Starting phenix.real_space_refine on Fri Jul 3 01:38:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gzo_51729/07_2026/9gzo_51729.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gzo_51729/07_2026/9gzo_51729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9gzo_51729/07_2026/9gzo_51729.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gzo_51729/07_2026/9gzo_51729.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gzo_51729/07_2026/9gzo_51729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gzo_51729/07_2026/9gzo_51729.map" } resolution = 3.15 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= 0.001 sd= 0.007 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 67 5.49 5 S 63 5.16 5 C 7099 2.51 5 N 2052 2.21 5 O 2169 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 11450 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 968, 7626 Classifications: {'peptide': 968} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 59, 'TRANS': 908} Chain breaks: 5 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'GLU:plan': 6, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "N" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 640 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "T" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 632 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "B" Number of atoms: 2475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2475 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 20, 'TRANS': 296} Chain breaks: 1 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 4, 'TRP:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 67 Chain: "R" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 77 Unusual residues: {'GTP': 1} Classifications: {'RNA': 2, 'undetermined': 1} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1, None: 1} Not linked: pdbres="GTP R 1 " pdbres=" G R 2 " Time building chain proxies: 2.07, per 1000 atoms: 0.18 Number of scatterers: 11450 At special positions: 0 Unit cell: (112.52, 109.61, 114.46, 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 63 16.00 P 67 15.00 O 2169 8.00 N 2052 7.00 C 7099 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: 0.90 Conformation dependent library (CDL) restraints added in 518.9 milliseconds 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2434 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 12 sheets defined 59.6% alpha, 6.4% beta 24 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 220 through 237 removed outlier: 3.576A pdb=" N ARG A 225 " --> pdb=" O GLY A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 252 removed outlier: 3.599A pdb=" N GLN A 252 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.729A pdb=" N LYS A 257 " --> pdb=" O ARG A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 273 Processing helix chain 'A' and resid 276 through 291 removed outlier: 3.589A pdb=" N LEU A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.532A pdb=" N ALA A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG A 308 " --> pdb=" O GLN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 323 removed outlier: 3.869A pdb=" N ILE A 316 " --> pdb=" O ASP A 312 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET A 323 " --> pdb=" O CYS A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 337 Processing helix chain 'A' and resid 340 through 355 removed outlier: 3.885A pdb=" N LYS A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 379 Processing helix chain 'A' and resid 392 through 410 Processing helix chain 'A' and resid 424 through 461 removed outlier: 3.550A pdb=" N LYS A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 473 Processing helix chain 'A' and resid 475 through 489 Processing helix chain 'A' and resid 496 through 521 Processing helix chain 'A' and resid 521 through 538 removed outlier: 3.735A pdb=" N ALA A 525 " --> pdb=" O GLY A 521 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N CYS A 535 " --> pdb=" O ARG A 531 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N LEU A 536 " --> pdb=" O LYS A 532 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU A 537 " --> pdb=" O TYR A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 556 Processing helix chain 'A' and resid 568 through 587 Processing helix chain 'A' and resid 624 through 635 Processing helix chain 'A' and resid 678 through 687 removed outlier: 3.618A pdb=" N LEU A 683 " --> pdb=" O GLN A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 705 Processing helix chain 'A' and resid 710 through 724 removed outlier: 3.501A pdb=" N LEU A 716 " --> pdb=" O ARG A 712 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA A 723 " --> pdb=" O GLN A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 789 Processing helix chain 'A' and resid 818 through 824 Processing helix chain 'A' and resid 836 through 850 Processing helix chain 'A' and resid 856 through 867 Processing helix chain 'A' and resid 867 through 877 Processing helix chain 'A' and resid 883 through 888 removed outlier: 3.528A pdb=" N MET A 886 " --> pdb=" O LYS A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 906 Processing helix chain 'A' and resid 909 through 912 Processing helix chain 'A' and resid 925 through 936 Processing helix chain 'A' and resid 937 through 944 removed outlier: 3.558A pdb=" N ALA A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 942 " --> pdb=" O SER A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 972 Processing helix chain 'A' and resid 975 through 981 removed outlier: 3.652A pdb=" N LEU A 981 " --> pdb=" O VAL A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 996 removed outlier: 5.109A pdb=" N GLN A 992 " --> pdb=" O LYS A 988 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N THR A 993 " --> pdb=" O VAL A 989 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1017 removed outlier: 3.534A pdb=" N GLN A1009 " --> pdb=" O GLY A1005 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU A1016 " --> pdb=" O LYS A1012 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU A1017 " --> pdb=" O ARG A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1023 No H-bonds generated for 'chain 'A' and resid 1021 through 1023' Processing helix chain 'A' and resid 1024 through 1044 removed outlier: 3.553A pdb=" N ARG A1034 " --> pdb=" O HIS A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1065 Processing helix chain 'A' and resid 1111 through 1117 Processing helix chain 'A' and resid 1118 through 1141 Processing helix chain 'A' and resid 1159 through 1175 removed outlier: 3.604A pdb=" N GLU A1169 " --> pdb=" O GLN A1165 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A1171 " --> pdb=" O CYS A1167 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1192 Processing helix chain 'A' and resid 1201 through 1210 Processing helix chain 'A' and resid 1218 through 1223 removed outlier: 3.733A pdb=" N GLN A1221 " --> pdb=" O ASP A1218 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 90 removed outlier: 3.849A pdb=" N GLN B 86 " --> pdb=" O GLU B 82 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 116 Processing helix chain 'B' and resid 129 through 140 removed outlier: 3.527A pdb=" N LEU B 133 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU B 140 " --> pdb=" O LEU B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 177 Processing helix chain 'B' and resid 199 through 214 Processing helix chain 'B' and resid 215 through 220 removed outlier: 3.638A pdb=" N PHE B 220 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 238 Processing helix chain 'B' and resid 248 through 256 Processing helix chain 'B' and resid 288 through 294 Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.546A pdb=" N PHE B 320 " --> pdb=" O ASN B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 343 removed outlier: 3.576A pdb=" N ARG B 340 " --> pdb=" O ILE B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 354 removed outlier: 3.640A pdb=" N ILE B 354 " --> pdb=" O ILE B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 379 removed outlier: 3.535A pdb=" N LYS B 371 " --> pdb=" O PRO B 367 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 411 through 415 removed outlier: 3.865A pdb=" N VAL A 414 " --> pdb=" O LEU A 639 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 589 through 590 Processing sheet with id=AA3, first strand: chain 'A' and resid 606 through 613 Processing sheet with id=AA4, first strand: chain 'A' and resid 794 through 795 Processing sheet with id=AA5, first strand: chain 'A' and resid 798 through 800 Processing sheet with id=AA6, first strand: chain 'A' and resid 831 through 832 removed outlier: 3.759A pdb=" N ARG A 831 " --> pdb=" O SER A 915 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 918 through 921 removed outlier: 3.846A pdb=" N TYR A1153 " --> pdb=" O GLN A 921 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A1147 " --> pdb=" O TRP A1154 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1069 through 1071 Processing sheet with id=AA9, first strand: chain 'A' and resid 1089 through 1091 removed outlier: 4.188A pdb=" N LYS A1089 " --> pdb=" O TYR A1100 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 72 through 75 removed outlier: 4.091A pdb=" N LYS B 72 " --> pdb=" O TYR B 274 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 99 through 101 removed outlier: 3.511A pdb=" N VAL B 192 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL B 191 " --> pdb=" O ASN B 226 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N PHE B 228 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N GLY B 193 " --> pdb=" O PHE B 228 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N HIS B 264 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLN B 300 " --> pdb=" O VAL B 262 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL B 262 " --> pdb=" O GLN B 300 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 123 through 124 removed outlier: 3.530A pdb=" N GLU B 124 " --> pdb=" O ILE B 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 539 hydrogen bonds defined for protein. 1581 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 55 hydrogen bonds 110 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 2.09 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2219 1.33 - 1.45: 3015 1.45 - 1.57: 6381 1.57 - 1.69: 140 1.69 - 1.81: 96 Bond restraints: 11851 Sorted by residual: bond pdb=" C3' DT T 27 " pdb=" C2' DT T 27 " ideal model delta sigma weight residual 1.516 1.687 -0.171 8.00e-03 1.56e+04 4.59e+02 bond pdb=" C3' DT T 8 " pdb=" C2' DT T 8 " ideal model delta sigma weight residual 1.516 1.620 -0.104 8.00e-03 1.56e+04 1.69e+02 bond pdb=" C3' DA N 24 " pdb=" C2' DA N 24 " ideal model delta sigma weight residual 1.516 1.597 -0.081 8.00e-03 1.56e+04 1.04e+02 bond pdb=" C3' DA N 46 " pdb=" C2' DA N 46 " ideal model delta sigma weight residual 1.516 1.597 -0.081 8.00e-03 1.56e+04 1.03e+02 bond pdb=" C2' DA N 23 " pdb=" C1' DA N 23 " ideal model delta sigma weight residual 1.518 1.610 -0.092 1.00e-02 1.00e+04 8.39e+01 ... (remaining 11846 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.07: 15990 3.07 - 6.14: 290 6.14 - 9.21: 50 9.21 - 12.28: 16 12.28 - 15.35: 6 Bond angle restraints: 16352 Sorted by residual: angle pdb=" C3' DA N 23 " pdb=" O3' DA N 23 " pdb=" P DA N 24 " ideal model delta sigma weight residual 120.20 104.85 15.35 1.50e+00 4.44e-01 1.05e+02 angle pdb=" C3' DT T 27 " pdb=" C2' DT T 27 " pdb=" C1' DT T 27 " ideal model delta sigma weight residual 102.50 91.36 11.14 1.20e+00 6.94e-01 8.62e+01 angle pdb=" C3' DC T 23 " pdb=" O3' DC T 23 " pdb=" P DA T 24 " ideal model delta sigma weight residual 120.20 106.30 13.90 1.50e+00 4.44e-01 8.59e+01 angle pdb=" CA PRO A 596 " pdb=" N PRO A 596 " pdb=" CD PRO A 596 " ideal model delta sigma weight residual 112.00 99.66 12.34 1.40e+00 5.10e-01 7.76e+01 angle pdb=" C3' DT T 29 " pdb=" O3' DT T 29 " pdb=" P DA T 30 " ideal model delta sigma weight residual 120.20 107.15 13.05 1.50e+00 4.44e-01 7.57e+01 ... (remaining 16347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.28: 6439 27.28 - 54.56: 508 54.56 - 81.85: 72 81.85 - 109.13: 4 109.13 - 136.41: 3 Dihedral angle restraints: 7026 sinusoidal: 3278 harmonic: 3748 Sorted by residual: dihedral pdb=" O3B GTP R 1 " pdb=" O3A GTP R 1 " pdb=" PB GTP R 1 " pdb=" PA GTP R 1 " ideal model delta sinusoidal sigma weight residual 291.08 154.67 136.41 1 2.00e+01 2.50e-03 4.14e+01 dihedral pdb=" O2G GTP R 1 " pdb=" O3B GTP R 1 " pdb=" PG GTP R 1 " pdb=" PB GTP R 1 " ideal model delta sinusoidal sigma weight residual 177.30 59.37 117.93 1 2.00e+01 2.50e-03 3.52e+01 dihedral pdb=" O3A GTP R 1 " pdb=" O3B GTP R 1 " pdb=" PB GTP R 1 " pdb=" PG GTP R 1 " ideal model delta sinusoidal sigma weight residual -56.21 -168.41 112.20 1 2.00e+01 2.50e-03 3.31e+01 ... (remaining 7023 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 1745 0.128 - 0.256: 42 0.256 - 0.384: 4 0.384 - 0.512: 27 0.512 - 0.640: 16 Chirality restraints: 1834 Sorted by residual: chirality pdb=" P DA T 1 " pdb=" OP1 DA T 1 " pdb=" OP2 DA T 1 " pdb=" O5' DA T 1 " both_signs ideal model delta sigma weight residual True 2.34 -2.98 -0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" P DG T 14 " pdb=" OP1 DG T 14 " pdb=" OP2 DG T 14 " pdb=" O5' DG T 14 " both_signs ideal model delta sigma weight residual True 2.34 -2.91 -0.57 2.00e-01 2.50e+01 8.18e+00 chirality pdb=" P DC T 16 " pdb=" OP1 DC T 16 " pdb=" OP2 DC T 16 " pdb=" O5' DC T 16 " both_signs ideal model delta sigma weight residual True 2.34 -2.90 -0.56 2.00e-01 2.50e+01 7.91e+00 ... (remaining 1831 not shown) Planarity restraints: 1864 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 94 " 0.059 5.00e-02 4.00e+02 8.89e-02 1.26e+01 pdb=" N PRO B 95 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO B 95 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 95 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 595 " 0.046 5.00e-02 4.00e+02 6.30e-02 6.35e+00 pdb=" N PRO A 596 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 596 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 596 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 770 " -0.010 2.00e-02 2.50e+03 1.94e-02 3.75e+00 pdb=" C ARG A 770 " 0.034 2.00e-02 2.50e+03 pdb=" O ARG A 770 " -0.012 2.00e-02 2.50e+03 pdb=" N GLU A 771 " -0.012 2.00e-02 2.50e+03 ... (remaining 1861 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 300 2.70 - 3.25: 11003 3.25 - 3.80: 18551 3.80 - 4.35: 24172 4.35 - 4.90: 38700 Nonbonded interactions: 92726 Sorted by model distance: nonbonded pdb=" O VAL A1172 " pdb=" OG SER A1176 " model vdw 2.148 3.040 nonbonded pdb=" O ASP A 295 " pdb=" OG SER A 298 " model vdw 2.205 3.040 nonbonded pdb=" OH TYR A1082 " pdb=" OP1 DC T 11 " model vdw 2.227 3.040 nonbonded pdb=" O TYR B 209 " pdb=" OG SER B 213 " model vdw 2.228 3.040 nonbonded pdb=" NE2 HIS A 608 " pdb=" OE1 GLN A1096 " model vdw 2.241 3.120 ... (remaining 92721 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.160 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: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.080 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 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 : 0.007 0.171 11852 Z= 0.558 Angle : 1.047 15.351 16352 Z= 0.642 Chirality : 0.093 0.640 1834 Planarity : 0.006 0.089 1864 Dihedral : 18.230 136.411 4592 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.56 % Allowed : 0.93 % Favored : 98.51 % 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 (0.23), residues: 1269 helix: 1.42 (0.19), residues: 719 sheet: -0.97 (0.53), residues: 89 loop : -0.62 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 976 TYR 0.021 0.002 TYR A1100 PHE 0.012 0.001 PHE A 465 TRP 0.030 0.001 TRP A 441 HIS 0.007 0.001 HIS A 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00726 / 0.56 (11851) covalent geometry : angle 1.04728 / 0.64 (16352) hydrogen bonds : bond 0.16371 / 10.88 ( 594) hydrogen bonds : angle 6.27194 / 4.53 ( 1691) Misc. bond : bond 0.04759 / 2.50 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 187 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 768 VAL cc_start: 0.8788 (t) cc_final: 0.8402 (t) REVERT: A 772 MET cc_start: 0.8051 (ptt) cc_final: 0.7661 (ptt) outliers start: 6 outliers final: 2 residues processed: 192 average time/residue: 0.0905 time to fit residues: 25.0616 Evaluate side-chains 140 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 138 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 922 ASP Chi-restraints excluded: chain A residue 1101 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 50.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 0.7980 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 929 GLN A1090 GLN B 111 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.091311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.069073 restraints weight = 35444.568| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 3.86 r_work: 0.3021 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11852 Z= 0.189 Angle : 0.682 9.217 16352 Z= 0.359 Chirality : 0.044 0.210 1834 Planarity : 0.005 0.057 1864 Dihedral : 19.509 136.962 2151 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.21 % Allowed : 7.63 % Favored : 91.16 % 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: 0.97 (0.23), residues: 1269 helix: 1.64 (0.19), residues: 726 sheet: -1.29 (0.52), residues: 82 loop : -0.54 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 967 TYR 0.015 0.001 TYR A1004 PHE 0.023 0.002 PHE A 465 TRP 0.016 0.001 TRP A 441 HIS 0.009 0.001 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.19 (11851) covalent geometry : angle 0.68166 / 0.36 (16352) hydrogen bonds : bond 0.05876 / 3.97 ( 594) hydrogen bonds : angle 4.39666 / 3.24 ( 1691) Misc. bond : bond 0.00202 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 ARG cc_start: 0.8455 (mmt90) cc_final: 0.7982 (mmt90) REVERT: A 616 GLN cc_start: 0.8020 (mt0) cc_final: 0.7640 (mm-40) REVERT: A 975 MET cc_start: 0.8948 (ttp) cc_final: 0.8558 (tmm) REVERT: A 1043 MET cc_start: 0.8358 (mtp) cc_final: 0.8070 (mtm) REVERT: B 167 MET cc_start: 0.8469 (ttm) cc_final: 0.7799 (tmm) REVERT: B 195 PHE cc_start: 0.8172 (m-80) cc_final: 0.7845 (m-80) REVERT: B 201 LYS cc_start: 0.9375 (mttm) cc_final: 0.8949 (mttt) REVERT: B 301 MET cc_start: 0.8313 (mpp) cc_final: 0.7955 (mpp) outliers start: 13 outliers final: 7 residues processed: 149 average time/residue: 0.0797 time to fit residues: 17.5007 Evaluate side-chains 140 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 133 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 922 ASP Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain B residue 305 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 5 optimal weight: 0.0010 chunk 106 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 97 optimal weight: 50.0000 chunk 96 optimal weight: 50.0000 chunk 31 optimal weight: 10.0000 chunk 114 optimal weight: 30.0000 chunk 22 optimal weight: 5.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN B 97 HIS B 111 GLN ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.092378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.069815 restraints weight = 35477.945| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 3.92 r_work: 0.3042 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11852 Z= 0.138 Angle : 0.594 8.748 16352 Z= 0.317 Chirality : 0.039 0.172 1834 Planarity : 0.005 0.048 1864 Dihedral : 19.482 133.622 2150 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.30 % Allowed : 10.14 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.24), residues: 1269 helix: 1.79 (0.19), residues: 723 sheet: -1.09 (0.52), residues: 82 loop : -0.49 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 94 TYR 0.014 0.001 TYR B 297 PHE 0.021 0.001 PHE B 320 TRP 0.009 0.001 TRP A1026 HIS 0.004 0.001 HIS B 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (11851) covalent geometry : angle 0.59387 / 0.32 (16352) hydrogen bonds : bond 0.04884 / 3.32 ( 594) hydrogen bonds : angle 4.11477 / 3.02 ( 1691) Misc. bond : bond 0.00173 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 VAL cc_start: 0.8369 (t) cc_final: 0.8114 (m) REVERT: A 616 GLN cc_start: 0.7979 (mt0) cc_final: 0.7480 (mm-40) REVERT: A 970 ASP cc_start: 0.8811 (t0) cc_final: 0.8204 (t0) REVERT: A 975 MET cc_start: 0.9039 (ttp) cc_final: 0.8816 (tmm) REVERT: B 167 MET cc_start: 0.8495 (ttm) cc_final: 0.7834 (tmm) REVERT: B 201 LYS cc_start: 0.9403 (mttm) cc_final: 0.9086 (mttt) REVERT: B 265 MET cc_start: 0.8967 (tmm) cc_final: 0.8709 (tmm) outliers start: 14 outliers final: 10 residues processed: 145 average time/residue: 0.0854 time to fit residues: 18.3397 Evaluate side-chains 138 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 922 ASP Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain B residue 305 GLN Chi-restraints excluded: chain B residue 324 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 59 optimal weight: 30.0000 chunk 102 optimal weight: 50.0000 chunk 23 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 chunk 10 optimal weight: 30.0000 chunk 104 optimal weight: 9.9990 chunk 120 optimal weight: 20.0000 chunk 7 optimal weight: 40.0000 chunk 129 optimal weight: 7.9990 chunk 83 optimal weight: 20.0000 chunk 31 optimal weight: 4.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.088988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.066638 restraints weight = 35962.408| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 3.86 r_work: 0.2974 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11852 Z= 0.242 Angle : 0.666 9.643 16352 Z= 0.347 Chirality : 0.042 0.329 1834 Planarity : 0.005 0.049 1864 Dihedral : 19.523 130.332 2150 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.40 % Allowed : 12.47 % Favored : 86.14 % 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: 0.85 (0.24), residues: 1269 helix: 1.55 (0.19), residues: 730 sheet: -1.06 (0.51), residues: 91 loop : -0.67 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 455 TYR 0.014 0.002 TYR B 297 PHE 0.017 0.002 PHE B 320 TRP 0.010 0.001 TRP A 553 HIS 0.006 0.001 HIS B 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.24 (11851) covalent geometry : angle 0.66563 / 0.35 (16352) hydrogen bonds : bond 0.05243 / 3.53 ( 594) hydrogen bonds : angle 4.27972 / 3.17 ( 1691) Misc. bond : bond 0.00045 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 ASP cc_start: 0.8512 (p0) cc_final: 0.8216 (p0) REVERT: A 495 GLU cc_start: 0.9070 (mt-10) cc_final: 0.8856 (mp0) REVERT: A 616 GLN cc_start: 0.8019 (mt0) cc_final: 0.7534 (mm-40) REVERT: A 632 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8773 (mp0) REVERT: A 868 MET cc_start: 0.8527 (mmm) cc_final: 0.8319 (mmm) REVERT: B 167 MET cc_start: 0.8493 (ttm) cc_final: 0.7844 (tmm) REVERT: B 201 LYS cc_start: 0.9462 (mttm) cc_final: 0.9169 (mtpt) REVERT: B 265 MET cc_start: 0.9022 (tmm) cc_final: 0.8812 (tmm) REVERT: B 301 MET cc_start: 0.8389 (mpp) cc_final: 0.8136 (mpp) outliers start: 15 outliers final: 11 residues processed: 138 average time/residue: 0.0803 time to fit residues: 16.6150 Evaluate side-chains 135 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 922 ASP Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 305 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 1 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 127 optimal weight: 20.0000 chunk 125 optimal weight: 0.0270 chunk 100 optimal weight: 30.0000 chunk 38 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 132 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 55 optimal weight: 6.9990 chunk 76 optimal weight: 20.0000 overall best weight: 7.0048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.088925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.066527 restraints weight = 35943.696| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 3.88 r_work: 0.2976 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11852 Z= 0.212 Angle : 0.641 10.542 16352 Z= 0.336 Chirality : 0.041 0.203 1834 Planarity : 0.005 0.047 1864 Dihedral : 19.503 126.594 2150 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.86 % Allowed : 13.30 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.24), residues: 1269 helix: 1.56 (0.19), residues: 730 sheet: -1.11 (0.51), residues: 91 loop : -0.69 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 94 TYR 0.013 0.001 TYR A1004 PHE 0.017 0.001 PHE B 320 TRP 0.009 0.001 TRP A 553 HIS 0.005 0.001 HIS B 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.21 (11851) covalent geometry : angle 0.64148 / 0.34 (16352) hydrogen bonds : bond 0.04872 / 3.29 ( 594) hydrogen bonds : angle 4.24120 / 3.12 ( 1691) Misc. bond : bond 0.00016 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 ASP cc_start: 0.8518 (p0) cc_final: 0.8214 (p0) REVERT: A 495 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8815 (mp0) REVERT: A 616 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7609 (mt0) REVERT: A 868 MET cc_start: 0.8503 (mmm) cc_final: 0.8292 (mmm) REVERT: A 970 ASP cc_start: 0.8951 (t70) cc_final: 0.8556 (t0) REVERT: A 975 MET cc_start: 0.9420 (tmm) cc_final: 0.9106 (tmm) REVERT: B 167 MET cc_start: 0.8557 (ttm) cc_final: 0.7879 (tmm) REVERT: B 201 LYS cc_start: 0.9467 (mttm) cc_final: 0.9175 (mtpt) REVERT: B 265 MET cc_start: 0.9053 (tmm) cc_final: 0.8825 (tmm) outliers start: 20 outliers final: 12 residues processed: 140 average time/residue: 0.0848 time to fit residues: 17.8113 Evaluate side-chains 135 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 616 GLN Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 965 VAL Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 305 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 87 optimal weight: 9.9990 chunk 59 optimal weight: 20.0000 chunk 42 optimal weight: 8.9990 chunk 12 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 72 optimal weight: 0.0970 chunk 13 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 overall best weight: 5.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 HIS ** 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 = 0.3678 r_free = 0.3678 target = 0.089420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.066924 restraints weight = 35660.532| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 3.87 r_work: 0.2984 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11852 Z= 0.172 Angle : 0.623 12.792 16352 Z= 0.324 Chirality : 0.040 0.188 1834 Planarity : 0.005 0.045 1864 Dihedral : 19.421 120.809 2148 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.77 % Allowed : 13.95 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.24), residues: 1269 helix: 1.67 (0.19), residues: 730 sheet: -0.67 (0.56), residues: 81 loop : -0.65 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 967 TYR 0.013 0.001 TYR A1004 PHE 0.016 0.001 PHE B 320 TRP 0.008 0.001 TRP A 553 HIS 0.004 0.001 HIS A 773 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (11851) covalent geometry : angle 0.62259 / 0.32 (16352) hydrogen bonds : bond 0.04536 / 3.06 ( 594) hydrogen bonds : angle 4.15113 / 3.05 ( 1691) Misc. bond : bond 0.00030 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 495 GLU cc_start: 0.9097 (mt-10) cc_final: 0.8816 (mp0) REVERT: A 616 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7650 (mt0) REVERT: A 868 MET cc_start: 0.8550 (mmm) cc_final: 0.8329 (mmm) REVERT: A 970 ASP cc_start: 0.9004 (t70) cc_final: 0.8554 (t0) REVERT: A 975 MET cc_start: 0.9403 (tmm) cc_final: 0.8947 (tmm) REVERT: A 992 GLN cc_start: 0.9385 (mm-40) cc_final: 0.8981 (mp10) REVERT: A 1097 SER cc_start: 0.8191 (m) cc_final: 0.7874 (t) REVERT: B 167 MET cc_start: 0.8582 (ttm) cc_final: 0.7919 (tmm) REVERT: B 201 LYS cc_start: 0.9454 (mttm) cc_final: 0.9156 (mtpt) REVERT: B 265 MET cc_start: 0.9044 (tmm) cc_final: 0.8782 (tmm) outliers start: 19 outliers final: 12 residues processed: 149 average time/residue: 0.0844 time to fit residues: 18.7713 Evaluate side-chains 145 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 616 GLN Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 305 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 0 optimal weight: 30.0000 chunk 106 optimal weight: 8.9990 chunk 112 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 98 optimal weight: 50.0000 chunk 11 optimal weight: 8.9990 chunk 45 optimal weight: 0.0980 chunk 104 optimal weight: 20.0000 chunk 6 optimal weight: 2.9990 chunk 102 optimal weight: 50.0000 chunk 34 optimal weight: 10.0000 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 HIS ** 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 = 0.3693 r_free = 0.3693 target = 0.090144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.067760 restraints weight = 35513.088| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 3.88 r_work: 0.3005 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11852 Z= 0.140 Angle : 0.607 12.478 16352 Z= 0.315 Chirality : 0.040 0.218 1834 Planarity : 0.005 0.045 1864 Dihedral : 19.327 116.486 2148 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.49 % Allowed : 14.79 % Favored : 83.72 % 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: 1.21 (0.24), residues: 1269 helix: 1.84 (0.20), residues: 723 sheet: -0.52 (0.58), residues: 77 loop : -0.59 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 94 TYR 0.011 0.001 TYR A1004 PHE 0.015 0.001 PHE B 320 TRP 0.009 0.001 TRP A 885 HIS 0.003 0.001 HIS A 624 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (11851) covalent geometry : angle 0.60713 / 0.32 (16352) hydrogen bonds : bond 0.04282 / 2.91 ( 594) hydrogen bonds : angle 4.08277 / 2.98 ( 1691) Misc. bond : bond 0.00039 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 495 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8802 (mp0) REVERT: A 616 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7653 (mt0) REVERT: A 886 MET cc_start: 0.9177 (ptp) cc_final: 0.8569 (mpp) REVERT: A 970 ASP cc_start: 0.9063 (t70) cc_final: 0.8517 (t0) REVERT: A 975 MET cc_start: 0.9397 (tmm) cc_final: 0.8774 (tmm) REVERT: A 992 GLN cc_start: 0.9384 (mm-40) cc_final: 0.8971 (mp10) REVERT: A 1013 ARG cc_start: 0.8914 (mmp80) cc_final: 0.8704 (mmp80) REVERT: A 1097 SER cc_start: 0.8140 (m) cc_final: 0.7857 (t) REVERT: B 167 MET cc_start: 0.8605 (ttm) cc_final: 0.7950 (tmm) REVERT: B 201 LYS cc_start: 0.9441 (mttm) cc_final: 0.9130 (mtpt) REVERT: B 227 MET cc_start: 0.8304 (mmm) cc_final: 0.8049 (mmm) REVERT: B 235 GLN cc_start: 0.9128 (mt0) cc_final: 0.8909 (mt0) REVERT: B 265 MET cc_start: 0.9064 (tmm) cc_final: 0.8809 (tmm) outliers start: 16 outliers final: 12 residues processed: 146 average time/residue: 0.0862 time to fit residues: 18.4912 Evaluate side-chains 145 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 616 GLN Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 305 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 69 optimal weight: 10.0000 chunk 99 optimal weight: 50.0000 chunk 62 optimal weight: 0.6980 chunk 8 optimal weight: 30.0000 chunk 67 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 96 optimal weight: 50.0000 chunk 63 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 HIS ** 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 = 0.3699 r_free = 0.3699 target = 0.090279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.067792 restraints weight = 35399.220| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.90 r_work: 0.3011 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11852 Z= 0.138 Angle : 0.607 12.415 16352 Z= 0.314 Chirality : 0.040 0.421 1834 Planarity : 0.005 0.046 1864 Dihedral : 19.258 113.494 2148 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.30 % Allowed : 15.07 % Favored : 83.63 % 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: 1.24 (0.24), residues: 1269 helix: 1.89 (0.20), residues: 723 sheet: -0.86 (0.59), residues: 72 loop : -0.55 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 94 TYR 0.011 0.001 TYR B 385 PHE 0.017 0.001 PHE B 320 TRP 0.009 0.001 TRP A 885 HIS 0.004 0.001 HIS A 773 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (11851) covalent geometry : angle 0.60705 / 0.31 (16352) hydrogen bonds : bond 0.04134 / 2.80 ( 594) hydrogen bonds : angle 4.08250 / 2.98 ( 1691) Misc. bond : bond 0.00043 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 495 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8790 (mp0) REVERT: A 616 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7651 (mm110) REVERT: A 772 MET cc_start: 0.6899 (ppp) cc_final: 0.6479 (ppp) REVERT: A 886 MET cc_start: 0.9213 (ptp) cc_final: 0.8930 (mpp) REVERT: A 970 ASP cc_start: 0.9041 (t70) cc_final: 0.8537 (t0) REVERT: A 975 MET cc_start: 0.9381 (tmm) cc_final: 0.8735 (tmm) REVERT: A 992 GLN cc_start: 0.9363 (mm-40) cc_final: 0.8956 (mp10) REVERT: A 1097 SER cc_start: 0.8144 (m) cc_final: 0.7886 (t) REVERT: B 167 MET cc_start: 0.8558 (ttm) cc_final: 0.7934 (tmm) REVERT: B 201 LYS cc_start: 0.9448 (mttm) cc_final: 0.9125 (mttt) REVERT: B 235 GLN cc_start: 0.9111 (mt0) cc_final: 0.8865 (mt0) REVERT: B 265 MET cc_start: 0.9051 (tmm) cc_final: 0.8813 (tmm) outliers start: 14 outliers final: 11 residues processed: 142 average time/residue: 0.0786 time to fit residues: 16.8423 Evaluate side-chains 143 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 616 GLN Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 305 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 80 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 23 optimal weight: 0.3980 chunk 29 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 110 optimal weight: 20.0000 chunk 28 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 overall best weight: 4.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 HIS ** 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 = 0.3686 r_free = 0.3686 target = 0.089528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.067188 restraints weight = 35321.700| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 3.87 r_work: 0.2999 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11852 Z= 0.166 Angle : 0.634 11.993 16352 Z= 0.325 Chirality : 0.040 0.283 1834 Planarity : 0.005 0.045 1864 Dihedral : 19.255 109.630 2148 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.67 % Allowed : 15.63 % Favored : 82.70 % 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: 1269 helix: 1.81 (0.20), residues: 722 sheet: -0.91 (0.60), residues: 72 loop : -0.59 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 94 TYR 0.011 0.001 TYR B 88 PHE 0.015 0.001 PHE B 320 TRP 0.008 0.001 TRP A 885 HIS 0.005 0.001 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 (11851) covalent geometry : angle 0.63441 / 0.33 (16352) hydrogen bonds : bond 0.04272 / 2.89 ( 594) hydrogen bonds : angle 4.15054 / 3.03 ( 1691) Misc. bond : bond 0.00028 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 482 MET cc_start: 0.6987 (ttt) cc_final: 0.6628 (ttt) REVERT: A 495 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8807 (mp0) REVERT: A 616 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7648 (mt0) REVERT: A 772 MET cc_start: 0.6879 (ppp) cc_final: 0.6482 (ppp) REVERT: A 886 MET cc_start: 0.9214 (ptp) cc_final: 0.8913 (mpp) REVERT: A 970 ASP cc_start: 0.9038 (t70) cc_final: 0.8406 (t0) REVERT: A 975 MET cc_start: 0.9374 (tmm) cc_final: 0.8633 (tmm) REVERT: A 992 GLN cc_start: 0.9364 (mm-40) cc_final: 0.8958 (mp10) REVERT: A 1097 SER cc_start: 0.8139 (m) cc_final: 0.7863 (t) REVERT: B 144 LEU cc_start: 0.9237 (tp) cc_final: 0.8983 (tp) REVERT: B 167 MET cc_start: 0.8547 (ttm) cc_final: 0.7926 (tmm) REVERT: B 201 LYS cc_start: 0.9457 (mttm) cc_final: 0.9136 (mttt) REVERT: B 235 GLN cc_start: 0.9123 (mt0) cc_final: 0.8870 (mt0) REVERT: B 265 MET cc_start: 0.9075 (tmm) cc_final: 0.8842 (tmm) outliers start: 18 outliers final: 14 residues processed: 141 average time/residue: 0.0862 time to fit residues: 17.9986 Evaluate side-chains 146 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 616 GLN Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 898 CYS Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 305 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 36 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 130 optimal weight: 20.0000 chunk 92 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 HIS ** 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 = 0.3704 r_free = 0.3704 target = 0.090420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.068133 restraints weight = 35279.304| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 3.90 r_work: 0.3018 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11852 Z= 0.136 Angle : 0.654 13.156 16352 Z= 0.334 Chirality : 0.041 0.282 1834 Planarity : 0.005 0.045 1864 Dihedral : 19.212 105.790 2148 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.40 % Allowed : 15.72 % Favored : 82.88 % 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: 1269 helix: 1.84 (0.20), residues: 719 sheet: -0.90 (0.60), residues: 72 loop : -0.57 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 94 TYR 0.012 0.001 TYR B 88 PHE 0.019 0.001 PHE B 320 TRP 0.009 0.001 TRP A 885 HIS 0.003 0.001 HIS B 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (11851) covalent geometry : angle 0.65431 / 0.33 (16352) hydrogen bonds : bond 0.04110 / 2.80 ( 594) hydrogen bonds : angle 4.12364 / 3.00 ( 1691) Misc. bond : bond 0.00043 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 482 MET cc_start: 0.6980 (ttt) cc_final: 0.6693 (ttt) REVERT: A 495 GLU cc_start: 0.9069 (mt-10) cc_final: 0.8819 (mp0) REVERT: A 616 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7625 (mm110) REVERT: A 772 MET cc_start: 0.6881 (ppp) cc_final: 0.6494 (ppp) REVERT: A 886 MET cc_start: 0.9171 (ptp) cc_final: 0.8880 (mpp) REVERT: A 970 ASP cc_start: 0.9047 (t70) cc_final: 0.8434 (t0) REVERT: A 975 MET cc_start: 0.9385 (tmm) cc_final: 0.8639 (tmm) REVERT: A 992 GLN cc_start: 0.9362 (mm-40) cc_final: 0.8959 (mp10) REVERT: A 1097 SER cc_start: 0.8196 (m) cc_final: 0.7946 (t) REVERT: B 167 MET cc_start: 0.8590 (ttm) cc_final: 0.7902 (tmm) REVERT: B 201 LYS cc_start: 0.9454 (mttm) cc_final: 0.9137 (mttt) REVERT: B 235 GLN cc_start: 0.9081 (mt0) cc_final: 0.8834 (mt0) REVERT: B 265 MET cc_start: 0.9084 (tmm) cc_final: 0.8848 (tmm) REVERT: B 315 MET cc_start: 0.9213 (pmm) cc_final: 0.8972 (pmm) outliers start: 15 outliers final: 14 residues processed: 144 average time/residue: 0.0862 time to fit residues: 18.6536 Evaluate side-chains 145 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 616 GLN Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 305 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 84 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 chunk 130 optimal weight: 20.0000 chunk 122 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 82 optimal weight: 50.0000 chunk 94 optimal weight: 1.9990 chunk 111 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 HIS ** 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 = 0.3695 r_free = 0.3695 target = 0.090017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.067472 restraints weight = 35778.673| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 3.92 r_work: 0.3007 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11852 Z= 0.155 Angle : 0.659 12.695 16352 Z= 0.339 Chirality : 0.041 0.262 1834 Planarity : 0.005 0.046 1864 Dihedral : 19.198 102.062 2148 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.49 % Allowed : 15.72 % Favored : 82.79 % 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: 1269 helix: 1.75 (0.20), residues: 721 sheet: -0.94 (0.60), residues: 72 loop : -0.58 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 455 TYR 0.015 0.001 TYR B 88 PHE 0.019 0.001 PHE B 320 TRP 0.008 0.001 TRP A 885 HIS 0.003 0.001 HIS A1138 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (11851) covalent geometry : angle 0.65885 / 0.34 (16352) hydrogen bonds : bond 0.04171 / 2.84 ( 594) hydrogen bonds : angle 4.17390 / 3.04 ( 1691) Misc. bond : bond 0.00036 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2681.03 seconds wall clock time: 46 minutes 31.63 seconds (2791.63 seconds total)