Starting phenix.real_space_refine on Fri Jul 3 00:58:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8c5s_16442/07_2026/8c5s_16442.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c5s_16442/07_2026/8c5s_16442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8c5s_16442/07_2026/8c5s_16442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c5s_16442/07_2026/8c5s_16442.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8c5s_16442/07_2026/8c5s_16442.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8c5s_16442/07_2026/8c5s_16442.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8c5s_16442/07_2026/8c5s_16442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c5s_16442/07_2026/8c5s_16442.map" } resolution = 3.75 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= 0.018 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 65 5.49 5 S 36 5.16 5 C 7038 2.51 5 N 1960 2.21 5 O 2213 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: 11312 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2758 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 316} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 7244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 924, 7244 Classifications: {'peptide': 924} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 44, 'TRANS': 879} Chain breaks: 2 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 6, 'ARG:plan': 3, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 80 Chain: "N" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 580 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "T" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 569 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "C" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 2} Link IDs: {'rna3p': 5} 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: 2.54, per 1000 atoms: 0.22 Number of scatterers: 11312 At special positions: 0 Unit cell: (104.76, 116.4, 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 36 16.00 P 65 15.00 O 2213 8.00 N 1960 7.00 C 7038 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: 0.81 Conformation dependent library (CDL) restraints added in 433.4 milliseconds 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2384 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 10 sheets defined 57.1% alpha, 7.5% beta 23 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'B' and resid 7 through 14 removed outlier: 3.686A pdb=" N LEU B 14 " --> pdb=" O ASP B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 37 removed outlier: 3.607A pdb=" N TYR B 29 " --> pdb=" O ASN B 25 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASP B 37 " --> pdb=" O PHE B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 42 removed outlier: 4.122A 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 90 Processing helix chain 'B' and resid 104 through 113 removed outlier: 4.098A pdb=" N TYR B 108 " --> pdb=" O ASP B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 157 removed outlier: 3.830A pdb=" N ILE B 147 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY B 155 " --> pdb=" O LEU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 164 removed outlier: 3.576A pdb=" N PHE B 163 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 181 Processing helix chain 'B' and resid 190 through 200 Processing helix chain 'B' and resid 210 through 215 Processing helix chain 'B' and resid 217 through 225 removed outlier: 4.070A pdb=" N GLU B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU B 223 " --> pdb=" O GLN B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 234 removed outlier: 3.617A pdb=" N ILE B 234 " --> pdb=" O ALA B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 266 Processing helix chain 'B' and resid 273 through 278 removed outlier: 3.578A pdb=" N VAL B 277 " --> pdb=" O PRO B 273 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N MET B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 273 through 278' Processing helix chain 'B' and resid 279 through 281 No H-bonds generated for 'chain 'B' and resid 279 through 281' Processing helix chain 'B' and resid 284 through 293 removed outlier: 3.618A pdb=" N TYR B 288 " --> pdb=" O GLY B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 300 removed outlier: 3.557A pdb=" N LEU B 299 " --> pdb=" O ASP B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 320 removed outlier: 3.548A pdb=" N GLU B 320 " --> pdb=" O LYS B 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 395 Processing helix chain 'A' and resid 397 through 421 removed outlier: 5.057A pdb=" N ASP A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ARG A 415 " --> pdb=" O PHE A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 442 removed outlier: 4.138A pdb=" N ALA A 440 " --> pdb=" O GLU A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 474 Proline residue: A 463 - end of helix Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 492 through 501 Proline residue: A 498 - end of helix removed outlier: 3.525A pdb=" N THR A 501 " --> pdb=" O GLY A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 517 Processing helix chain 'A' and resid 531 through 552 removed outlier: 3.571A pdb=" N LEU A 552 " --> pdb=" O SER A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 612 Processing helix chain 'A' and resid 652 through 662 Processing helix chain 'A' and resid 703 through 717 removed outlier: 4.074A pdb=" N VAL A 707 " --> pdb=" O SER A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 731 Processing helix chain 'A' and resid 738 through 749 Processing helix chain 'A' and resid 775 through 813 removed outlier: 3.568A pdb=" N LEU A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 848 removed outlier: 3.588A pdb=" N LEU A 848 " --> pdb=" O MET A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 872 Processing helix chain 'A' and resid 879 through 889 Processing helix chain 'A' and resid 890 through 900 removed outlier: 3.526A pdb=" N ASN A 900 " --> pdb=" O ASP A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 911 Processing helix chain 'A' and resid 913 through 930 Processing helix chain 'A' and resid 948 through 959 Processing helix chain 'A' and resid 961 through 966 Processing helix chain 'A' and resid 977 through 994 Processing helix chain 'A' and resid 998 through 1004 Processing helix chain 'A' and resid 1009 through 1021 removed outlier: 4.068A pdb=" N VAL A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL A1021 " --> pdb=" O VAL A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1036 Processing helix chain 'A' and resid 1037 through 1041 removed outlier: 3.926A pdb=" N PHE A1041 " --> pdb=" O SER A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1063 Processing helix chain 'A' and resid 1067 through 1085 removed outlier: 3.514A pdb=" N LEU A1071 " --> pdb=" O HIS A1067 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A1072 " --> pdb=" O SER A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1180 removed outlier: 3.995A pdb=" N GLN A1153 " --> pdb=" O ASN A1149 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS A1154 " --> pdb=" O ALA A1150 " (cutoff:3.500A) Proline residue: A1158 - end of helix removed outlier: 3.833A pdb=" N ALA A1167 " --> pdb=" O HIS A1163 " (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 1257 Processing helix chain 'A' and resid 1264 through 1281 removed outlier: 3.697A pdb=" N SER A1281 " --> pdb=" O GLU A1277 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1292 Processing helix chain 'A' and resid 1295 through 1300 Processing helix chain 'A' and resid 1305 through 1311 removed outlier: 3.834A pdb=" N GLU A1310 " --> pdb=" O LEU A1306 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1345 removed outlier: 3.557A pdb=" N VAL A1342 " --> pdb=" O ASP A1339 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASN A1345 " --> pdb=" O VAL A1342 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.647A pdb=" N GLU B 77 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER B 74 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU B 76 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 10.435A pdb=" N LYS B 165 " --> pdb=" O ASP B 130 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N PHE B 132 " --> pdb=" O LYS B 165 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LYS B 167 " --> pdb=" O PHE B 132 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA B 206 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLU B 246 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LEU B 204 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N ILE B 227 " --> pdb=" O LYS B 203 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ILE B 205 " --> pdb=" O ILE B 227 " (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 614 through 616 Processing sheet with id=AA4, first strand: chain 'A' and resid 818 through 819 Processing sheet with id=AA5, first strand: chain 'A' and resid 822 through 824 Processing sheet with id=AA6, first strand: chain 'A' and resid 855 through 856 removed outlier: 3.969A pdb=" N LYS A 855 " --> pdb=" O SER A 938 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER A 938 " --> pdb=" O LYS A 855 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 942 through 944 removed outlier: 3.648A pdb=" N THR A1193 " --> pdb=" O VAL A 942 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1087 through 1088 Processing sheet with id=AA9, first strand: chain 'A' and resid 1109 through 1111 Processing sheet with id=AB1, first strand: chain 'A' and resid 1127 through 1131 508 hydrogen bonds defined for protein. 1461 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 51 hydrogen bonds 102 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 2.48 Time building geometry restraints manager: 1.05 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: 3140 1.34 - 1.45: 2231 1.45 - 1.57: 6142 1.57 - 1.69: 133 1.69 - 1.81: 62 Bond restraints: 11708 Sorted by residual: bond pdb=" C3' DG N 113 " pdb=" C2' DG N 113 " ideal model delta sigma weight residual 1.516 1.623 -0.107 8.00e-03 1.56e+04 1.79e+02 bond pdb=" C3' DG N 136 " pdb=" C2' DG N 136 " ideal model delta sigma weight residual 1.516 1.620 -0.104 8.00e-03 1.56e+04 1.69e+02 bond pdb=" C3' DT N 111 " pdb=" C2' DT N 111 " ideal model delta sigma weight residual 1.516 1.619 -0.103 8.00e-03 1.56e+04 1.65e+02 bond pdb=" C3' DT T 20 " pdb=" C2' DT T 20 " ideal model delta sigma weight residual 1.516 1.608 -0.092 8.00e-03 1.56e+04 1.31e+02 bond pdb=" C3' DT T 14 " pdb=" C2' DT T 14 " ideal model delta sigma weight residual 1.516 1.594 -0.078 8.00e-03 1.56e+04 9.49e+01 ... (remaining 11703 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.50: 15971 4.50 - 9.00: 139 9.00 - 13.50: 22 13.50 - 18.00: 5 18.00 - 22.50: 3 Bond angle restraints: 16140 Sorted by residual: angle pdb=" C3' DA T 35 " pdb=" O3' DA T 35 " pdb=" P DT T 36 " ideal model delta sigma weight residual 120.20 99.37 20.83 1.50e+00 4.44e-01 1.93e+02 angle pdb=" C3' A C 104 " pdb=" O3' A C 104 " pdb=" P A C 105 " ideal model delta sigma weight residual 120.20 101.23 18.97 1.50e+00 4.44e-01 1.60e+02 angle pdb=" C3' DC T 17 " pdb=" O3' DC T 17 " pdb=" P DA T 18 " ideal model delta sigma weight residual 120.20 135.17 -14.97 1.50e+00 4.44e-01 9.96e+01 angle pdb=" O4' DG T 16 " pdb=" C1' DG T 16 " pdb=" C2' DG T 16 " ideal model delta sigma weight residual 105.90 113.12 -7.22 8.00e-01 1.56e+00 8.16e+01 angle pdb=" C3' DT T 19 " pdb=" O3' DT T 19 " pdb=" P DT T 20 " ideal model delta sigma weight residual 120.20 107.31 12.89 1.50e+00 4.44e-01 7.38e+01 ... (remaining 16135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.06: 6434 30.06 - 60.11: 437 60.11 - 90.17: 23 90.17 - 120.22: 2 120.22 - 150.28: 4 Dihedral angle restraints: 6900 sinusoidal: 3220 harmonic: 3680 Sorted by residual: dihedral pdb=" O5' GTP C 201 " pdb=" O3A GTP C 201 " pdb=" PA GTP C 201 " pdb=" PB GTP C 201 " ideal model delta sinusoidal sigma weight residual -85.88 55.19 -141.07 1 2.00e+01 2.50e-03 4.27e+01 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 303.79 167.39 136.40 1 2.00e+01 2.50e-03 4.14e+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 -18.61 123.20 1 2.00e+01 2.50e-03 3.71e+01 ... (remaining 6897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 1717 0.136 - 0.273: 31 0.273 - 0.409: 8 0.409 - 0.546: 23 0.546 - 0.682: 9 Chirality restraints: 1788 Sorted by residual: chirality pdb=" C1' DG T 16 " pdb=" O4' DG T 16 " pdb=" C2' DG T 16 " pdb=" N9 DG T 16 " both_signs ideal model delta sigma weight residual False 2.43 1.75 0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" P DT N 109 " pdb=" OP1 DT N 109 " pdb=" OP2 DT N 109 " pdb=" O5' DT N 109 " both_signs ideal model delta sigma weight residual True 2.34 -2.97 -0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" P DC T 10 " pdb=" OP1 DC T 10 " pdb=" OP2 DC T 10 " pdb=" O5' DC T 10 " both_signs ideal model delta sigma weight residual True 2.34 -2.97 -0.63 2.00e-01 2.50e+01 9.96e+00 ... (remaining 1785 not shown) Planarity restraints: 1841 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 900 " -0.056 5.00e-02 4.00e+02 8.44e-02 1.14e+01 pdb=" N PRO A 901 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO A 901 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 901 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 767 " 0.057 5.00e-02 4.00e+02 8.34e-02 1.11e+01 pdb=" N PRO A 768 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO A 768 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 768 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 462 " -0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO A 463 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 463 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 463 " -0.027 5.00e-02 4.00e+02 ... (remaining 1838 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 34 2.45 - 3.07: 7210 3.07 - 3.68: 17158 3.68 - 4.29: 25016 4.29 - 4.90: 40963 Nonbonded interactions: 90381 Sorted by model distance: nonbonded pdb=" OE1 GLN B 336 " pdb=" N2 DG T 25 " model vdw 1.842 3.120 nonbonded pdb=" O ASN A 900 " pdb=" OD1 ASN A 900 " model vdw 2.082 3.040 nonbonded pdb=" OG1 THR A1132 " pdb=" O GLN A1135 " model vdw 2.223 3.040 nonbonded pdb=" OE1 GLN A 944 " pdb=" OG SER A1351 " model vdw 2.253 3.040 nonbonded pdb=" OG SER A 794 " pdb=" N7 DG T 25 " model vdw 2.267 3.120 ... (remaining 90376 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 group one per residue 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: 0.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.470 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 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 0.121 11709 Z= 0.552 Angle : 1.038 22.496 16140 Z= 0.582 Chirality : 0.089 0.682 1788 Planarity : 0.005 0.084 1841 Dihedral : 18.357 150.277 4516 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % 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: 0.62 (0.24), residues: 1252 helix: 1.71 (0.21), residues: 649 sheet: -0.89 (0.49), residues: 111 loop : -1.04 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 264 TYR 0.024 0.001 TYR B 161 PHE 0.029 0.001 PHE A1338 TRP 0.023 0.001 TRP A 915 HIS 0.004 0.001 HIS A1169 Details of bonding type rmsd/Z covalent geometry : bond 0.00680 / 0.55 (11708) covalent geometry : angle 1.03844 / 0.58 (16140) hydrogen bonds : bond 0.14756 / 9.77 ( 559) hydrogen bonds : angle 6.18565 / 4.37 ( 1563) Misc. bond : bond 0.01822 / 0.96 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.297 Fit side-chains REVERT: A 476 LEU cc_start: 0.6034 (mt) cc_final: 0.5205 (tt) REVERT: A 1005 LYS cc_start: 0.7467 (tmmt) cc_final: 0.7193 (tttp) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.0986 time to fit residues: 26.3472 Evaluate side-chains 150 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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: 8.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.0020 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 40.0000 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 overall best weight: 4.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 137 ASN B 187 HIS A 492 ASN A 900 ASN ** A 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.159523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.131774 restraints weight = 15434.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.133395 restraints weight = 11225.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.133607 restraints weight = 9520.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.133836 restraints weight = 8913.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.134248 restraints weight = 8361.023| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11709 Z= 0.191 Angle : 0.650 9.657 16140 Z= 0.348 Chirality : 0.045 0.244 1788 Planarity : 0.005 0.056 1841 Dihedral : 19.903 162.394 2089 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.07 % Favored : 95.85 % Rotamer: Outliers : 1.86 % Allowed : 7.83 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.24), residues: 1252 helix: 1.61 (0.21), residues: 662 sheet: -0.92 (0.45), residues: 129 loop : -1.18 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 79 TYR 0.026 0.002 TYR B 161 PHE 0.015 0.001 PHE A1161 TRP 0.015 0.002 TRP A 915 HIS 0.010 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 (11708) covalent geometry : angle 0.65044 / 0.35 (16140) hydrogen bonds : bond 0.05491 / 3.57 ( 559) hydrogen bonds : angle 4.66968 / 3.34 ( 1563) Misc. bond : bond 0.00012 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.397 Fit side-chains REVERT: B 137 ASN cc_start: 0.9019 (OUTLIER) cc_final: 0.8573 (t0) REVERT: A 439 LYS cc_start: 0.6505 (tttt) cc_final: 0.6128 (tttt) outliers start: 20 outliers final: 14 residues processed: 170 average time/residue: 0.0986 time to fit residues: 24.4456 Evaluate side-chains 162 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 996 LYS Chi-restraints excluded: chain A residue 1096 PHE Chi-restraints excluded: chain A residue 1146 ASN Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1189 ASP Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 16 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 86 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 137 ASN A 900 ASN A 987 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.158125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.130038 restraints weight = 15494.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.132525 restraints weight = 12402.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.134016 restraints weight = 9223.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.134465 restraints weight = 7676.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.134537 restraints weight = 7103.324| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11709 Z= 0.168 Angle : 0.607 9.376 16140 Z= 0.323 Chirality : 0.042 0.180 1788 Planarity : 0.005 0.052 1841 Dihedral : 19.676 172.780 2089 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.55 % Favored : 95.37 % Rotamer: Outliers : 2.14 % Allowed : 11.09 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.24), residues: 1252 helix: 1.63 (0.21), residues: 664 sheet: -0.98 (0.44), residues: 129 loop : -1.21 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 264 TYR 0.026 0.001 TYR B 161 PHE 0.017 0.001 PHE A1338 TRP 0.015 0.001 TRP A 915 HIS 0.003 0.001 HIS A1169 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (11708) covalent geometry : angle 0.60683 / 0.32 (16140) hydrogen bonds : bond 0.05137 / 3.35 ( 559) hydrogen bonds : angle 4.52670 / 3.24 ( 1563) Misc. bond : bond 0.00101 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.401 Fit side-chains REVERT: B 137 ASN cc_start: 0.8855 (OUTLIER) cc_final: 0.8262 (t0) REVERT: B 321 TRP cc_start: 0.7964 (t60) cc_final: 0.7348 (t60) REVERT: A 439 LYS cc_start: 0.6538 (tttt) cc_final: 0.6152 (tttt) outliers start: 23 outliers final: 18 residues processed: 162 average time/residue: 0.1022 time to fit residues: 23.8837 Evaluate side-chains 164 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 692 TYR Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain A residue 996 LYS Chi-restraints excluded: chain A residue 1096 PHE Chi-restraints excluded: chain A residue 1146 ASN Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1189 ASP Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 125 optimal weight: 40.0000 chunk 24 optimal weight: 7.9990 chunk 29 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 72 optimal weight: 8.9990 chunk 86 optimal weight: 8.9990 chunk 4 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 137 ASN A 900 ASN A 987 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.159340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.131384 restraints weight = 15505.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.134300 restraints weight = 12362.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.135452 restraints weight = 9130.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.135980 restraints weight = 7561.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.136543 restraints weight = 7081.554| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11709 Z= 0.158 Angle : 0.599 10.098 16140 Z= 0.317 Chirality : 0.042 0.186 1788 Planarity : 0.004 0.053 1841 Dihedral : 19.320 144.578 2089 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.15 % Favored : 95.77 % Rotamer: Outliers : 2.52 % Allowed : 13.05 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.24), residues: 1252 helix: 1.64 (0.21), residues: 664 sheet: -1.04 (0.44), residues: 129 loop : -1.22 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 264 TYR 0.020 0.001 TYR A 690 PHE 0.015 0.001 PHE A 826 TRP 0.015 0.001 TRP A 915 HIS 0.003 0.001 HIS A1169 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (11708) covalent geometry : angle 0.59946 / 0.32 (16140) hydrogen bonds : bond 0.04830 / 3.16 ( 559) hydrogen bonds : angle 4.46880 / 3.19 ( 1563) Misc. bond : bond 0.00083 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 0.373 Fit side-chains REVERT: B 137 ASN cc_start: 0.8881 (OUTLIER) cc_final: 0.8298 (t0) REVERT: B 247 MET cc_start: 0.8390 (mmt) cc_final: 0.7966 (tpp) REVERT: B 321 TRP cc_start: 0.8014 (t60) cc_final: 0.7232 (t60) REVERT: A 1215 VAL cc_start: 0.7639 (OUTLIER) cc_final: 0.7365 (t) outliers start: 27 outliers final: 20 residues processed: 168 average time/residue: 0.0927 time to fit residues: 22.4934 Evaluate side-chains 168 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 692 TYR Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain A residue 996 LYS Chi-restraints excluded: chain A residue 1096 PHE Chi-restraints excluded: chain A residue 1146 ASN Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1189 ASP Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 21 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 73 optimal weight: 0.1980 chunk 80 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 137 ASN A 900 ASN A 968 ASN A 987 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.161480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.134236 restraints weight = 15343.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.135374 restraints weight = 11482.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.135774 restraints weight = 9815.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.135953 restraints weight = 9198.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.137783 restraints weight = 8640.842| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11709 Z= 0.125 Angle : 0.568 10.088 16140 Z= 0.301 Chirality : 0.041 0.183 1788 Planarity : 0.004 0.051 1841 Dihedral : 19.078 138.390 2089 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.33 % Allowed : 14.35 % Favored : 83.32 % 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: 0.59 (0.24), residues: 1252 helix: 1.74 (0.21), residues: 664 sheet: -1.02 (0.43), residues: 129 loop : -1.20 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 264 TYR 0.016 0.001 TYR B 288 PHE 0.019 0.001 PHE A1338 TRP 0.015 0.001 TRP A 915 HIS 0.003 0.001 HIS A1169 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (11708) covalent geometry : angle 0.56808 / 0.30 (16140) hydrogen bonds : bond 0.04382 / 2.85 ( 559) hydrogen bonds : angle 4.33390 / 3.09 ( 1563) Misc. bond : bond 0.00093 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 0.396 Fit side-chains REVERT: B 137 ASN cc_start: 0.8843 (OUTLIER) cc_final: 0.8201 (t0) REVERT: B 321 TRP cc_start: 0.7995 (t60) cc_final: 0.7399 (t60) REVERT: A 503 ILE cc_start: 0.7927 (OUTLIER) cc_final: 0.7605 (mp) REVERT: A 1215 VAL cc_start: 0.7687 (OUTLIER) cc_final: 0.7423 (t) outliers start: 25 outliers final: 15 residues processed: 176 average time/residue: 0.0939 time to fit residues: 24.1599 Evaluate side-chains 166 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain A residue 996 LYS Chi-restraints excluded: chain A residue 1096 PHE Chi-restraints excluded: chain A residue 1146 ASN Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1189 ASP Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1296 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 1 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 49 optimal weight: 30.0000 chunk 103 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 61 optimal weight: 0.0170 chunk 74 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 52 optimal weight: 20.0000 overall best weight: 4.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 137 ASN A 987 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.158365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.130690 restraints weight = 15564.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.132619 restraints weight = 11946.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.133561 restraints weight = 9211.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.134066 restraints weight = 8204.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.136056 restraints weight = 7550.060| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11709 Z= 0.176 Angle : 0.603 9.110 16140 Z= 0.318 Chirality : 0.042 0.184 1788 Planarity : 0.004 0.054 1841 Dihedral : 19.045 138.159 2089 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.55 % Favored : 95.37 % Rotamer: Outliers : 2.42 % Allowed : 14.82 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.24), residues: 1252 helix: 1.67 (0.21), residues: 664 sheet: -1.00 (0.43), residues: 129 loop : -1.24 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 264 TYR 0.013 0.001 TYR B 42 PHE 0.015 0.001 PHE A 826 TRP 0.016 0.002 TRP A 915 HIS 0.003 0.001 HIS B 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (11708) covalent geometry : angle 0.60289 / 0.32 (16140) hydrogen bonds : bond 0.04724 / 3.08 ( 559) hydrogen bonds : angle 4.37318 / 3.12 ( 1563) Misc. bond : bond 0.00065 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.400 Fit side-chains REVERT: B 114 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7484 (mp0) REVERT: B 137 ASN cc_start: 0.8868 (OUTLIER) cc_final: 0.8209 (t0) REVERT: B 321 TRP cc_start: 0.8059 (t60) cc_final: 0.7384 (t60) REVERT: A 503 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7678 (mp) REVERT: A 519 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7353 (pp) REVERT: A 1215 VAL cc_start: 0.7678 (OUTLIER) cc_final: 0.7416 (t) outliers start: 26 outliers final: 18 residues processed: 169 average time/residue: 0.0968 time to fit residues: 23.9169 Evaluate side-chains 169 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain A residue 996 LYS Chi-restraints excluded: chain A residue 1096 PHE Chi-restraints excluded: chain A residue 1146 ASN Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1189 ASP Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 8.9990 chunk 57 optimal weight: 9.9990 chunk 38 optimal weight: 20.0000 chunk 51 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 88 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 137 ASN B 287 GLN A 987 GLN 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 = 0.157619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.129589 restraints weight = 15532.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.132196 restraints weight = 12273.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.133433 restraints weight = 9320.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.133967 restraints weight = 7913.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.134271 restraints weight = 7267.712| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11709 Z= 0.183 Angle : 0.611 9.217 16140 Z= 0.323 Chirality : 0.042 0.183 1788 Planarity : 0.004 0.054 1841 Dihedral : 19.035 137.907 2089 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.79 % Favored : 95.13 % Rotamer: Outliers : 2.70 % Allowed : 15.38 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.24), residues: 1252 helix: 1.62 (0.21), residues: 664 sheet: -1.00 (0.43), residues: 129 loop : -1.28 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 264 TYR 0.014 0.001 TYR B 42 PHE 0.021 0.001 PHE A1338 TRP 0.017 0.002 TRP A 915 HIS 0.003 0.001 HIS B 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (11708) covalent geometry : angle 0.61113 / 0.32 (16140) hydrogen bonds : bond 0.04808 / 3.13 ( 559) hydrogen bonds : angle 4.39116 / 3.14 ( 1563) Misc. bond : bond 0.00053 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.431 Fit side-chains REVERT: B 114 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7551 (mp0) REVERT: B 137 ASN cc_start: 0.8856 (OUTLIER) cc_final: 0.8210 (t0) REVERT: B 321 TRP cc_start: 0.8075 (t60) cc_final: 0.7473 (t60) REVERT: A 503 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7733 (mp) REVERT: A 519 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7303 (pp) REVERT: A 1215 VAL cc_start: 0.7690 (OUTLIER) cc_final: 0.7424 (t) REVERT: A 1271 PHE cc_start: 0.4934 (m-80) cc_final: 0.3989 (t80) outliers start: 29 outliers final: 19 residues processed: 173 average time/residue: 0.0935 time to fit residues: 23.9982 Evaluate side-chains 170 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain A residue 996 LYS Chi-restraints excluded: chain A residue 1096 PHE Chi-restraints excluded: chain A residue 1146 ASN Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1189 ASP Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 2 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 125 optimal weight: 50.0000 chunk 71 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 137 ASN B 287 GLN A 639 GLN A 987 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.159323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.132571 restraints weight = 15402.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.133152 restraints weight = 11240.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.134380 restraints weight = 9445.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.136350 restraints weight = 8101.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.136467 restraints weight = 6925.632| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11709 Z= 0.134 Angle : 0.579 9.167 16140 Z= 0.307 Chirality : 0.041 0.178 1788 Planarity : 0.004 0.053 1841 Dihedral : 18.937 137.247 2089 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.31 % Favored : 95.61 % Rotamer: Outliers : 2.98 % Allowed : 15.75 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.24), residues: 1252 helix: 1.67 (0.21), residues: 664 sheet: -0.99 (0.42), residues: 129 loop : -1.27 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 264 TYR 0.010 0.001 TYR B 42 PHE 0.022 0.001 PHE A1338 TRP 0.023 0.001 TRP A 915 HIS 0.003 0.001 HIS A1169 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (11708) covalent geometry : angle 0.57896 / 0.31 (16140) hydrogen bonds : bond 0.04378 / 2.85 ( 559) hydrogen bonds : angle 4.28114 / 3.07 ( 1563) Misc. bond : bond 0.00077 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 0.377 Fit side-chains REVERT: B 114 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7475 (mp0) REVERT: B 137 ASN cc_start: 0.8800 (OUTLIER) cc_final: 0.8118 (t0) REVERT: B 321 TRP cc_start: 0.8066 (t60) cc_final: 0.7512 (t60) REVERT: A 461 MET cc_start: 0.7948 (ttm) cc_final: 0.7261 (ttm) REVERT: A 503 ILE cc_start: 0.7961 (OUTLIER) cc_final: 0.7678 (mp) REVERT: A 519 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.6972 (pp) REVERT: A 1215 VAL cc_start: 0.7687 (OUTLIER) cc_final: 0.7385 (t) REVERT: A 1271 PHE cc_start: 0.5005 (m-80) cc_final: 0.4094 (t80) outliers start: 32 outliers final: 20 residues processed: 176 average time/residue: 0.0984 time to fit residues: 25.4181 Evaluate side-chains 174 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain A residue 996 LYS Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1096 PHE Chi-restraints excluded: chain A residue 1146 ASN Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1189 ASP Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 99 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 90 optimal weight: 20.0000 chunk 115 optimal weight: 6.9990 chunk 119 optimal weight: 30.0000 chunk 65 optimal weight: 0.0980 chunk 124 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 137 ASN B 287 GLN A 987 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.157818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.130456 restraints weight = 15360.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.131971 restraints weight = 11951.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.132975 restraints weight = 9384.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.133772 restraints weight = 8240.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.135127 restraints weight = 7518.161| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11709 Z= 0.164 Angle : 0.602 9.400 16140 Z= 0.318 Chirality : 0.042 0.181 1788 Planarity : 0.004 0.054 1841 Dihedral : 18.918 137.199 2089 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.71 % Favored : 95.21 % Rotamer: Outliers : 2.89 % Allowed : 16.31 % Favored : 80.80 % 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: 0.44 (0.24), residues: 1252 helix: 1.62 (0.21), residues: 664 sheet: -1.00 (0.42), residues: 129 loop : -1.32 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 264 TYR 0.012 0.001 TYR B 42 PHE 0.025 0.001 PHE A1338 TRP 0.022 0.002 TRP A 915 HIS 0.002 0.001 HIS A 953 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (11708) covalent geometry : angle 0.60204 / 0.32 (16140) hydrogen bonds : bond 0.04569 / 2.97 ( 559) hydrogen bonds : angle 4.32360 / 3.09 ( 1563) Misc. bond : bond 0.00064 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 0.400 Fit side-chains REVERT: B 114 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7487 (mp0) REVERT: B 137 ASN cc_start: 0.8791 (OUTLIER) cc_final: 0.8051 (t0) REVERT: B 321 TRP cc_start: 0.8077 (t60) cc_final: 0.7446 (t60) REVERT: A 461 MET cc_start: 0.7907 (ttm) cc_final: 0.7263 (ttm) REVERT: A 503 ILE cc_start: 0.8006 (OUTLIER) cc_final: 0.7705 (mp) REVERT: A 519 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.6993 (pp) REVERT: A 1215 VAL cc_start: 0.7719 (OUTLIER) cc_final: 0.7436 (t) REVERT: A 1271 PHE cc_start: 0.5029 (m-80) cc_final: 0.4114 (t80) outliers start: 31 outliers final: 21 residues processed: 173 average time/residue: 0.0956 time to fit residues: 24.4471 Evaluate side-chains 176 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain A residue 996 LYS Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1096 PHE Chi-restraints excluded: chain A residue 1146 ASN Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1189 ASP Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 30 optimal weight: 0.0040 chunk 35 optimal weight: 7.9990 chunk 100 optimal weight: 0.0370 chunk 10 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 116 optimal weight: 30.0000 chunk 115 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 overall best weight: 2.8076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 287 GLN A 987 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.159171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.132194 restraints weight = 15354.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.133653 restraints weight = 11485.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.134536 restraints weight = 9020.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.135180 restraints weight = 8375.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.137010 restraints weight = 7466.901| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 11709 Z= 0.142 Angle : 0.592 9.110 16140 Z= 0.311 Chirality : 0.041 0.178 1788 Planarity : 0.004 0.054 1841 Dihedral : 18.872 136.739 2089 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.63 % Favored : 95.29 % Rotamer: Outliers : 2.42 % Allowed : 16.78 % Favored : 80.80 % 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: 0.48 (0.24), residues: 1252 helix: 1.66 (0.21), residues: 664 sheet: -0.98 (0.42), residues: 129 loop : -1.30 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 264 TYR 0.029 0.001 TYR B 73 PHE 0.025 0.001 PHE A1338 TRP 0.025 0.001 TRP A 915 HIS 0.003 0.001 HIS A1169 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (11708) covalent geometry : angle 0.59172 / 0.31 (16140) hydrogen bonds : bond 0.04373 / 2.84 ( 559) hydrogen bonds : angle 4.28244 / 3.07 ( 1563) Misc. bond : bond 0.00071 / 0.04 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.388 Fit side-chains REVERT: B 114 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: B 321 TRP cc_start: 0.8064 (t60) cc_final: 0.7459 (t60) REVERT: A 461 MET cc_start: 0.7886 (ttm) cc_final: 0.7261 (ttm) REVERT: A 503 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7675 (mp) REVERT: A 519 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.6940 (pp) REVERT: A 1215 VAL cc_start: 0.7729 (OUTLIER) cc_final: 0.7450 (t) REVERT: A 1271 PHE cc_start: 0.4976 (m-80) cc_final: 0.4095 (t80) outliers start: 26 outliers final: 21 residues processed: 172 average time/residue: 0.1016 time to fit residues: 25.4760 Evaluate side-chains 175 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain A residue 996 LYS Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1096 PHE Chi-restraints excluded: chain A residue 1146 ASN Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1189 ASP Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 5 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 125 optimal weight: 40.0000 chunk 128 optimal weight: 20.0000 chunk 12 optimal weight: 8.9990 chunk 79 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 287 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.160085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.133318 restraints weight = 15367.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.134493 restraints weight = 11389.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.135693 restraints weight = 9188.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.136510 restraints weight = 7954.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.137364 restraints weight = 7297.535| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11709 Z= 0.137 Angle : 0.588 8.839 16140 Z= 0.307 Chirality : 0.040 0.178 1788 Planarity : 0.004 0.053 1841 Dihedral : 18.821 136.183 2089 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.55 % Favored : 95.37 % Rotamer: Outliers : 2.42 % Allowed : 16.96 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.24), residues: 1252 helix: 1.64 (0.21), residues: 671 sheet: -1.00 (0.43), residues: 124 loop : -1.29 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 264 TYR 0.030 0.001 TYR B 161 PHE 0.025 0.001 PHE A1338 TRP 0.033 0.001 TRP A 915 HIS 0.003 0.001 HIS A1169 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (11708) covalent geometry : angle 0.58769 / 0.31 (16140) hydrogen bonds : bond 0.04248 / 2.76 ( 559) hydrogen bonds : angle 4.24126 / 3.04 ( 1563) Misc. bond : bond 0.00069 / 0.04 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1546.85 seconds wall clock time: 27 minutes 38.48 seconds (1658.48 seconds total)