 (11548) covalent geometry : angle 0.68923 / 0.40 (15914) hydrogen bonds : bond 0.13915 / 9.10 ( 586) hydrogen bonds : angle 5.32629 / 3.64 ( 1638) Misc. bond : bond 0.05346 / 2.81 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.273 Fit side-chains REVERT: A 467 GLU cc_start: 0.6632 (tp30) cc_final: 0.6321 (tp30) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.0898 time to fit residues: 21.1906 Evaluate side-chains 138 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 35 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 449 ASN A 658 GLN A 966 GLN A1032 GLN A1231 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.161534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.127758 restraints weight = 22809.678| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.17 r_work: 0.3126 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3114 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3114 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11549 Z= 0.233 Angle : 0.690 9.263 15914 Z= 0.368 Chirality : 0.048 0.226 1762 Planarity : 0.005 0.048 1828 Dihedral : 18.510 112.143 2041 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.95 % Allowed : 6.34 % Favored : 92.71 % 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: 0.66 (0.24), residues: 1250 helix: 1.40 (0.20), residues: 690 sheet: 0.66 (0.54), residues: 98 loop : -1.09 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 79 TYR 0.017 0.002 TYR A 496 PHE 0.020 0.002 PHE B 229 TRP 0.011 0.002 TRP A 907 HIS 0.010 0.002 HIS A 943 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.23 (11548) covalent geometry : angle 0.69041 / 0.37 (15914) hydrogen bonds : bond 0.05760 / 3.69 ( 586) hydrogen bonds : angle 4.37140 / 3.03 ( 1638) Misc. bond : bond 0.00416 / 0.22 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 151 time to evaluate : 0.236 Fit side-chains REVERT: B 25 ASN cc_start: 0.7119 (t0) cc_final: 0.6837 (t0) REVERT: B 116 ARG cc_start: 0.7258 (mmm-85) cc_final: 0.7057 (mmm-85) REVERT: A 461 MET cc_start: 0.8805 (tmm) cc_final: 0.8118 (ttt) REVERT: A 468 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7324 (mm-30) outliers start: 10 outliers final: 8 residues processed: 153 average time/residue: 0.0997 time to fit residues: 21.4910 Evaluate side-chains 153 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 145 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1054 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 6.9990 chunk 111 optimal weight: 8.9990 chunk 73 optimal weight: 8.9990 chunk 104 optimal weight: 4.9990 chunk 12 optimal weight: 0.0570 chunk 15 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 890 HIS A1032 GLN A1231 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.165973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.131671 restraints weight = 21316.111| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.99 r_work: 0.3217 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11549 Z= 0.124 Angle : 0.567 8.604 15914 Z= 0.307 Chirality : 0.042 0.199 1762 Planarity : 0.004 0.042 1828 Dihedral : 18.463 108.930 2041 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.85 % Allowed : 7.39 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.24), residues: 1250 helix: 1.81 (0.20), residues: 691 sheet: 0.52 (0.51), residues: 103 loop : -0.96 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1220 TYR 0.018 0.002 TYR B 42 PHE 0.012 0.001 PHE A 886 TRP 0.009 0.001 TRP A 455 HIS 0.007 0.001 HIS A1057 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (11548) covalent geometry : angle 0.56681 / 0.31 (15914) hydrogen bonds : bond 0.04678 / 2.93 ( 586) hydrogen bonds : angle 3.99595 / 2.79 ( 1638) Misc. bond : bond 0.00147 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 157 time to evaluate : 0.250 Fit side-chains REVERT: B 25 ASN cc_start: 0.6929 (t0) cc_final: 0.6641 (t0) REVERT: B 214 LYS cc_start: 0.8144 (mmtm) cc_final: 0.7886 (mmtm) REVERT: A 461 MET cc_start: 0.8675 (tmm) cc_final: 0.8032 (ttt) REVERT: A 888 GLU cc_start: 0.7254 (mt-10) cc_final: 0.6648 (mt-10) REVERT: A 1019 THR cc_start: 0.8764 (m) cc_final: 0.8477 (m) REVERT: A 1105 MET cc_start: 0.8533 (mmm) cc_final: 0.8309 (mmp) REVERT: A 1351 SER cc_start: 0.7182 (m) cc_final: 0.6594 (p) outliers start: 9 outliers final: 7 residues processed: 158 average time/residue: 0.1013 time to fit residues: 22.4519 Evaluate side-chains 152 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 145 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1233 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 50 optimal weight: 0.9990 chunk 128 optimal weight: 30.0000 chunk 46 optimal weight: 0.9980 chunk 54 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 5 optimal weight: 0.2980 chunk 119 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1231 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.166931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.131877 restraints weight = 18435.256| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.87 r_work: 0.3227 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11549 Z= 0.117 Angle : 0.549 8.393 15914 Z= 0.295 Chirality : 0.041 0.184 1762 Planarity : 0.004 0.042 1828 Dihedral : 18.463 107.377 2041 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.14 % Allowed : 8.14 % Favored : 90.72 % 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: 1.28 (0.24), residues: 1250 helix: 1.97 (0.20), residues: 690 sheet: 0.64 (0.51), residues: 103 loop : -0.87 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1220 TYR 0.016 0.001 TYR A 496 PHE 0.013 0.001 PHE A 886 TRP 0.008 0.001 TRP A 864 HIS 0.007 0.001 HIS A1057 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.12 (11548) covalent geometry : angle 0.54900 / 0.30 (15914) hydrogen bonds : bond 0.04312 / 2.72 ( 586) hydrogen bonds : angle 3.85908 / 2.69 ( 1638) Misc. bond : bond 0.00071 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 0.379 Fit side-chains REVERT: B 25 ASN cc_start: 0.6948 (t0) cc_final: 0.6674 (t0) REVERT: B 168 MET cc_start: 0.7964 (mmm) cc_final: 0.7607 (tpt) REVERT: A 461 MET cc_start: 0.8689 (tmm) cc_final: 0.8225 (ttt) REVERT: A 467 GLU cc_start: 0.7196 (tp30) cc_final: 0.6903 (tp30) REVERT: A 888 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6757 (mt-10) REVERT: A 988 LYS cc_start: 0.7138 (tmtt) cc_final: 0.6768 (tppt) REVERT: A 1019 THR cc_start: 0.8914 (m) cc_final: 0.8639 (m) REVERT: A 1105 MET cc_start: 0.8603 (mmm) cc_final: 0.8335 (mmp) REVERT: A 1351 SER cc_start: 0.7214 (m) cc_final: 0.6622 (p) outliers start: 12 outliers final: 10 residues processed: 152 average time/residue: 0.0928 time to fit residues: 20.0975 Evaluate side-chains 156 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1231 ASN Chi-restraints excluded: chain A residue 1233 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 128 optimal weight: 20.0000 chunk 113 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 123 GLN ** 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 = 0.3761 r_free = 0.3761 target = 0.163824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.129308 restraints weight = 21332.145| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.99 r_work: 0.3187 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11549 Z= 0.177 Angle : 0.591 8.857 15914 Z= 0.316 Chirality : 0.043 0.190 1762 Planarity : 0.005 0.055 1828 Dihedral : 18.606 107.797 2041 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.14 % Allowed : 9.19 % Favored : 89.68 % 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: 1.07 (0.24), residues: 1250 helix: 1.78 (0.20), residues: 689 sheet: 0.67 (0.53), residues: 103 loop : -0.97 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 189 TYR 0.016 0.002 TYR A 496 PHE 0.014 0.001 PHE A 886 TRP 0.009 0.001 TRP A 864 HIS 0.008 0.001 HIS A 943 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (11548) covalent geometry : angle 0.59103 / 0.32 (15914) hydrogen bonds : bond 0.04788 / 3.08 ( 586) hydrogen bonds : angle 3.94583 / 2.75 ( 1638) Misc. bond : bond 0.00036 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 0.331 Fit side-chains REVERT: B 25 ASN cc_start: 0.7044 (t0) cc_final: 0.6770 (t0) REVERT: B 168 MET cc_start: 0.8075 (mmm) cc_final: 0.7735 (tpt) REVERT: B 214 LYS cc_start: 0.8080 (mmtm) cc_final: 0.7789 (mmtm) REVERT: A 461 MET cc_start: 0.8761 (tmm) cc_final: 0.8395 (ttt) REVERT: A 888 GLU cc_start: 0.7358 (mt-10) cc_final: 0.6786 (mt-10) REVERT: A 988 LYS cc_start: 0.7120 (tmtt) cc_final: 0.6774 (tppt) REVERT: A 1019 THR cc_start: 0.8856 (m) cc_final: 0.8584 (m) outliers start: 12 outliers final: 10 residues processed: 150 average time/residue: 0.0915 time to fit residues: 19.7989 Evaluate side-chains 154 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 144 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 794 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 75 optimal weight: 0.0570 chunk 125 optimal weight: 50.0000 chunk 62 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 12 optimal weight: 0.1980 chunk 110 optimal weight: 4.9990 chunk 122 optimal weight: 20.0000 chunk 84 optimal weight: 0.8980 chunk 14 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 overall best weight: 3.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 96 GLN ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 890 HIS A1231 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.165270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.131061 restraints weight = 18090.654| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.00 r_work: 0.3209 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11549 Z= 0.135 Angle : 0.560 8.730 15914 Z= 0.300 Chirality : 0.041 0.176 1762 Planarity : 0.004 0.045 1828 Dihedral : 18.604 107.528 2041 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.33 % Allowed : 9.75 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.24), residues: 1250 helix: 1.85 (0.20), residues: 690 sheet: 0.71 (0.53), residues: 103 loop : -0.95 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 533 TYR 0.016 0.001 TYR A 496 PHE 0.013 0.001 PHE A 886 TRP 0.009 0.001 TRP A 864 HIS 0.006 0.001 HIS A1057 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (11548) covalent geometry : angle 0.56035 / 0.30 (15914) hydrogen bonds : bond 0.04455 / 2.86 ( 586) hydrogen bonds : angle 3.90400 / 2.71 ( 1638) Misc. bond : bond 0.00054 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 0.380 Fit side-chains REVERT: B 25 ASN cc_start: 0.7071 (t0) cc_final: 0.6805 (t0) REVERT: B 168 MET cc_start: 0.8041 (mmm) cc_final: 0.7762 (tpt) REVERT: B 214 LYS cc_start: 0.8092 (mmtm) cc_final: 0.7802 (mmtm) REVERT: A 461 MET cc_start: 0.8734 (tmm) cc_final: 0.8402 (ttt) REVERT: A 533 ARG cc_start: 0.7629 (ttt180) cc_final: 0.7334 (tpt-90) REVERT: A 888 GLU cc_start: 0.7373 (mt-10) cc_final: 0.6817 (mt-10) REVERT: A 926 GLU cc_start: 0.7513 (tt0) cc_final: 0.7228 (tt0) REVERT: A 988 LYS cc_start: 0.7220 (tmtt) cc_final: 0.6874 (tppt) REVERT: A 1019 THR cc_start: 0.8988 (m) cc_final: 0.8724 (m) REVERT: A 1230 LYS cc_start: 0.7791 (mmmm) cc_final: 0.7583 (mmmm) outliers start: 14 outliers final: 12 residues processed: 150 average time/residue: 0.0953 time to fit residues: 20.4085 Evaluate side-chains 156 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 1231 ASN Chi-restraints excluded: chain A residue 1233 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 53 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 122 optimal weight: 0.4980 chunk 34 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 chunk 120 optimal weight: 40.0000 chunk 83 optimal weight: 6.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 123 GLN ** 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 = 0.3778 r_free = 0.3778 target = 0.165516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.131173 restraints weight = 21249.751| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.03 r_work: 0.3196 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11549 Z= 0.128 Angle : 0.553 8.682 15914 Z= 0.296 Chirality : 0.041 0.176 1762 Planarity : 0.004 0.048 1828 Dihedral : 18.586 107.266 2041 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.23 % Allowed : 10.51 % Favored : 88.26 % 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: 1.17 (0.24), residues: 1250 helix: 1.88 (0.20), residues: 690 sheet: 0.71 (0.53), residues: 103 loop : -0.95 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1220 TYR 0.016 0.001 TYR A 496 PHE 0.014 0.001 PHE A 886 TRP 0.008 0.001 TRP A 864 HIS 0.006 0.001 HIS A1057 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (11548) covalent geometry : angle 0.55347 / 0.30 (15914) hydrogen bonds : bond 0.04364 / 2.80 ( 586) hydrogen bonds : angle 3.87048 / 2.69 ( 1638) Misc. bond : bond 0.00054 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.316 Fit side-chains REVERT: B 25 ASN cc_start: 0.7055 (t0) cc_final: 0.6770 (t0) REVERT: B 214 LYS cc_start: 0.8056 (mmtm) cc_final: 0.7765 (mmtm) REVERT: A 461 MET cc_start: 0.8736 (tmm) cc_final: 0.8414 (ttt) REVERT: A 533 ARG cc_start: 0.7665 (ttt180) cc_final: 0.7378 (tpt-90) REVERT: A 888 GLU cc_start: 0.7390 (mt-10) cc_final: 0.6864 (mt-10) REVERT: A 926 GLU cc_start: 0.7541 (tt0) cc_final: 0.7319 (tt0) REVERT: A 988 LYS cc_start: 0.7192 (tmtt) cc_final: 0.6863 (tppt) REVERT: A 1019 THR cc_start: 0.9034 (m) cc_final: 0.8761 (m) REVERT: A 1105 MET cc_start: 0.8431 (mmm) cc_final: 0.8218 (mmp) REVERT: A 1230 LYS cc_start: 0.7612 (mmmm) cc_final: 0.7395 (mmmm) REVERT: A 1231 ASN cc_start: 0.7188 (p0) cc_final: 0.6908 (p0) outliers start: 13 outliers final: 11 residues processed: 153 average time/residue: 0.0889 time to fit residues: 19.4705 Evaluate side-chains 155 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 1018 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 120 optimal weight: 50.0000 chunk 58 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 82 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 42 optimal weight: 40.0000 chunk 28 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1231 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.160997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.126820 restraints weight = 18491.789| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.89 r_work: 0.3157 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3144 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11549 Z= 0.237 Angle : 0.672 9.353 15914 Z= 0.356 Chirality : 0.046 0.208 1762 Planarity : 0.005 0.060 1828 Dihedral : 18.835 108.898 2041 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.76 % Favored : 96.16 % Rotamer: Outliers : 1.42 % Allowed : 10.89 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.24), residues: 1250 helix: 1.38 (0.20), residues: 691 sheet: 0.62 (0.52), residues: 101 loop : -1.24 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 984 TYR 0.016 0.002 TYR A 496 PHE 0.014 0.002 PHE A 886 TRP 0.010 0.002 TRP A 864 HIS 0.010 0.002 HIS A 943 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.24 (11548) covalent geometry : angle 0.67186 / 0.36 (15914) hydrogen bonds : bond 0.05651 / 3.70 ( 586) hydrogen bonds : angle 4.21568 / 2.92 ( 1638) Misc. bond : bond 0.00037 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 0.288 Fit side-chains REVERT: B 25 ASN cc_start: 0.7215 (t0) cc_final: 0.6903 (t0) REVERT: B 214 LYS cc_start: 0.8085 (mmtm) cc_final: 0.7743 (mmtm) REVERT: A 386 ILE cc_start: 0.7244 (mp) cc_final: 0.6973 (tt) REVERT: A 461 MET cc_start: 0.8858 (tmm) cc_final: 0.8471 (ttt) REVERT: A 536 ILE cc_start: 0.8558 (mp) cc_final: 0.8286 (mp) REVERT: A 988 LYS cc_start: 0.7180 (tmtt) cc_final: 0.6968 (tppt) REVERT: A 1105 MET cc_start: 0.8430 (mmm) cc_final: 0.8136 (mmp) REVERT: A 1201 MET cc_start: 0.8722 (ttp) cc_final: 0.8480 (ttp) REVERT: A 1230 LYS cc_start: 0.7813 (mmmm) cc_final: 0.7603 (tptm) outliers start: 15 outliers final: 10 residues processed: 152 average time/residue: 0.0945 time to fit residues: 20.2947 Evaluate side-chains 152 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 142 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 520 ASN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 794 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 96 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 10.0000 chunk 11 optimal weight: 0.2980 chunk 59 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 42 optimal weight: 40.0000 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1231 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.164384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.130567 restraints weight = 17463.916| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.99 r_work: 0.3189 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11549 Z= 0.127 Angle : 0.569 8.795 15914 Z= 0.305 Chirality : 0.041 0.179 1762 Planarity : 0.004 0.054 1828 Dihedral : 18.689 108.354 2041 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.85 % Allowed : 11.65 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.24), residues: 1250 helix: 1.74 (0.20), residues: 691 sheet: 0.54 (0.52), residues: 103 loop : -1.08 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1220 TYR 0.016 0.001 TYR A 496 PHE 0.013 0.001 PHE B 163 TRP 0.010 0.001 TRP A 455 HIS 0.006 0.001 HIS A1057 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 (11548) covalent geometry : angle 0.56868 / 0.31 (15914) hydrogen bonds : bond 0.04479 / 2.88 ( 586) hydrogen bonds : angle 3.96828 / 2.77 ( 1638) Misc. bond : bond 0.00073 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 145 time to evaluate : 0.377 Fit side-chains REVERT: B 25 ASN cc_start: 0.7054 (t0) cc_final: 0.6757 (t0) REVERT: B 214 LYS cc_start: 0.8051 (mmtm) cc_final: 0.7765 (mmtm) REVERT: A 461 MET cc_start: 0.8805 (tmm) cc_final: 0.8452 (ttt) REVERT: A 988 LYS cc_start: 0.7090 (tmtt) cc_final: 0.6786 (tppt) REVERT: A 1105 MET cc_start: 0.8470 (mmm) cc_final: 0.8268 (mmp) outliers start: 9 outliers final: 9 residues processed: 149 average time/residue: 0.1151 time to fit residues: 24.5068 Evaluate side-chains 150 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 141 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 1125 GLU Chi-restraints excluded: chain A residue 1231 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 12 optimal weight: 0.0980 chunk 110 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 2 optimal weight: 30.0000 chunk 78 optimal weight: 10.0000 chunk 54 optimal weight: 0.2980 chunk 72 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 105 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 123 GLN ** 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 = 0.3761 r_free = 0.3761 target = 0.164099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.130190 restraints weight = 18051.888| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.84 r_work: 0.3212 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.176 11549 Z= 0.180 Angle : 0.836 59.188 15914 Z= 0.487 Chirality : 0.045 0.761 1762 Planarity : 0.005 0.054 1828 Dihedral : 18.695 108.350 2041 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.85 % Allowed : 11.93 % Favored : 87.22 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.24), residues: 1250 helix: 1.75 (0.20), residues: 691 sheet: 0.53 (0.52), residues: 103 loop : -1.07 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1250 TYR 0.016 0.001 TYR A 496 PHE 0.013 0.001 PHE A 886 TRP 0.010 0.001 TRP A 455 HIS 0.006 0.001 HIS A1057 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.18 (11548) covalent geometry : angle 0.83593 / 0.49 (15914) hydrogen bonds : bond 0.04488 / 2.89 ( 586) hydrogen bonds : angle 3.96646 / 2.77 ( 1638) Misc. bond : bond 0.00069 / 0.04 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 0.412 Fit side-chains REVERT: B 25 ASN cc_start: 0.7210 (t0) cc_final: 0.6885 (t0) REVERT: B 214 LYS cc_start: 0.8053 (mmtm) cc_final: 0.7792 (mmtm) REVERT: A 461 MET cc_start: 0.8843 (tmm) cc_final: 0.8463 (ttt) REVERT: A 988 LYS cc_start: 0.7143 (tmtt) cc_final: 0.6859 (tppt) outliers start: 9 outliers final: 8 residues processed: 146 average time/residue: 0.1133 time to fit residues: 23.7922 Evaluate side-chains 150 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 142 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 1125 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 6.9990 chunk 124 optimal weight: 20.0000 chunk 61 optimal weight: 9.9990 chunk 65 optimal weight: 0.0370 chunk 38 optimal weight: 0.0170 chunk 48 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 22 optimal weight: 9.9990 chunk 108 optimal weight: 9.9990 chunk 27 optimal weight: 0.9990 chunk 84 optimal weight: 9.9990 overall best weight: 0.6102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 123 GLN ** 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 = 0.3763 r_free = 0.3763 target = 0.164271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.130247 restraints weight = 16035.303| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.84 r_work: 0.3212 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.175 11549 Z= 0.180 Angle : 0.836 59.200 15914 Z= 0.487 Chirality : 0.045 0.759 1762 Planarity : 0.005 0.054 1828 Dihedral : 18.695 108.350 2041 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.76 % Allowed : 12.03 % Favored : 87.22 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.24), residues: 1250 helix: 1.75 (0.20), residues: 691 sheet: 0.53 (0.52), residues: 103 loop : -1.07 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1250 TYR 0.016 0.001 TYR A 496 PHE 0.013 0.001 PHE A 886 TRP 0.010 0.001 TRP A 455 HIS 0.006 0.001 HIS A1057 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.18 (11548) covalent geometry : angle 0.83581 / 0.49 (15914) hydrogen bonds : bond 0.04488 / 2.89 ( 586) hydrogen bonds : angle 3.96646 / 2.77 ( 1638) Misc. bond : bond 0.00069 / 0.04 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2452.40 seconds wall clock time: 42 minutes 42.56 seconds (2562.56 seconds total)