Starting phenix.real_space_refine (version: dev) on Wed Feb 22 15:18:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4c_14493/02_2023/7z4c_14493.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4c_14493/02_2023/7z4c_14493.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4c_14493/02_2023/7z4c_14493.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4c_14493/02_2023/7z4c_14493.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4c_14493/02_2023/7z4c_14493.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4c_14493/02_2023/7z4c_14493.pdb" } resolution = 3.87 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 ------------------------------------------------------------------------------- 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= 0.002 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3714 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "B TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 14180 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 589 Classifications: {'DNA': 29} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 28} Chain: "D" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 592 Classifications: {'DNA': 29} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 28} Chain: "A" Number of atoms: 1910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 1910 Classifications: {'DNA': 1, 'RNA': 89} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 46, 'rna3p_pyr': 30} Link IDs: {'rna2p': 13, 'rna3p': 76} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A%5*END:plan2': 1, ' A%5*END:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 11089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1357, 11089 Classifications: {'peptide': 1357} Link IDs: {'PTRANS': 35, 'TRANS': 1321} Chain breaks: 1 Time building chain proxies: 8.76, per 1000 atoms: 0.62 Number of scatterers: 14180 At special positions: 0 Unit cell: (92.3, 124.15, 124.8, 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 23 16.00 P 145 15.00 O 3043 8.00 N 2483 7.00 C 8486 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 - 3.50 Amino acid : False - 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=0, symmetry=0 Time building additional restraints: 6.50 Conformation dependent library (CDL) restraints added in 1.9 seconds 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2580 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 10 sheets defined 54.4% alpha, 8.1% beta 51 base pairs and 93 stacking pairs defined. Time for finding SS restraints: 4.35 Creating SS restraints... Processing helix chain 'B' and resid 59 through 86 Processing helix chain 'B' and resid 86 through 94 Processing helix chain 'B' and resid 96 through 103 Processing helix chain 'B' and resid 107 through 111 Processing helix chain 'B' and resid 121 through 132 Processing helix chain 'B' and resid 134 through 145 Processing helix chain 'B' and resid 150 through 164 removed outlier: 3.763A pdb=" N PHE B 164 " --> pdb=" O HIS B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 196 Processing helix chain 'B' and resid 207 through 214 Processing helix chain 'B' and resid 217 through 228 Processing helix chain 'B' and resid 236 through 247 Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 270 through 283 removed outlier: 3.759A pdb=" N ASP B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN B 281 " --> pdb=" O ASN B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 306 removed outlier: 3.905A pdb=" N ILE B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 343 removed outlier: 3.715A pdb=" N SER B 320 " --> pdb=" O PRO B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 353 removed outlier: 3.522A pdb=" N ASP B 353 " --> pdb=" O GLU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 364 Processing helix chain 'B' and resid 368 through 383 Proline residue: B 378 - end of helix Processing helix chain 'B' and resid 386 through 395 Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.900A pdb=" N GLY B 408 " --> pdb=" O PHE B 405 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER B 409 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 427 removed outlier: 4.351A pdb=" N HIS B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 436 removed outlier: 3.603A pdb=" N LYS B 434 " --> pdb=" O TYR B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 446 Processing helix chain 'B' and resid 477 through 482 removed outlier: 3.779A pdb=" N VAL B 482 " --> pdb=" O PHE B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 496 removed outlier: 3.899A pdb=" N THR B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 525 removed outlier: 3.554A pdb=" N GLU B 523 " --> pdb=" O THR B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 552 Processing helix chain 'B' and resid 560 through 568 removed outlier: 3.657A pdb=" N TYR B 568 " --> pdb=" O LEU B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 602 Processing helix chain 'B' and resid 603 through 609 Processing helix chain 'B' and resid 612 through 625 Processing helix chain 'B' and resid 628 through 637 Processing helix chain 'B' and resid 638 through 643 removed outlier: 4.529A pdb=" N HIS B 641 " --> pdb=" O THR B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 654 Processing helix chain 'B' and resid 664 through 669 Processing helix chain 'B' and resid 678 through 685 Processing helix chain 'B' and resid 692 through 698 Processing helix chain 'B' and resid 702 through 713 removed outlier: 4.276A pdb=" N GLU B 706 " --> pdb=" O LEU B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 727 Processing helix chain 'B' and resid 730 through 751 Processing helix chain 'B' and resid 776 through 792 Processing helix chain 'B' and resid 794 through 799 Processing helix chain 'B' and resid 804 through 807 removed outlier: 3.705A pdb=" N GLN B 807 " --> pdb=" O THR B 804 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 804 through 807' Processing helix chain 'B' and resid 808 through 817 removed outlier: 3.642A pdb=" N TYR B 812 " --> pdb=" O ASN B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 865 removed outlier: 3.538A pdb=" N GLY B 865 " --> pdb=" O LYS B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 889 removed outlier: 3.555A pdb=" N VAL B 876 " --> pdb=" O SER B 872 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASN B 881 " --> pdb=" O LYS B 877 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N TYR B 882 " --> pdb=" O LYS B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 893 through 901 Processing helix chain 'B' and resid 901 through 906 Processing helix chain 'B' and resid 909 through 922 Processing helix chain 'B' and resid 926 through 940 Processing helix chain 'B' and resid 959 through 970 removed outlier: 4.206A pdb=" N VAL B 963 " --> pdb=" O LYS B 959 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE B 970 " --> pdb=" O PHE B 966 " (cutoff:3.500A) Processing helix chain 'B' and resid 980 through 1001 removed outlier: 4.530A pdb=" N ALA B 984 " --> pdb=" O ASN B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1009 Processing helix chain 'B' and resid 1043 through 1047 Processing helix chain 'B' and resid 1078 through 1088 Processing helix chain 'B' and resid 1127 through 1132 removed outlier: 3.513A pdb=" N TYR B1131 " --> pdb=" O ASP B1127 " (cutoff:3.500A) Processing helix chain 'B' and resid 1168 through 1177 removed outlier: 4.582A pdb=" N SER B1172 " --> pdb=" O ILE B1168 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N SER B1173 " --> pdb=" O MET B1169 " (cutoff:3.500A) Processing helix chain 'B' and resid 1177 through 1186 Processing helix chain 'B' and resid 1207 through 1209 No H-bonds generated for 'chain 'B' and resid 1207 through 1209' Processing helix chain 'B' and resid 1229 through 1241 Processing helix chain 'B' and resid 1248 through 1262 Processing helix chain 'B' and resid 1264 through 1278 removed outlier: 3.616A pdb=" N SER B1274 " --> pdb=" O ILE B1270 " (cutoff:3.500A) Processing helix chain 'B' and resid 1283 through 1297 Processing helix chain 'B' and resid 1306 through 1311 removed outlier: 3.976A pdb=" N HIS B1311 " --> pdb=" O GLU B1307 " (cutoff:3.500A) Processing helix chain 'B' and resid 1312 through 1317 removed outlier: 3.592A pdb=" N LEU B1315 " --> pdb=" O LEU B1312 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN B1317 " --> pdb=" O THR B1314 " (cutoff:3.500A) Processing helix chain 'B' and resid 1340 through 1344 Processing helix chain 'B' and resid 1363 through 1365 No H-bonds generated for 'chain 'B' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'B' and resid 954 through 957 removed outlier: 4.152A pdb=" N ASN B 758 " --> pdb=" O TYR B 5 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 29 through 32 Processing sheet with id=AA3, first strand: chain 'B' and resid 34 through 35 removed outlier: 3.821A pdb=" N LEU B 35 " --> pdb=" O GLU B1357 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG B1359 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU B1203 " --> pdb=" O ILE B1348 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER B1202 " --> pdb=" O LEU B1214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 538 through 539 removed outlier: 3.759A pdb=" N ALA B 538 " --> pdb=" O TYR B 529 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR B 529 " --> pdb=" O ALA B 538 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 837 through 840 removed outlier: 3.874A pdb=" N ASP B 837 " --> pdb=" O THR B 858 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR B 858 " --> pdb=" O ASP B 837 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1049 through 1051 Processing sheet with id=AA7, first strand: chain 'B' and resid 1063 through 1065 Processing sheet with id=AA8, first strand: chain 'B' and resid 1106 through 1111 removed outlier: 6.866A pdb=" N LYS B1107 " --> pdb=" O PRO B1137 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N SER B1109 " --> pdb=" O ASP B1135 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASP B1135 " --> pdb=" O SER B1109 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY B1133 " --> pdb=" O LEU B1111 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1156 through 1167 removed outlier: 3.730A pdb=" N GLU B1162 " --> pdb=" O VAL B1145 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL B1145 " --> pdb=" O GLU B1162 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR B1141 " --> pdb=" O ILE B1166 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1324 through 1326 512 hydrogen bonds defined for protein. 1467 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 125 hydrogen bonds 242 hydrogen bond angles 0 basepair planarities 51 basepair parallelities 93 stacking parallelities Total time for adding SS restraints: 8.12 Time building geometry restraints manager: 6.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3110 1.33 - 1.45: 3728 1.45 - 1.57: 7575 1.57 - 1.69: 290 1.69 - 1.81: 44 Bond restraints: 14747 Sorted by residual: bond pdb=" C PHE B 446 " pdb=" N ARG B 447 " ideal model delta sigma weight residual 1.332 1.359 -0.027 1.26e-02 6.30e+03 4.69e+00 bond pdb=" CA SER B1106 " pdb=" CB SER B1106 " ideal model delta sigma weight residual 1.530 1.489 0.041 1.93e-02 2.68e+03 4.43e+00 bond pdb=" N ARG B1333 " pdb=" CA ARG B1333 " ideal model delta sigma weight residual 1.456 1.481 -0.025 1.22e-02 6.72e+03 4.33e+00 bond pdb=" N SER B1106 " pdb=" CA SER B1106 " ideal model delta sigma weight residual 1.458 1.477 -0.019 1.27e-02 6.20e+03 2.14e+00 bond pdb=" CB VAL B 452 " pdb=" CG1 VAL B 452 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.01e+00 ... (remaining 14742 not shown) Histogram of bond angle deviations from ideal: 99.53 - 106.41: 1063 106.41 - 113.29: 8153 113.29 - 120.18: 5307 120.18 - 127.06: 5599 127.06 - 133.94: 414 Bond angle restraints: 20536 Sorted by residual: angle pdb=" O PHE B 446 " pdb=" C PHE B 446 " pdb=" N ARG B 447 " ideal model delta sigma weight residual 122.96 128.75 -5.79 1.26e+00 6.30e-01 2.11e+01 angle pdb=" CA PHE B 446 " pdb=" C PHE B 446 " pdb=" N ARG B 447 " ideal model delta sigma weight residual 116.43 110.53 5.90 1.37e+00 5.33e-01 1.86e+01 angle pdb=" C PHE B 446 " pdb=" N ARG B 447 " pdb=" CA ARG B 447 " ideal model delta sigma weight residual 122.39 116.69 5.70 1.48e+00 4.57e-01 1.48e+01 angle pdb=" CA PHE B1105 " pdb=" C PHE B1105 " pdb=" N SER B1106 " ideal model delta sigma weight residual 117.63 114.39 3.24 1.25e+00 6.40e-01 6.72e+00 angle pdb=" CA ARG B1333 " pdb=" C ARG B1333 " pdb=" O ARG B1333 " ideal model delta sigma weight residual 121.16 118.52 2.64 1.12e+00 7.97e-01 5.57e+00 ... (remaining 20531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 8245 35.93 - 71.86: 336 71.86 - 107.78: 4 107.78 - 143.71: 1 143.71 - 179.64: 2 Dihedral angle restraints: 8588 sinusoidal: 4598 harmonic: 3990 Sorted by residual: dihedral pdb=" C4' DA D -2 " pdb=" C3' DA D -2 " pdb=" O3' DA D -2 " pdb=" P DT D -1 " ideal model delta sinusoidal sigma weight residual -140.00 39.64 -179.64 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' U A 80 " pdb=" C3' U A 80 " pdb=" O3' U A 80 " pdb=" P G A 81 " ideal model delta sinusoidal sigma weight residual -140.00 27.05 -167.05 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DC C 5 " pdb=" C3' DC C 5 " pdb=" O3' DC C 5 " pdb=" P DT C 6 " ideal model delta sinusoidal sigma weight residual 220.00 81.09 138.91 1 3.50e+01 8.16e-04 1.37e+01 ... (remaining 8585 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1763 0.035 - 0.069: 447 0.069 - 0.104: 100 0.104 - 0.138: 30 0.138 - 0.173: 2 Chirality restraints: 2342 Sorted by residual: chirality pdb=" C1' A A 12 " pdb=" O4' A A 12 " pdb=" C2' A A 12 " pdb=" N9 A A 12 " both_signs ideal model delta sigma weight residual False 2.46 2.28 0.17 2.00e-01 2.50e+01 7.48e-01 chirality pdb=" C2' G A 16 " pdb=" C3' G A 16 " pdb=" O2' G A 16 " pdb=" C1' G A 16 " both_signs ideal model delta sigma weight residual False -2.75 -2.59 -0.16 2.00e-01 2.50e+01 6.36e-01 chirality pdb=" C1' A A 41 " pdb=" O4' A A 41 " pdb=" C2' A A 41 " pdb=" N9 A A 41 " both_signs ideal model delta sigma weight residual False 2.46 2.32 0.14 2.00e-01 2.50e+01 4.75e-01 ... (remaining 2339 not shown) Planarity restraints: 2093 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U A 13 " -0.025 2.00e-02 2.50e+03 1.27e-02 3.64e+00 pdb=" N1 U A 13 " 0.027 2.00e-02 2.50e+03 pdb=" C2 U A 13 " 0.005 2.00e-02 2.50e+03 pdb=" O2 U A 13 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U A 13 " -0.002 2.00e-02 2.50e+03 pdb=" C4 U A 13 " -0.003 2.00e-02 2.50e+03 pdb=" O4 U A 13 " -0.008 2.00e-02 2.50e+03 pdb=" C5 U A 13 " 0.000 2.00e-02 2.50e+03 pdb=" C6 U A 13 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 454 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.31e+00 pdb=" C PRO B 454 " 0.031 2.00e-02 2.50e+03 pdb=" O PRO B 454 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU B 455 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A 12 " -0.023 2.00e-02 2.50e+03 1.05e-02 3.06e+00 pdb=" N9 A A 12 " 0.025 2.00e-02 2.50e+03 pdb=" C8 A A 12 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A A 12 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A A 12 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A A 12 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A A 12 " -0.004 2.00e-02 2.50e+03 pdb=" N1 A A 12 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A A 12 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A A 12 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A A 12 " 0.003 2.00e-02 2.50e+03 ... (remaining 2090 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2437 2.77 - 3.30: 13375 3.30 - 3.83: 24711 3.83 - 4.37: 28632 4.37 - 4.90: 45023 Nonbonded interactions: 114178 Sorted by model distance: nonbonded pdb=" OG1 THR B 474 " pdb=" OD1 ASN B 477 " model vdw 2.232 2.440 nonbonded pdb=" O LEU B 551 " pdb=" OG1 THR B 555 " model vdw 2.235 2.440 nonbonded pdb=" O HIS B 799 " pdb=" OH TYR B 815 " model vdw 2.245 2.440 nonbonded pdb=" O2' U A 56 " pdb=" N2 G A 58 " model vdw 2.253 2.520 nonbonded pdb=" OE1 GLU B1357 " pdb=" NH1 ARG B1359 " model vdw 2.265 2.520 ... (remaining 114173 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 145 5.49 5 S 23 5.16 5 C 8486 2.51 5 N 2483 2.21 5 O 3043 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 4.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 12.580 Check model and map are aligned: 0.190 Process input model: 45.940 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.150 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 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 : 0.003 0.047 14747 Z= 0.172 Angle : 0.451 5.903 20536 Z= 0.255 Chirality : 0.034 0.173 2342 Planarity : 0.003 0.031 2093 Dihedral : 15.324 179.639 6008 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer Outliers : 2.06 % 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: 1.06 (0.23), residues: 1353 helix: 1.93 (0.21), residues: 656 sheet: -0.18 (0.48), residues: 118 loop : -0.52 (0.24), residues: 579 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 135 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 6 residues processed: 156 average time/residue: 0.3085 time to fit residues: 68.4222 Evaluate side-chains 80 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 74 time to evaluate : 1.551 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1472 time to fit residues: 3.6035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 116 optimal weight: 0.9980 chunk 44 optimal weight: 8.9990 chunk 70 optimal weight: 30.0000 chunk 86 optimal weight: 1.9990 chunk 134 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 415 HIS B 698 HIS B 826 GLN B 854 ASN B 885 GLN ** B 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1041 ASN B1305 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 14747 Z= 0.225 Angle : 0.533 10.771 20536 Z= 0.283 Chirality : 0.036 0.198 2342 Planarity : 0.003 0.037 2093 Dihedral : 17.834 177.257 3125 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer Outliers : 1.64 % 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: 1.28 (0.23), residues: 1353 helix: 2.12 (0.21), residues: 661 sheet: 0.36 (0.54), residues: 95 loop : -0.53 (0.24), residues: 597 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 77 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 10 residues processed: 92 average time/residue: 0.2982 time to fit residues: 41.9334 Evaluate side-chains 68 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 58 time to evaluate : 1.470 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1381 time to fit residues: 4.5914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 37 optimal weight: 20.0000 chunk 134 optimal weight: 0.0980 chunk 145 optimal weight: 9.9990 chunk 119 optimal weight: 20.0000 chunk 133 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 14747 Z= 0.174 Angle : 0.503 10.026 20536 Z= 0.263 Chirality : 0.035 0.209 2342 Planarity : 0.003 0.047 2093 Dihedral : 17.774 176.192 3125 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 0.58 % 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: 1.32 (0.23), residues: 1353 helix: 2.14 (0.21), residues: 664 sheet: 0.45 (0.54), residues: 95 loop : -0.52 (0.24), residues: 594 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 74 average time/residue: 0.2811 time to fit residues: 31.8202 Evaluate side-chains 63 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 1.610 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1320 time to fit residues: 2.3703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 6.9990 chunk 101 optimal weight: 8.9990 chunk 69 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 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 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 511 HIS ** B 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 14747 Z= 0.314 Angle : 0.594 13.036 20536 Z= 0.316 Chirality : 0.037 0.228 2342 Planarity : 0.004 0.051 2093 Dihedral : 18.035 175.656 3125 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 1.48 % 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: 0.97 (0.23), residues: 1353 helix: 1.76 (0.20), residues: 673 sheet: 0.37 (0.52), residues: 93 loop : -0.62 (0.24), residues: 587 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 59 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 13 residues processed: 71 average time/residue: 0.3041 time to fit residues: 32.6764 Evaluate side-chains 67 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 54 time to evaluate : 1.570 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1797 time to fit residues: 5.7719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 20.0000 chunk 81 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 98 optimal weight: 30.0000 chunk 0 optimal weight: 8.9990 chunk 73 optimal weight: 5.9990 chunk 128 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 ASN B 556 ASN ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1234 ASN B1286 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.060 14747 Z= 0.390 Angle : 0.671 11.397 20536 Z= 0.358 Chirality : 0.039 0.277 2342 Planarity : 0.004 0.045 2093 Dihedral : 18.348 175.887 3125 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 21.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer Outliers : 1.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.40 (0.22), residues: 1353 helix: 1.19 (0.20), residues: 675 sheet: 0.46 (0.62), residues: 70 loop : -0.78 (0.23), residues: 608 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 53 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 10 residues processed: 73 average time/residue: 0.2923 time to fit residues: 32.4082 Evaluate side-chains 60 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 50 time to evaluate : 1.542 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1364 time to fit residues: 4.4523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 143 optimal weight: 9.9990 chunk 118 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 47 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 808 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 14747 Z= 0.134 Angle : 0.513 10.402 20536 Z= 0.270 Chirality : 0.035 0.284 2342 Planarity : 0.003 0.043 2093 Dihedral : 17.875 176.593 3125 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer Outliers : 0.90 % 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: 1.03 (0.23), residues: 1353 helix: 1.73 (0.21), residues: 683 sheet: 0.48 (0.55), residues: 93 loop : -0.53 (0.25), residues: 577 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 73 average time/residue: 0.3038 time to fit residues: 33.5250 Evaluate side-chains 61 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 1.608 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1436 time to fit residues: 3.4760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 81 optimal weight: 30.0000 chunk 104 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 142 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 65 optimal weight: 8.9990 chunk 88 optimal weight: 0.0170 overall best weight: 1.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 HIS ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1234 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 14747 Z= 0.157 Angle : 0.515 10.810 20536 Z= 0.271 Chirality : 0.035 0.259 2342 Planarity : 0.003 0.044 2093 Dihedral : 17.797 176.674 3125 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer Outliers : 0.58 % 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: 1.11 (0.23), residues: 1353 helix: 1.82 (0.21), residues: 683 sheet: 0.40 (0.54), residues: 93 loop : -0.51 (0.25), residues: 577 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 54 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 58 average time/residue: 0.2682 time to fit residues: 25.0922 Evaluate side-chains 55 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 1.559 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1661 time to fit residues: 2.8356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 42 optimal weight: 20.0000 chunk 28 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 97 optimal weight: 20.0000 chunk 70 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 14747 Z= 0.223 Angle : 0.558 14.933 20536 Z= 0.291 Chirality : 0.036 0.256 2342 Planarity : 0.003 0.045 2093 Dihedral : 17.902 176.607 3125 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer Outliers : 0.58 % 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: 1.05 (0.23), residues: 1353 helix: 1.76 (0.21), residues: 677 sheet: 0.38 (0.54), residues: 93 loop : -0.50 (0.25), residues: 583 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 57 average time/residue: 0.2710 time to fit residues: 24.8935 Evaluate side-chains 53 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 50 time to evaluate : 1.498 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1329 time to fit residues: 2.8230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 132 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 125 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 140 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1044 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 14747 Z= 0.155 Angle : 0.519 13.123 20536 Z= 0.274 Chirality : 0.035 0.242 2342 Planarity : 0.003 0.046 2093 Dihedral : 17.765 176.827 3125 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.16 (0.23), residues: 1353 helix: 1.82 (0.21), residues: 678 sheet: 0.47 (0.58), residues: 83 loop : -0.39 (0.25), residues: 592 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 1.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 58 average time/residue: 0.2949 time to fit residues: 26.9848 Evaluate side-chains 51 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 1.609 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1895 time to fit residues: 2.5342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 135 optimal weight: 0.9980 chunk 117 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 71 optimal weight: 20.0000 chunk 93 optimal weight: 5.9990 chunk 125 optimal weight: 0.0010 overall best weight: 3.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 14747 Z= 0.203 Angle : 0.560 11.682 20536 Z= 0.292 Chirality : 0.036 0.235 2342 Planarity : 0.003 0.045 2093 Dihedral : 17.816 176.604 3125 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer Outliers : 0.33 % 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: 0.99 (0.23), residues: 1353 helix: 1.68 (0.21), residues: 678 sheet: 0.47 (0.58), residues: 83 loop : -0.48 (0.25), residues: 592 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 51 average time/residue: 0.2747 time to fit residues: 23.5854 Evaluate side-chains 51 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 1.521 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1363 time to fit residues: 2.3087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 4.9990 chunk 108 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 120 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 6 optimal weight: 10.0000 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.049209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.035109 restraints weight = 110435.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.036375 restraints weight = 54772.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.037083 restraints weight = 35853.840| |-----------------------------------------------------------------------------| r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 14747 Z= 0.145 Angle : 0.536 12.480 20536 Z= 0.275 Chirality : 0.035 0.222 2342 Planarity : 0.003 0.045 2093 Dihedral : 17.629 176.928 3125 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer Outliers : 0.00 % 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: 1.05 (0.23), residues: 1353 helix: 1.69 (0.21), residues: 684 sheet: 0.37 (0.57), residues: 83 loop : -0.42 (0.25), residues: 586 =============================================================================== Job complete usr+sys time: 2299.23 seconds wall clock time: 43 minutes 17.68 seconds (2597.68 seconds total)