Starting phenix.real_space_refine on Fri Jul 3 00:17:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8atv_15664/07_2026/8atv_15664.cif Found real_map, /net/cci-nas-00/data/ceres_data/8atv_15664/07_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_15664/07_2026/8atv_15664.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8atv_15664/07_2026/8atv_15664.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8atv_15664/07_2026/8atv_15664.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8atv_15664/07_2026/8atv_15664.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8atv_15664/07_2026/8atv_15664.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8atv_15664/07_2026/8atv_15664.cif" } 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-dev-6108/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: {'RNA': 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: 3.49, per 1000 atoms: 0.31 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: 0.89 Conformation dependent library (CDL) restraints added in 532.2 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: 1.10 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: 2.42 Time building geometry restraints manager: 1.11 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 1.50e-02 4.44e+03 8.26e+01 bond pdb=" O3' DA T 13 " pdb=" P DT T 14 " ideal model delta sigma weight residual 1.607 1.494 0.113 1.50e-02 4.44e+03 5.67e+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' DC T 25 " pdb=" P DA T 26 " ideal model delta sigma weight residual 1.607 1.510 0.097 1.50e-02 4.44e+03 4.17e+01 bond pdb=" C4' DT T 20 " pdb=" O4' DT T 20 " ideal model delta sigma weight residual 1.446 1.501 -0.055 1.00e-02 1.00e+04 3.08e+01 ... (remaining 11543 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 15726 2.63 - 5.26: 157 5.26 - 7.89: 19 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=" 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=" 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 angle pdb=" C LEU A 755 " pdb=" CA LEU A 755 " pdb=" CB LEU A 755 " ideal model delta sigma weight residual 117.23 110.74 6.49 1.36e+00 5.41e-01 2.28e+01 angle pdb=" C3' DT T 14 " pdb=" O3' DT T 14 " pdb=" P DG T 15 " ideal model delta sigma weight residual 120.20 127.00 -6.80 1.50e+00 4.44e-01 2.06e+01 ... (remaining 15909 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.58: 6263 27.58 - 55.17: 486 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: 1705 0.108 - 0.216: 51 0.216 - 0.324: 3 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.170 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: 0.160 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 12.750 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.130 ------------------------------------------------------------------------------- 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= 0.289 Angle : 0.683 13.149 15914 Z= 0.397 Chirality : 0.050 0.540 1762 Planarity : 0.004 0.042 1828 Dihedral : 17.943 137.923 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 / 0.29 (11548) covalent geometry : angle 0.68270 / 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 : 0.389 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: 0.0945 time to fit residues: 22.1749 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 : 0.243 ------------------------------------------------------------------------------- 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 = 0.3739 r_free = 0.3739 target = 0.161847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.127755 restraints weight = 22795.397| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.21 r_work: 0.3130 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 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 = 0.3111 r_free = 0.3111 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: 0.3111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 11549 Z= 0.233 Angle : 0.684 9.386 15914 Z= 0.367 Chirality : 0.047 0.233 1762 Planarity : 0.005 0.048 1828 Dihedral : 18.402 111.089 2041 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.95 % Allowed : 6.25 % Favored : 92.80 % 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: 0.67 (0.24), residues: 1250 helix: 1.41 (0.20), residues: 690 sheet: 0.65 (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 0.019 0.002 PHE B 229 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 0.00529 / 0.23 (11548) covalent geometry : angle 0.68367 / 0.37 (15914) hydrogen bonds : bond 0.05804 / 3.72 ( 586) hydrogen bonds : angle 4.37571 / 3.04 ( 1638) Misc. bond : bond 0.00182 / 0.10 ( 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 : 0.530 Fit side-chains REVERT: B 25 ASN cc_start: 0.7105 (t0) cc_final: 0.6833 (t0) REVERT: B 116 ARG cc_start: 0.7263 (mmm-85) cc_final: 0.7061 (mmm-85) REVERT: A 461 MET cc_start: 0.8803 (tmm) cc_final: 0.8117 (ttt) REVERT: A 468 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7338 (mm-30) outliers start: 10 outliers final: 8 residues processed: 153 average time/residue: 0.1016 time to fit residues: 21.9371 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 : 0.246 ------------------------------------------------------------------------------- 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: 3.9990 chunk 111 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 chunk 104 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 = 0.3733 r_free = 0.3733 target = 0.161361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.127384 restraints weight = 21464.852| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.08 r_work: 0.3123 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11549 Z= 0.205 Angle : 0.645 9.128 15914 Z= 0.347 Chirality : 0.045 0.212 1762 Planarity : 0.005 0.050 1828 Dihedral : 18.673 109.873 2041 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.60 % Favored : 96.32 % Rotamer: Outliers : 1.33 % Allowed : 7.86 % Favored : 90.81 % 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: 0.55 (0.24), residues: 1250 helix: 1.36 (0.20), residues: 692 sheet: 0.36 (0.52), residues: 103 loop : -1.18 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1220 TYR 0.017 0.002 TYR B 42 PHE 0.014 0.002 PHE A 886 TRP 0.011 0.001 TRP A 864 HIS 0.010 0.002 HIS A 943 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.21 (11548) covalent geometry : angle 0.64472 / 0.35 (15914) hydrogen bonds : bond 0.05629 / 3.62 ( 586) hydrogen bonds : angle 4.27082 / 2.97 ( 1638) Misc. bond : bond 0.00069 / 0.04 ( 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 163 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.276 Fit side-chains REVERT: B 25 ASN cc_start: 0.7168 (t0) cc_final: 0.6874 (t0) REVERT: B 214 LYS cc_start: 0.8183 (mmtm) cc_final: 0.7883 (mmtm) REVERT: B 319 MET cc_start: 0.7851 (mtt) cc_final: 0.7621 (mtt) REVERT: A 461 MET cc_start: 0.8803 (tmm) cc_final: 0.8200 (ttt) REVERT: A 1105 MET cc_start: 0.8554 (mmm) cc_final: 0.8251 (mmp) REVERT: A 1201 MET cc_start: 0.8724 (ttp) cc_final: 0.8433 (ttp) outliers start: 14 outliers final: 12 residues processed: 152 average time/residue: 0.1087 time to fit residues: 23.2298 Evaluate side-chains 154 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain A residue 1024 VAL 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: 10.0000 chunk 128 optimal weight: 20.0000 chunk 46 optimal weight: 8.9990 chunk 54 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 119 optimal weight: 0.0000 overall best weight: 4.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 96 GLN A1231 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.162621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.128596 restraints weight = 18519.969| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.80 r_work: 0.3161 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11549 Z= 0.164 Angle : 0.604 8.817 15914 Z= 0.325 Chirality : 0.043 0.195 1762 Planarity : 0.005 0.053 1828 Dihedral : 18.718 110.057 2041 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.52 % Favored : 96.40 % Rotamer: Outliers : 1.52 % Allowed : 9.47 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.24), residues: 1250 helix: 1.53 (0.20), residues: 691 sheet: 0.43 (0.52), residues: 103 loop : -1.14 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1220 TYR 0.016 0.002 TYR A 496 PHE 0.014 0.001 PHE B 163 TRP 0.010 0.001 TRP A 864 HIS 0.007 0.001 HIS A 943 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (11548) covalent geometry : angle 0.60399 / 0.33 (15914) hydrogen bonds : bond 0.05086 / 3.26 ( 586) hydrogen bonds : angle 4.12001 / 2.88 ( 1638) Misc. bond : bond 0.00006 / 0.00 ( 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 160 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.428 Fit side-chains REVERT: B 25 ASN cc_start: 0.7154 (t0) cc_final: 0.6841 (t0) REVERT: B 214 LYS cc_start: 0.8170 (mmtm) cc_final: 0.7903 (mmtm) REVERT: A 461 MET cc_start: 0.8809 (tmm) cc_final: 0.8306 (ttt) REVERT: A 468 GLU cc_start: 0.8071 (tp30) cc_final: 0.7824 (tp30) REVERT: A 988 LYS cc_start: 0.7131 (tmtt) cc_final: 0.6744 (tppt) REVERT: A 1201 MET cc_start: 0.8699 (ttp) cc_final: 0.8366 (ttp) outliers start: 16 outliers final: 14 residues processed: 148 average time/residue: 0.1113 time to fit residues: 23.1312 Evaluate side-chains 158 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 277 VAL 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 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: 5.9990 chunk 10 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 128 optimal weight: 20.0000 chunk 113 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.163697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.130986 restraints weight = 21159.426| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.92 r_work: 0.3150 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 11549 Z= 0.240 Angle : 0.671 11.641 15914 Z= 0.357 Chirality : 0.046 0.208 1762 Planarity : 0.005 0.059 1828 Dihedral : 18.880 110.670 2041 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.92 % Favored : 96.00 % Rotamer: Outliers : 1.61 % Allowed : 10.32 % Favored : 88.07 % 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: 0.42 (0.24), residues: 1250 helix: 1.25 (0.20), residues: 691 sheet: 0.35 (0.53), residues: 103 loop : -1.24 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 984 TYR 0.017 0.002 TYR A 496 PHE 0.014 0.002 PHE A 886 TRP 0.011 0.002 TRP A 682 HIS 0.010 0.002 HIS A 943 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.24 (11548) covalent geometry : angle 0.67144 / 0.36 (15914) hydrogen bonds : bond 0.05648 / 3.66 ( 586) hydrogen bonds : angle 4.26534 / 2.97 ( 1638) Misc. bond : bond 0.00021 / 0.01 ( 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 162 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 0.342 Fit side-chains REVERT: B 25 ASN cc_start: 0.7178 (t0) cc_final: 0.6863 (t0) REVERT: B 214 LYS cc_start: 0.8148 (mmtm) cc_final: 0.7854 (mmtm) REVERT: A 461 MET cc_start: 0.8868 (tmm) cc_final: 0.8390 (ttt) REVERT: A 468 GLU cc_start: 0.8166 (tp30) cc_final: 0.7930 (tp30) REVERT: A 988 LYS cc_start: 0.7197 (tmtt) cc_final: 0.6832 (tppt) REVERT: A 1230 LYS cc_start: 0.7723 (mmmm) cc_final: 0.7496 (tptm) outliers start: 17 outliers final: 14 residues processed: 150 average time/residue: 0.1188 time to fit residues: 24.8522 Evaluate side-chains 155 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 276 THR Chi-restraints excluded: chain B residue 277 VAL 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 602 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 75 optimal weight: 0.8980 chunk 125 optimal weight: 50.0000 chunk 62 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1032 GLN A1231 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.162632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.128748 restraints weight = 18099.456| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.75 r_work: 0.3172 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11549 Z= 0.152 Angle : 0.591 8.823 15914 Z= 0.318 Chirality : 0.042 0.190 1762 Planarity : 0.004 0.056 1828 Dihedral : 18.804 110.505 2041 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.52 % Favored : 96.40 % Rotamer: Outliers : 1.61 % Allowed : 10.98 % 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: 0.71 (0.24), residues: 1250 helix: 1.51 (0.20), residues: 691 sheet: 0.45 (0.53), residues: 103 loop : -1.15 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1250 TYR 0.016 0.002 TYR A 496 PHE 0.014 0.001 PHE B 163 TRP 0.010 0.001 TRP A 864 HIS 0.006 0.001 HIS A1057 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (11548) covalent geometry : angle 0.59126 / 0.32 (15914) hydrogen bonds : bond 0.04896 / 3.14 ( 586) hydrogen bonds : angle 4.06828 / 2.84 ( 1638) Misc. bond : bond 0.00047 / 0.02 ( 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 159 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.313 Fit side-chains REVERT: B 25 ASN cc_start: 0.7137 (t0) cc_final: 0.6846 (t0) REVERT: B 214 LYS cc_start: 0.8149 (mmtm) cc_final: 0.7917 (mmtm) REVERT: A 461 MET cc_start: 0.8839 (tmm) cc_final: 0.8383 (ttt) REVERT: A 988 LYS cc_start: 0.7223 (tmtt) cc_final: 0.6830 (tppt) REVERT: A 1105 MET cc_start: 0.8496 (mmm) cc_final: 0.8238 (mmp) outliers start: 17 outliers final: 15 residues processed: 147 average time/residue: 0.0974 time to fit residues: 20.0369 Evaluate side-chains 154 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 277 VAL 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 611 VAL 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 1125 GLU 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: 20.0000 chunk 92 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 5 optimal weight: 0.0040 chunk 122 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 120 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 overall best weight: 2.9798 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.163317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.129462 restraints weight = 21288.714| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.04 r_work: 0.3164 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1397 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= 0.141 Angle : 0.579 8.731 15914 Z= 0.311 Chirality : 0.042 0.186 1762 Planarity : 0.004 0.055 1828 Dihedral : 18.761 110.193 2041 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.23 % Allowed : 12.31 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.24), residues: 1250 helix: 1.62 (0.20), residues: 689 sheet: 0.48 (0.53), residues: 103 loop : -1.13 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1228 TYR 0.015 0.001 TYR A 496 PHE 0.012 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 0.00300 / 0.14 (11548) covalent geometry : angle 0.57887 / 0.31 (15914) hydrogen bonds : bond 0.04742 / 3.04 ( 586) hydrogen bonds : angle 3.99339 / 2.79 ( 1638) Misc. bond : bond 0.00049 / 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 155 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.389 Fit side-chains REVERT: B 25 ASN cc_start: 0.7117 (t0) cc_final: 0.6831 (t0) REVERT: B 214 LYS cc_start: 0.8107 (mmtm) cc_final: 0.7875 (mmtm) REVERT: A 461 MET cc_start: 0.8854 (tmm) cc_final: 0.8380 (ttt) REVERT: A 533 ARG cc_start: 0.7684 (ttt180) cc_final: 0.7469 (tpt-90) REVERT: A 988 LYS cc_start: 0.7184 (tmtt) cc_final: 0.6829 (tppt) REVERT: A 1105 MET cc_start: 0.8538 (mmm) cc_final: 0.8312 (mmp) REVERT: A 1230 LYS cc_start: 0.7613 (mmmm) cc_final: 0.7391 (tptm) REVERT: A 1272 GLU cc_start: 0.3541 (tp30) cc_final: 0.3292 (tp30) outliers start: 13 outliers final: 12 residues processed: 146 average time/residue: 0.1042 time to fit residues: 21.1269 Evaluate side-chains 152 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 276 THR Chi-restraints excluded: chain B residue 277 VAL 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 611 VAL 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 1125 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 120 optimal weight: 10.0000 chunk 58 optimal weight: 0.6980 chunk 111 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 28 optimal weight: 20.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- 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 = 0.3781 r_free = 0.3781 target = 0.166104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.132485 restraints weight = 18170.388| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.75 r_work: 0.3184 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11549 Z= 0.166 Angle : 0.595 8.877 15914 Z= 0.319 Chirality : 0.043 0.192 1762 Planarity : 0.005 0.056 1828 Dihedral : 18.776 110.124 2041 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.68 % Favored : 96.24 % Rotamer: Outliers : 1.61 % Allowed : 12.22 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.24), residues: 1250 helix: 1.54 (0.20), residues: 691 sheet: 0.44 (0.53), residues: 103 loop : -1.15 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 189 TYR 0.015 0.002 TYR A 496 PHE 0.013 0.001 PHE A 886 TRP 0.010 0.001 TRP A 864 HIS 0.006 0.001 HIS A1057 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (11548) covalent geometry : angle 0.59472 / 0.32 (15914) hydrogen bonds : bond 0.04941 / 3.20 ( 586) hydrogen bonds : angle 4.02067 / 2.81 ( 1638) Misc. bond : bond 0.00041 / 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 160 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.290 Fit side-chains REVERT: B 25 ASN cc_start: 0.7289 (t0) cc_final: 0.6973 (t0) REVERT: B 214 LYS cc_start: 0.8085 (mmtm) cc_final: 0.7854 (mmtm) REVERT: A 461 MET cc_start: 0.8917 (tmm) cc_final: 0.8464 (ttt) REVERT: A 827 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7778 (mtm110) REVERT: A 988 LYS cc_start: 0.7204 (tmtt) cc_final: 0.6871 (tppt) REVERT: A 1105 MET cc_start: 0.8609 (mmm) cc_final: 0.8343 (mmp) REVERT: A 1230 LYS cc_start: 0.7755 (mmmm) cc_final: 0.7533 (tptm) outliers start: 17 outliers final: 14 residues processed: 149 average time/residue: 0.1108 time to fit residues: 23.3866 Evaluate side-chains 157 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 277 VAL 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 611 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 827 ARG Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1125 GLU Chi-restraints excluded: chain A residue 1231 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 96 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 22 optimal weight: 20.0000 chunk 11 optimal weight: 0.1980 chunk 59 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 42 optimal weight: 30.0000 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 890 HIS A1231 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.164819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.130569 restraints weight = 17402.285| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.91 r_work: 0.3206 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 11549 Z= 0.123 Angle : 0.558 8.541 15914 Z= 0.300 Chirality : 0.041 0.172 1762 Planarity : 0.004 0.051 1828 Dihedral : 18.670 109.385 2041 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.95 % Allowed : 12.69 % Favored : 86.36 % 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: 1.01 (0.24), residues: 1250 helix: 1.81 (0.21), residues: 688 sheet: 0.50 (0.53), residues: 103 loop : -1.08 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 533 TYR 0.015 0.001 TYR A 496 PHE 0.012 0.001 PHE A 826 TRP 0.010 0.001 TRP A 864 HIS 0.007 0.001 HIS A1057 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (11548) covalent geometry : angle 0.55792 / 0.30 (15914) hydrogen bonds : bond 0.04350 / 2.79 ( 586) hydrogen bonds : angle 3.88262 / 2.72 ( 1638) Misc. bond : bond 0.00062 / 0.03 ( 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 158 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 148 time to evaluate : 0.403 Fit side-chains REVERT: B 25 ASN cc_start: 0.7057 (t0) cc_final: 0.6766 (t0) REVERT: B 214 LYS cc_start: 0.8084 (mmtm) cc_final: 0.7855 (mmtm) REVERT: A 461 MET cc_start: 0.8818 (tmm) cc_final: 0.8424 (ttt) REVERT: A 988 LYS cc_start: 0.7116 (tmtt) cc_final: 0.6766 (tppt) REVERT: A 1105 MET cc_start: 0.8549 (mmm) cc_final: 0.8309 (mmp) outliers start: 10 outliers final: 7 residues processed: 151 average time/residue: 0.1082 time to fit residues: 23.1058 Evaluate side-chains 146 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 139 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 193 SER 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 1125 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 12 optimal weight: 5.9990 chunk 110 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 2 optimal weight: 30.0000 chunk 78 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 72 optimal weight: 8.9990 chunk 98 optimal weight: 5.9990 chunk 105 optimal weight: 0.4980 chunk 66 optimal weight: 5.9990 chunk 101 optimal weight: 20.0000 overall best weight: 2.2988 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.165132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.131030 restraints weight = 18067.338| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.82 r_work: 0.3226 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 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 = 0.3080 r_free = 0.3080 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: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11549 Z= 0.128 Angle : 0.553 8.543 15914 Z= 0.297 Chirality : 0.041 0.180 1762 Planarity : 0.004 0.054 1828 Dihedral : 18.641 108.769 2041 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.95 % Allowed : 13.16 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.24), residues: 1250 helix: 1.82 (0.20), residues: 689 sheet: 0.52 (0.53), residues: 103 loop : -1.06 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 827 TYR 0.014 0.001 TYR A 496 PHE 0.012 0.001 PHE A 886 TRP 0.009 0.001 TRP A 864 HIS 0.007 0.001 HIS A1057 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (11548) covalent geometry : angle 0.55269 / 0.30 (15914) hydrogen bonds : bond 0.04357 / 2.82 ( 586) hydrogen bonds : angle 3.88833 / 2.72 ( 1638) Misc. bond : bond 0.00049 / 0.03 ( 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 153 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 143 time to evaluate : 0.387 Fit side-chains REVERT: B 25 ASN cc_start: 0.7181 (t0) cc_final: 0.6844 (t0) REVERT: B 85 PHE cc_start: 0.7919 (t80) cc_final: 0.7614 (t80) REVERT: B 214 LYS cc_start: 0.8063 (mmtm) cc_final: 0.7855 (mmtm) REVERT: A 827 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7758 (mtm110) REVERT: A 988 LYS cc_start: 0.7113 (tmtt) cc_final: 0.6805 (tppt) REVERT: A 1105 MET cc_start: 0.8647 (mmm) cc_final: 0.8414 (mmp) REVERT: A 1118 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7649 (mp) REVERT: A 1231 ASN cc_start: 0.7437 (p0) cc_final: 0.7160 (p0) outliers start: 10 outliers final: 8 residues processed: 147 average time/residue: 0.1122 time to fit residues: 23.3966 Evaluate side-chains 150 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 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 827 ARG Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1118 ILE 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: 2.9990 chunk 124 optimal weight: 20.0000 chunk 61 optimal weight: 5.9990 chunk 65 optimal weight: 0.1980 chunk 38 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 108 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- 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 = 0.3786 r_free = 0.3786 target = 0.166282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.134217 restraints weight = 15978.748| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.48 r_work: 0.3244 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11549 Z= 0.117 Angle : 0.538 8.363 15914 Z= 0.290 Chirality : 0.040 0.171 1762 Planarity : 0.004 0.054 1828 Dihedral : 18.592 107.649 2041 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.95 % Allowed : 13.26 % Favored : 85.80 % 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: 1.14 (0.24), residues: 1250 helix: 1.91 (0.21), residues: 689 sheet: 0.49 (0.53), residues: 103 loop : -0.99 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1220 TYR 0.015 0.001 TYR A 496 PHE 0.012 0.001 PHE A 826 TRP 0.016 0.001 TRP B 24 HIS 0.007 0.001 HIS A1057 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 (11548) covalent geometry : angle 0.53828 / 0.29 (15914) hydrogen bonds : bond 0.04072 / 2.62 ( 586) hydrogen bonds : angle 3.81580 / 2.66 ( 1638) Misc. bond : bond 0.00049 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2574.92 seconds wall clock time: 44 minutes 48.11 seconds (2688.11 seconds total)