Starting phenix.real_space_refine on Tue Jun 10 03:32:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c5s_16442/06_2025/8c5s_16442.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c5s_16442/06_2025/8c5s_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8c5s_16442/06_2025/8c5s_16442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c5s_16442/06_2025/8c5s_16442.map" model { file = "/net/cci-nas-00/data/ceres_data/8c5s_16442/06_2025/8c5s_16442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c5s_16442/06_2025/8c5s_16442.cif" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 2, 'GLU:plan': 9, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 6} 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: 6.94, per 1000 atoms: 0.61 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: 2.97 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 3.93 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: 4.97 Time building geometry restraints manager: 3.52 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=" O3' DC T 24 " pdb=" P DG T 25 " ideal model delta sigma weight residual 1.607 1.728 -0.121 1.50e-02 4.44e+03 6.56e+01 bond pdb=" O3' DT N 135 " pdb=" P DG N 136 " ideal model delta sigma weight residual 1.607 1.495 0.112 1.50e-02 4.44e+03 5.56e+01 bond pdb=" O3' DC T 17 " pdb=" P DA T 18 " ideal model delta sigma weight residual 1.607 1.499 0.108 1.50e-02 4.44e+03 5.16e+01 bond pdb=" O3' DA T 31 " pdb=" P DT T 32 " ideal model delta sigma weight residual 1.607 1.506 0.101 1.50e-02 4.44e+03 4.56e+01 bond pdb=" O3' DA T 34 " pdb=" P DA T 35 " ideal model delta sigma weight residual 1.607 1.523 0.084 1.50e-02 4.44e+03 3.15e+01 ... (remaining 11703 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.50: 15979 4.50 - 9.00: 129 9.00 - 13.50: 24 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=" O3' DG N 136 " pdb=" C3' DG N 136 " pdb=" C2' DG N 136 " ideal model delta sigma weight residual 111.50 98.40 13.10 1.50e+00 4.44e-01 7.62e+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: 6440 30.06 - 60.11: 443 60.11 - 90.17: 25 90.17 - 120.22: 2 120.22 - 150.28: 4 Dihedral angle restraints: 6914 sinusoidal: 3234 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 6911 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 1716 0.134 - 0.268: 32 0.268 - 0.402: 7 0.402 - 0.536: 25 0.536 - 0.670: 8 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 2.42 1.75 0.67 2.00e-01 2.50e+01 1.12e+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 2.35 -2.97 -0.62 2.00e-01 2.50e+01 9.69e+00 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 2.35 -2.97 -0.62 2.00e-01 2.50e+01 9.64e+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: 0.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 32.220 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 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= 0.348 Angle : 1.037 22.496 16140 Z= 0.543 Chirality : 0.087 0.670 1788 Planarity : 0.005 0.084 1841 Dihedral : 18.483 150.277 4530 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.023 0.001 TRP A 915 HIS 0.004 0.001 HIS A1169 PHE 0.029 0.001 PHE A1338 TYR 0.024 0.001 TYR B 161 ARG 0.004 0.000 ARG B 264 Details of bonding type rmsd hydrogen bonds : bond 0.14756 ( 559) hydrogen bonds : angle 6.18565 ( 1563) covalent geometry : bond 0.00658 (11708) covalent geometry : angle 1.03711 (16140) Misc. bond : bond 0.01822 ( 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 : 1.149 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: 0.2883 time to fit residues: 77.2295 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 : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 117 optimal weight: 20.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN B 187 HIS A 492 ASN A 900 ASN A 987 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.161971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.135196 restraints weight = 15171.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.135675 restraints weight = 11394.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.137209 restraints weight = 9418.783| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11709 Z= 0.138 Angle : 0.570 9.573 16140 Z= 0.303 Chirality : 0.039 0.142 1788 Planarity : 0.005 0.057 1841 Dihedral : 19.943 167.118 2103 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.77 % Allowed : 7.27 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.25), residues: 1252 helix: 1.72 (0.21), residues: 667 sheet: -0.83 (0.45), residues: 129 loop : -1.10 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 915 HIS 0.010 0.001 HIS B 187 PHE 0.013 0.001 PHE B 118 TYR 0.026 0.001 TYR B 161 ARG 0.003 0.000 ARG A 883 Details of bonding type rmsd hydrogen bonds : bond 0.05021 ( 559) hydrogen bonds : angle 4.48062 ( 1563) covalent geometry : bond 0.00310 (11708) covalent geometry : angle 0.56999 (16140) Misc. bond : bond 0.00122 ( 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 182 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 1.073 Fit side-chains REVERT: A 439 LYS cc_start: 0.6560 (tttt) cc_final: 0.6167 (tttt) REVERT: A 476 LEU cc_start: 0.6073 (mt) cc_final: 0.5191 (tt) outliers start: 19 outliers final: 12 residues processed: 172 average time/residue: 0.2366 time to fit residues: 57.7240 Evaluate side-chains 164 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 896 ASP 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 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 116 optimal weight: 30.0000 chunk 9 optimal weight: 30.0000 chunk 28 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 30.0000 chunk 34 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 52 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 HIS A 900 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.156391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.128994 restraints weight = 15571.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.130869 restraints weight = 12796.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.132079 restraints weight = 11015.796| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 11709 Z= 0.243 Angle : 0.659 8.653 16140 Z= 0.346 Chirality : 0.043 0.155 1788 Planarity : 0.005 0.055 1841 Dihedral : 19.512 141.126 2103 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.19 % Favored : 94.73 % Rotamer: Outliers : 1.96 % Allowed : 12.02 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.24), residues: 1252 helix: 1.53 (0.21), residues: 661 sheet: -0.99 (0.44), residues: 131 loop : -1.33 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 915 HIS 0.005 0.001 HIS A 868 PHE 0.021 0.002 PHE B 318 TYR 0.024 0.002 TYR B 161 ARG 0.003 0.001 ARG B 79 Details of bonding type rmsd hydrogen bonds : bond 0.05517 ( 559) hydrogen bonds : angle 4.59450 ( 1563) covalent geometry : bond 0.00572 (11708) covalent geometry : angle 0.65915 (16140) Misc. bond : bond 0.00052 ( 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 173 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 1.253 Fit side-chains REVERT: B 247 MET cc_start: 0.8438 (mmt) cc_final: 0.8086 (tpp) REVERT: B 321 TRP cc_start: 0.8135 (t60) cc_final: 0.7493 (t60) outliers start: 21 outliers final: 15 residues processed: 167 average time/residue: 0.2405 time to fit residues: 58.3874 Evaluate side-chains 158 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 602 SER 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 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 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 74 optimal weight: 4.9990 chunk 32 optimal weight: 0.0470 chunk 47 optimal weight: 8.9990 chunk 59 optimal weight: 0.0670 chunk 50 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 114 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 overall best weight: 1.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN A 900 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.160343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.131963 restraints weight = 15310.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.134624 restraints weight = 10853.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.136422 restraints weight = 8684.485| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1601 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= 0.122 Angle : 0.557 10.166 16140 Z= 0.292 Chirality : 0.038 0.151 1788 Planarity : 0.004 0.053 1841 Dihedral : 19.049 136.182 2103 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.68 % Allowed : 14.54 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.24), residues: 1252 helix: 1.72 (0.21), residues: 664 sheet: -1.02 (0.43), residues: 129 loop : -1.19 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 915 HIS 0.004 0.001 HIS A1169 PHE 0.014 0.001 PHE A 826 TYR 0.024 0.001 TYR B 161 ARG 0.003 0.000 ARG B 264 Details of bonding type rmsd hydrogen bonds : bond 0.04147 ( 559) hydrogen bonds : angle 4.22992 ( 1563) covalent geometry : bond 0.00272 (11708) covalent geometry : angle 0.55690 (16140) Misc. bond : bond 0.00086 ( 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: 18 poor density : 160 time to evaluate : 1.080 Fit side-chains REVERT: B 137 ASN cc_start: 0.8988 (OUTLIER) cc_final: 0.8382 (t0) REVERT: B 247 MET cc_start: 0.8397 (mmt) cc_final: 0.7892 (tpp) REVERT: B 321 TRP cc_start: 0.7952 (t60) cc_final: 0.7337 (t60) REVERT: A 1215 VAL cc_start: 0.7684 (OUTLIER) cc_final: 0.7411 (t) outliers start: 18 outliers final: 10 residues processed: 172 average time/residue: 0.2280 time to fit residues: 56.8444 Evaluate side-chains 160 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 2.101 ------------------------------------------------------------------------------- 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 651 ILE Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 784 LEU 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 1215 VAL Chi-restraints excluded: chain A residue 1296 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 76 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 chunk 120 optimal weight: 30.0000 chunk 112 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 27 optimal weight: 20.0000 chunk 20 optimal weight: 2.9990 chunk 90 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN A 900 ASN A 968 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.156189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.128987 restraints weight = 15369.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.129893 restraints weight = 12839.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.131545 restraints weight = 10978.736| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11709 Z= 0.202 Angle : 0.615 9.707 16140 Z= 0.321 Chirality : 0.041 0.158 1788 Planarity : 0.005 0.055 1841 Dihedral : 19.046 136.189 2103 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.79 % Favored : 95.13 % Rotamer: Outliers : 2.33 % Allowed : 15.19 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.24), residues: 1252 helix: 1.64 (0.21), residues: 662 sheet: -1.05 (0.43), residues: 129 loop : -1.26 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 915 HIS 0.003 0.001 HIS B 187 PHE 0.018 0.001 PHE A1338 TYR 0.027 0.002 TYR B 161 ARG 0.004 0.000 ARG B 264 Details of bonding type rmsd hydrogen bonds : bond 0.04808 ( 559) hydrogen bonds : angle 4.37340 ( 1563) covalent geometry : bond 0.00478 (11708) covalent geometry : angle 0.61505 (16140) Misc. bond : bond 0.00047 ( 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 174 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 1.116 Fit side-chains REVERT: B 114 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7577 (mp0) REVERT: B 137 ASN cc_start: 0.9026 (OUTLIER) cc_final: 0.8501 (t0) REVERT: B 321 TRP cc_start: 0.8107 (t60) cc_final: 0.7505 (t60) REVERT: A 1215 VAL cc_start: 0.7717 (OUTLIER) cc_final: 0.7446 (t) REVERT: A 1271 PHE cc_start: 0.4889 (m-80) cc_final: 0.3954 (t80) outliers start: 25 outliers final: 16 residues processed: 167 average time/residue: 0.2219 time to fit residues: 53.8376 Evaluate side-chains 166 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 1.118 ------------------------------------------------------------------------------- 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 602 SER Chi-restraints excluded: chain A residue 651 ILE 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 84 optimal weight: 0.2980 chunk 28 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 49 optimal weight: 30.0000 chunk 124 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN B 287 GLN A 900 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.158176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.130988 restraints weight = 15534.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.132098 restraints weight = 11747.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.133219 restraints weight = 9454.240| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1876 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= 0.149 Angle : 0.574 9.140 16140 Z= 0.301 Chirality : 0.039 0.153 1788 Planarity : 0.004 0.054 1841 Dihedral : 18.960 135.746 2103 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.39 % Favored : 95.53 % Rotamer: Outliers : 2.89 % Allowed : 15.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.24), residues: 1252 helix: 1.70 (0.21), residues: 664 sheet: -1.06 (0.43), residues: 129 loop : -1.25 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 915 HIS 0.003 0.001 HIS A1169 PHE 0.019 0.001 PHE A1338 TYR 0.026 0.001 TYR B 161 ARG 0.003 0.000 ARG B 264 Details of bonding type rmsd hydrogen bonds : bond 0.04340 ( 559) hydrogen bonds : angle 4.24799 ( 1563) covalent geometry : bond 0.00346 (11708) covalent geometry : angle 0.57396 (16140) Misc. bond : bond 0.00069 ( 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 185 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 1.230 Fit side-chains REVERT: B 114 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7575 (mp0) REVERT: B 137 ASN cc_start: 0.9052 (OUTLIER) cc_final: 0.8722 (t0) REVERT: B 321 TRP cc_start: 0.8099 (t60) cc_final: 0.7544 (t60) REVERT: A 519 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.6937 (pp) REVERT: A 1215 VAL cc_start: 0.7685 (OUTLIER) cc_final: 0.7410 (t) REVERT: A 1271 PHE cc_start: 0.5014 (m-80) cc_final: 0.4089 (t80) outliers start: 31 outliers final: 18 residues processed: 174 average time/residue: 0.2322 time to fit residues: 58.5759 Evaluate side-chains 170 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 1.184 ------------------------------------------------------------------------------- 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 519 LEU Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 651 ILE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 55 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN B 287 GLN A 900 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.158163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.130950 restraints weight = 15676.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.132267 restraints weight = 12772.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.133874 restraints weight = 10957.711| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11709 Z= 0.144 Angle : 0.573 9.121 16140 Z= 0.298 Chirality : 0.039 0.151 1788 Planarity : 0.004 0.054 1841 Dihedral : 18.913 135.367 2103 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.70 % Allowed : 15.75 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.24), residues: 1252 helix: 1.70 (0.21), residues: 664 sheet: -1.06 (0.43), residues: 129 loop : -1.26 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 915 HIS 0.003 0.001 HIS A1169 PHE 0.020 0.001 PHE A1338 TYR 0.022 0.001 TYR B 73 ARG 0.003 0.000 ARG B 264 Details of bonding type rmsd hydrogen bonds : bond 0.04254 ( 559) hydrogen bonds : angle 4.22962 ( 1563) covalent geometry : bond 0.00335 (11708) covalent geometry : angle 0.57316 (16140) Misc. bond : bond 0.00066 ( 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 183 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 1.110 Fit side-chains REVERT: B 114 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7541 (mp0) REVERT: B 137 ASN cc_start: 0.8967 (OUTLIER) cc_final: 0.8563 (t0) REVERT: B 321 TRP cc_start: 0.8055 (t60) cc_final: 0.7451 (t60) REVERT: A 519 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.7050 (pp) REVERT: A 1215 VAL cc_start: 0.7727 (OUTLIER) cc_final: 0.7426 (t) REVERT: A 1271 PHE cc_start: 0.4850 (m-80) cc_final: 0.3928 (t80) outliers start: 29 outliers final: 20 residues processed: 172 average time/residue: 0.2317 time to fit residues: 57.8829 Evaluate side-chains 173 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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 395 LEU Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 651 ILE 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 122 optimal weight: 20.0000 chunk 40 optimal weight: 9.9990 chunk 126 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 32 optimal weight: 0.0170 chunk 39 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 47 optimal weight: 0.0670 chunk 102 optimal weight: 0.5980 chunk 97 optimal weight: 10.0000 overall best weight: 2.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN B 287 GLN A 639 GLN A 900 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.159819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.132936 restraints weight = 15500.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.133861 restraints weight = 11459.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.135170 restraints weight = 9416.357| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11709 Z= 0.140 Angle : 0.568 8.898 16140 Z= 0.295 Chirality : 0.039 0.155 1788 Planarity : 0.004 0.054 1841 Dihedral : 18.848 134.988 2103 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.39 % Favored : 95.53 % Rotamer: Outliers : 2.80 % Allowed : 16.22 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.24), residues: 1252 helix: 1.73 (0.21), residues: 665 sheet: -1.05 (0.42), residues: 129 loop : -1.25 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 915 HIS 0.003 0.001 HIS A1169 PHE 0.021 0.001 PHE A1338 TYR 0.021 0.001 TYR B 73 ARG 0.004 0.000 ARG B 264 Details of bonding type rmsd hydrogen bonds : bond 0.04135 ( 559) hydrogen bonds : angle 4.18445 ( 1563) covalent geometry : bond 0.00326 (11708) covalent geometry : angle 0.56835 (16140) Misc. bond : bond 0.00064 ( 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 180 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 1.197 Fit side-chains REVERT: B 114 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7495 (mp0) REVERT: B 137 ASN cc_start: 0.8968 (OUTLIER) cc_final: 0.8601 (t0) REVERT: B 321 TRP cc_start: 0.8083 (t60) cc_final: 0.7729 (t60) REVERT: A 519 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.7012 (pp) REVERT: A 1051 SER cc_start: 0.7402 (t) cc_final: 0.7093 (p) REVERT: A 1215 VAL cc_start: 0.7720 (OUTLIER) cc_final: 0.7431 (t) REVERT: A 1271 PHE cc_start: 0.4961 (m-80) cc_final: 0.4126 (t80) outliers start: 30 outliers final: 21 residues processed: 171 average time/residue: 0.2312 time to fit residues: 57.7332 Evaluate side-chains 171 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 1.202 ------------------------------------------------------------------------------- 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 304 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 784 LEU 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 8 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 109 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 100 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN B 287 GLN A 900 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.159455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.132138 restraints weight = 15419.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.133142 restraints weight = 11521.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.134808 restraints weight = 9657.384| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11709 Z= 0.130 Angle : 0.567 8.782 16140 Z= 0.295 Chirality : 0.038 0.146 1788 Planarity : 0.004 0.053 1841 Dihedral : 18.781 134.621 2103 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.24 % Allowed : 17.05 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.24), residues: 1252 helix: 1.70 (0.21), residues: 672 sheet: -1.07 (0.43), residues: 124 loop : -1.25 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 915 HIS 0.003 0.001 HIS A1169 PHE 0.024 0.001 PHE A1338 TYR 0.021 0.001 TYR B 73 ARG 0.004 0.000 ARG B 264 Details of bonding type rmsd hydrogen bonds : bond 0.04006 ( 559) hydrogen bonds : angle 4.14172 ( 1563) covalent geometry : bond 0.00300 (11708) covalent geometry : angle 0.56724 (16140) Misc. bond : bond 0.00063 ( 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 174 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 1.228 Fit side-chains REVERT: B 114 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7477 (mp0) REVERT: B 137 ASN cc_start: 0.8930 (OUTLIER) cc_final: 0.8399 (t0) REVERT: B 321 TRP cc_start: 0.8055 (t60) cc_final: 0.7697 (t60) REVERT: A 519 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.6971 (pp) REVERT: A 1051 SER cc_start: 0.7401 (t) cc_final: 0.7067 (p) REVERT: A 1215 VAL cc_start: 0.7798 (OUTLIER) cc_final: 0.7526 (t) REVERT: A 1271 PHE cc_start: 0.5012 (m-80) cc_final: 0.4211 (t80) outliers start: 24 outliers final: 18 residues processed: 167 average time/residue: 0.2439 time to fit residues: 58.6898 Evaluate side-chains 170 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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 304 ILE 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 519 LEU Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 784 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 0 optimal weight: 20.0000 chunk 18 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN B 287 GLN A 900 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.159731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.132327 restraints weight = 15462.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.134030 restraints weight = 10827.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.135413 restraints weight = 8627.317| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11709 Z= 0.148 Angle : 0.573 8.697 16140 Z= 0.299 Chirality : 0.039 0.152 1788 Planarity : 0.004 0.054 1841 Dihedral : 18.780 134.626 2103 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.47 % Favored : 95.45 % Rotamer: Outliers : 2.52 % Allowed : 17.05 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.24), residues: 1252 helix: 1.69 (0.21), residues: 672 sheet: -1.12 (0.43), residues: 125 loop : -1.24 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 915 HIS 0.003 0.001 HIS A1169 PHE 0.024 0.001 PHE A1338 TYR 0.021 0.001 TYR B 73 ARG 0.004 0.000 ARG B 264 Details of bonding type rmsd hydrogen bonds : bond 0.04131 ( 559) hydrogen bonds : angle 4.14917 ( 1563) covalent geometry : bond 0.00346 (11708) covalent geometry : angle 0.57328 (16140) Misc. bond : bond 0.00054 ( 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 176 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 1.179 Fit side-chains REVERT: B 114 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7471 (mp0) REVERT: B 137 ASN cc_start: 0.8932 (OUTLIER) cc_final: 0.8339 (t0) REVERT: B 321 TRP cc_start: 0.8103 (t60) cc_final: 0.7703 (t60) REVERT: A 461 MET cc_start: 0.7885 (ttm) cc_final: 0.6979 (ttm) REVERT: A 519 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.6981 (pp) REVERT: A 1051 SER cc_start: 0.7383 (t) cc_final: 0.7048 (p) REVERT: A 1215 VAL cc_start: 0.7805 (OUTLIER) cc_final: 0.7529 (t) REVERT: A 1271 PHE cc_start: 0.5035 (m-80) cc_final: 0.4224 (t80) outliers start: 27 outliers final: 20 residues processed: 167 average time/residue: 0.2549 time to fit residues: 61.8685 Evaluate side-chains 172 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 1.244 ------------------------------------------------------------------------------- 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 304 ILE 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 519 LEU Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 651 ILE 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 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 26 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 110 optimal weight: 9.9990 chunk 118 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN B 287 GLN A 900 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.156776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.129650 restraints weight = 15497.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.130678 restraints weight = 12842.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.131589 restraints weight = 11166.747| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11709 Z= 0.198 Angle : 0.611 9.085 16140 Z= 0.320 Chirality : 0.041 0.148 1788 Planarity : 0.004 0.055 1841 Dihedral : 18.870 135.140 2103 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.03 % Favored : 94.89 % Rotamer: Outliers : 2.70 % Allowed : 16.87 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.24), residues: 1252 helix: 1.59 (0.21), residues: 672 sheet: -1.12 (0.43), residues: 125 loop : -1.27 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 915 HIS 0.003 0.001 HIS B 187 PHE 0.024 0.002 PHE A1338 TYR 0.021 0.002 TYR B 73 ARG 0.004 0.000 ARG B 264 Details of bonding type rmsd hydrogen bonds : bond 0.04597 ( 559) hydrogen bonds : angle 4.26893 ( 1563) covalent geometry : bond 0.00471 (11708) covalent geometry : angle 0.61111 (16140) Misc. bond : bond 0.00046 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3281.92 seconds wall clock time: 58 minutes 23.89 seconds (3503.89 seconds total)