Starting phenix.real_space_refine (version: dev) on Mon Dec 12 23:18:51 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4g_14496/12_2022/7z4g_14496.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4g_14496/12_2022/7z4g_14496.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4g_14496/12_2022/7z4g_14496.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4g_14496/12_2022/7z4g_14496.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4g_14496/12_2022/7z4g_14496.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4g_14496/12_2022/7z4g_14496.pdb" } resolution = 3.64 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= 0.001 sd= 0.006 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 943": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 12714 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1932 Classifications: {'DNA': 1, 'RNA': 90} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 48, 'rna3p_pyr': 30} Link IDs: {'rna2p': 12, 'rna3p': 78} 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: 9711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1188, 9711 Classifications: {'peptide': 1188} Link IDs: {'PTRANS': 32, 'TRANS': 1155} Chain breaks: 4 Chain: "C" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 625 Classifications: {'DNA': 31} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 30} Chain: "D" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 446 Inner-chain residues flagged as termini: ['pdbres=" DA D -2 "'] Classifications: {'DNA': 22} Modifications used: {'5*END': 2} Link IDs: {'rna3p': 21} Time building chain proxies: 7.79, per 1000 atoms: 0.61 Number of scatterers: 12714 At special positions: 0 Unit cell: (86.45, 130, 122.85, 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 19 16.00 P 140 15.00 O 2747 8.00 N 2223 7.00 C 7585 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: 6.34 Conformation dependent library (CDL) restraints added in 1.4 seconds 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 10 sheets defined 55.3% alpha, 9.1% beta 53 base pairs and 85 stacking pairs defined. Time for finding SS restraints: 4.36 Creating SS restraints... Processing helix chain 'B' and resid 22 through 26 removed outlier: 3.569A pdb=" N LYS B 26 " --> pdb=" O ASP B 23 " (cutoff:3.500A) 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 104 through 106 No H-bonds generated for 'chain 'B' and resid 104 through 106' Processing helix chain 'B' and resid 121 through 132 Processing helix chain 'B' and resid 134 through 145 removed outlier: 3.553A pdb=" N LEU B 138 " --> pdb=" O THR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 164 Processing helix chain 'B' and resid 182 through 196 Processing helix chain 'B' and resid 207 through 213 Processing helix chain 'B' and resid 217 through 228 Processing helix chain 'B' and resid 236 through 247 Processing helix chain 'B' and resid 251 through 256 removed outlier: 4.332A pdb=" N ASN B 255 " --> pdb=" O ASN B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 279 Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 286 through 306 removed outlier: 3.983A pdb=" N ASP B 304 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ILE B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 343 Processing helix chain 'B' and resid 343 through 352 removed outlier: 3.585A pdb=" N TYR B 347 " --> pdb=" O LEU B 343 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS B 348 " --> pdb=" O PRO B 344 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLU B 349 " --> pdb=" O GLU B 345 " (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 387 through 395 Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.869A pdb=" N ASN B 407 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY B 408 " --> pdb=" O PHE B 405 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N SER B 409 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 427 removed outlier: 4.117A pdb=" N HIS B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 436 Processing helix chain 'B' and resid 436 through 446 Processing helix chain 'B' and resid 477 through 482 Processing helix chain 'B' and resid 483 through 494 removed outlier: 3.556A pdb=" N ILE B 492 " --> pdb=" O ALA B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 526 removed outlier: 4.146A pdb=" N LYS B 526 " --> pdb=" O ASN B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 552 Processing helix chain 'B' and resid 560 through 568 removed outlier: 3.567A 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 626 removed outlier: 3.520A pdb=" N THR B 622 " --> pdb=" O ASP B 618 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE B 626 " --> pdb=" O THR B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 637 Processing helix chain 'B' and resid 638 through 640 No H-bonds generated for 'chain 'B' and resid 638 through 640' 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 712 removed outlier: 4.241A pdb=" N GLU B 706 " --> pdb=" O LEU B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 726 Processing helix chain 'B' and resid 730 through 751 Processing helix chain 'B' and resid 911 through 922 Processing helix chain 'B' and resid 925 through 940 removed outlier: 3.796A pdb=" N LYS B 929 " --> pdb=" O ARG B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 970 removed outlier: 3.879A pdb=" N VAL B 963 " --> pdb=" O LYS B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 980 through 1001 removed outlier: 4.112A 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 1076 through 1088 removed outlier: 3.905A pdb=" N PHE B1080 " --> pdb=" O LYS B1076 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ALA B1081 " --> pdb=" O GLY B1077 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1132 Processing helix chain 'B' and resid 1170 through 1177 Processing helix chain 'B' and resid 1177 through 1185 removed outlier: 3.561A pdb=" N LYS B1185 " --> pdb=" O PHE B1181 " (cutoff:3.500A) Processing helix chain 'B' and resid 1229 through 1241 removed outlier: 3.570A pdb=" N HIS B1241 " --> pdb=" O TYR B1237 " (cutoff:3.500A) Processing helix chain 'B' and resid 1249 through 1264 Processing helix chain 'B' and resid 1265 through 1280 removed outlier: 3.652A pdb=" N ILE B1269 " --> pdb=" O TYR B1265 " (cutoff:3.500A) Processing helix chain 'B' and resid 1283 through 1297 Processing helix chain 'B' and resid 1298 through 1300 No H-bonds generated for 'chain 'B' and resid 1298 through 1300' Processing helix chain 'B' and resid 1301 through 1313 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 958 removed outlier: 6.296A pdb=" N ILE B 759 " --> pdb=" O ILE B 956 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU B 958 " --> pdb=" O ILE B 759 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE B 761 " --> pdb=" O LEU B 958 " (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 507 through 509 removed outlier: 5.485A pdb=" N LEU B 508 " --> pdb=" O GLY B 660 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 538 through 539 removed outlier: 3.847A pdb=" N ALA B 538 " --> pdb=" O TYR B 529 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS B 528 " --> pdb=" O SER B 581 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER B 581 " --> pdb=" O LYS B 528 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1049 through 1051 Processing sheet with id=AA6, first strand: chain 'B' and resid 1063 through 1065 Processing sheet with id=AA7, first strand: chain 'B' and resid 1107 through 1111 removed outlier: 6.909A pdb=" N SER B1109 " --> pdb=" O ASP B1135 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASP B1135 " --> pdb=" O SER B1109 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1156 through 1167 removed outlier: 3.557A pdb=" N LYS B1158 " --> pdb=" O VAL B1149 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL B1149 " --> pdb=" O LYS B1158 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU B1162 " --> pdb=" O VAL B1145 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL B1145 " --> pdb=" O GLU B1162 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR B1141 " --> pdb=" O ILE B1166 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE B1196 " --> pdb=" O LEU B1144 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1219 through 1222 removed outlier: 6.249A pdb=" N GLU B1219 " --> pdb=" O ALA B1215 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER B1202 " --> pdb=" O LEU B1214 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU B1203 " --> pdb=" O ILE B1348 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1324 through 1326 457 hydrogen bonds defined for protein. 1326 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 133 hydrogen bonds 262 hydrogen bond angles 0 basepair planarities 53 basepair parallelities 85 stacking parallelities Total time for adding SS restraints: 7.02 Time building geometry restraints manager: 6.74 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: 2820 1.33 - 1.45: 3374 1.45 - 1.57: 6738 1.57 - 1.69: 281 1.69 - 1.81: 36 Bond restraints: 13249 Sorted by residual: bond pdb=" O3' DT C 12 " pdb=" P DA C 13 " ideal model delta sigma weight residual 1.607 1.633 -0.026 1.50e-02 4.44e+03 3.10e+00 bond pdb=" CG LEU B1266 " pdb=" CD2 LEU B1266 " ideal model delta sigma weight residual 1.521 1.574 -0.053 3.30e-02 9.18e+02 2.59e+00 bond pdb=" N ARG B 655 " pdb=" CA ARG B 655 " ideal model delta sigma weight residual 1.462 1.484 -0.021 1.32e-02 5.74e+03 2.55e+00 bond pdb=" CA ARG B 655 " pdb=" C ARG B 655 " ideal model delta sigma weight residual 1.529 1.515 0.014 1.04e-02 9.25e+03 1.89e+00 bond pdb=" C GLY B 752 " pdb=" N ARG B 753 " ideal model delta sigma weight residual 1.333 1.314 0.019 1.39e-02 5.18e+03 1.80e+00 ... (remaining 13244 not shown) Histogram of bond angle deviations from ideal: 99.87 - 106.69: 1037 106.69 - 113.51: 7463 113.51 - 120.33: 4925 120.33 - 127.15: 4709 127.15 - 133.97: 371 Bond angle restraints: 18505 Sorted by residual: angle pdb=" N ARG B 655 " pdb=" CA ARG B 655 " pdb=" C ARG B 655 " ideal model delta sigma weight residual 107.20 114.34 -7.14 1.70e+00 3.46e-01 1.76e+01 angle pdb=" O3' DT C 11 " pdb=" C3' DT C 11 " pdb=" C2' DT C 11 " ideal model delta sigma weight residual 111.50 106.48 5.02 1.50e+00 4.44e-01 1.12e+01 angle pdb=" C2' DC C 10 " pdb=" C1' DC C 10 " pdb=" N1 DC C 10 " ideal model delta sigma weight residual 113.50 118.22 -4.72 1.50e+00 4.44e-01 9.91e+00 angle pdb=" C3' DT C 11 " pdb=" C2' DT C 11 " pdb=" C1' DT C 11 " ideal model delta sigma weight residual 101.60 105.26 -3.66 1.50e+00 4.44e-01 5.96e+00 angle pdb=" C2' C A 83 " pdb=" C1' C A 83 " pdb=" N1 C A 83 " ideal model delta sigma weight residual 112.00 108.35 3.65 1.50e+00 4.44e-01 5.91e+00 ... (remaining 18500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 6953 17.09 - 34.18: 454 34.18 - 51.27: 182 51.27 - 68.35: 69 68.35 - 85.44: 6 Dihedral angle restraints: 7664 sinusoidal: 4171 harmonic: 3493 Sorted by residual: dihedral pdb=" CA LYS B1263 " pdb=" C LYS B1263 " pdb=" N HIS B1264 " pdb=" CA HIS B1264 " ideal model delta harmonic sigma weight residual 180.00 162.68 17.32 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CG ARG B 753 " pdb=" CD ARG B 753 " pdb=" NE ARG B 753 " pdb=" CZ ARG B 753 " ideal model delta sinusoidal sigma weight residual 180.00 135.51 44.49 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" O5' U A 44 " pdb=" C5' U A 44 " pdb=" C4' U A 44 " pdb=" C3' U A 44 " ideal model delta sinusoidal sigma weight residual -65.00 -5.23 -59.77 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 7661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1797 0.046 - 0.092: 275 0.092 - 0.137: 53 0.137 - 0.183: 2 0.183 - 0.229: 1 Chirality restraints: 2128 Sorted by residual: chirality pdb=" CA ARG B 753 " pdb=" N ARG B 753 " pdb=" C ARG B 753 " pdb=" CB ARG B 753 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA ILE B 956 " pdb=" N ILE B 956 " pdb=" C ILE B 956 " pdb=" CB ILE B 956 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.99e-01 chirality pdb=" C1' A A 42 " pdb=" O4' A A 42 " pdb=" C2' A A 42 " pdb=" N9 A A 42 " both_signs ideal model delta sigma weight residual False 2.46 2.31 0.15 2.00e-01 2.50e+01 5.34e-01 ... (remaining 2125 not shown) Planarity restraints: 1842 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 993 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.78e+00 pdb=" C VAL B 993 " 0.042 2.00e-02 2.50e+03 pdb=" O VAL B 993 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY B 994 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 991 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.11e+00 pdb=" C ALA B 991 " 0.039 2.00e-02 2.50e+03 pdb=" O ALA B 991 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL B 992 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 83 " -0.025 2.00e-02 2.50e+03 1.39e-02 4.36e+00 pdb=" N1 C A 83 " 0.031 2.00e-02 2.50e+03 pdb=" C2 C A 83 " 0.008 2.00e-02 2.50e+03 pdb=" O2 C A 83 " -0.002 2.00e-02 2.50e+03 pdb=" N3 C A 83 " -0.001 2.00e-02 2.50e+03 pdb=" C4 C A 83 " -0.005 2.00e-02 2.50e+03 pdb=" N4 C A 83 " -0.006 2.00e-02 2.50e+03 pdb=" C5 C A 83 " -0.002 2.00e-02 2.50e+03 pdb=" C6 C A 83 " 0.003 2.00e-02 2.50e+03 ... (remaining 1839 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1550 2.75 - 3.29: 12666 3.29 - 3.82: 23604 3.82 - 4.36: 27947 4.36 - 4.90: 42620 Nonbonded interactions: 108387 Sorted by model distance: nonbonded pdb=" O LYS B 209 " pdb=" OG SER B 213 " model vdw 2.209 2.440 nonbonded pdb=" O2' G A 58 " pdb=" O LEU B 455 " model vdw 2.210 2.440 nonbonded pdb=" NZ LYS B 140 " pdb=" OD2 ASP B 144 " model vdw 2.210 2.520 nonbonded pdb=" NZ LYS B1161 " pdb=" OD1 ASP B1344 " model vdw 2.210 2.520 nonbonded pdb=" O GLU B1304 " pdb=" ND2 ASN B1308 " model vdw 2.219 2.520 ... (remaining 108382 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 140 5.49 5 S 19 5.16 5 C 7585 2.51 5 N 2223 2.21 5 O 2747 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: 2.000 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: 0.020 Extract box with map and model: 12.000 Check model and map are aligned: 0.200 Convert atoms to be neutral: 0.110 Process input model: 42.790 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 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 0.053 13249 Z= 0.189 Angle : 0.478 7.138 18505 Z= 0.269 Chirality : 0.034 0.229 2128 Planarity : 0.004 0.034 1842 Dihedral : 13.818 85.443 5400 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer Outliers : 1.03 % 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: 1.30 (0.25), residues: 1178 helix: 1.99 (0.23), residues: 590 sheet: -0.09 (0.61), residues: 78 loop : -0.29 (0.27), residues: 510 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 216 time to evaluate : 1.942 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 222 average time/residue: 0.3532 time to fit residues: 107.3669 Evaluate side-chains 107 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 105 time to evaluate : 1.949 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1664 time to fit residues: 2.9127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.0010 chunk 100 optimal weight: 20.0000 chunk 55 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 40 optimal weight: 0.4980 chunk 62 optimal weight: 0.0010 chunk 77 optimal weight: 9.9990 chunk 119 optimal weight: 9.9990 overall best weight: 1.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 HIS ** B 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 GLN B 920 GLN B1101 GLN B1234 ASN ** B1311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 13249 Z= 0.192 Angle : 0.548 9.582 18505 Z= 0.287 Chirality : 0.035 0.188 2128 Planarity : 0.003 0.037 1842 Dihedral : 15.277 86.554 2891 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer Outliers : 3.38 % 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: 1.39 (0.25), residues: 1178 helix: 1.93 (0.22), residues: 596 sheet: 0.56 (0.65), residues: 76 loop : -0.20 (0.28), residues: 506 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 122 time to evaluate : 1.399 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 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: 36 outliers final: 20 residues processed: 141 average time/residue: 0.3408 time to fit residues: 67.4416 Evaluate side-chains 113 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 93 time to evaluate : 1.324 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1426 time to fit residues: 6.8033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 99 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 33 optimal weight: 20.0000 chunk 120 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 40 optimal weight: 0.0670 chunk 96 optimal weight: 20.0000 overall best weight: 5.2130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 GLN B 240 ASN B 255 ASN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 698 HIS ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 985 HIS ** B 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.046 13249 Z= 0.351 Angle : 0.679 11.010 18505 Z= 0.354 Chirality : 0.040 0.176 2128 Planarity : 0.005 0.051 1842 Dihedral : 15.783 88.613 2891 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 26.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 3.01 % 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: 0.79 (0.24), residues: 1178 helix: 1.32 (0.21), residues: 600 sheet: 0.18 (0.58), residues: 76 loop : -0.31 (0.28), residues: 502 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 92 time to evaluate : 1.516 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 19 residues processed: 116 average time/residue: 0.2876 time to fit residues: 49.4698 Evaluate side-chains 93 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 74 time to evaluate : 1.438 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1735 time to fit residues: 8.0621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 80 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 chunk 114 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 ASN ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 ASN B 255 ASN ** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 511 HIS ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 982 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 13249 Z= 0.286 Angle : 0.600 10.425 18505 Z= 0.317 Chirality : 0.037 0.150 2128 Planarity : 0.005 0.136 1842 Dihedral : 15.804 90.547 2891 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 23.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 2.26 % 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: 0.80 (0.25), residues: 1178 helix: 1.39 (0.21), residues: 598 sheet: 0.12 (0.57), residues: 78 loop : -0.39 (0.28), residues: 502 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 85 time to evaluate : 1.254 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 revert: symmetry clash outliers start: 24 outliers final: 15 residues processed: 101 average time/residue: 0.2771 time to fit residues: 40.6350 Evaluate side-chains 87 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 1.377 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1255 time to fit residues: 5.1908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 0.4980 chunk 1 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 88 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 114 optimal weight: 4.9990 chunk 32 optimal weight: 20.0000 chunk 42 optimal weight: 3.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 GLN B 394 ASN ** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1262 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 13249 Z= 0.237 Angle : 0.565 10.642 18505 Z= 0.298 Chirality : 0.036 0.163 2128 Planarity : 0.005 0.114 1842 Dihedral : 15.683 90.305 2891 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 20.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer Outliers : 1.22 % 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: 0.80 (0.25), residues: 1178 helix: 1.40 (0.21), residues: 598 sheet: 0.06 (0.57), residues: 78 loop : -0.38 (0.28), residues: 502 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 1.366 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: 13 outliers final: 9 residues processed: 89 average time/residue: 0.2341 time to fit residues: 32.2011 Evaluate side-chains 79 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 1.340 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1873 time to fit residues: 4.5906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 74 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 127 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 chunk 59 optimal weight: 0.0170 chunk 10 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 123 optimal weight: 20.0000 overall best weight: 3.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 ASN ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 13249 Z= 0.221 Angle : 0.557 13.318 18505 Z= 0.291 Chirality : 0.036 0.181 2128 Planarity : 0.004 0.051 1842 Dihedral : 15.630 90.367 2891 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 20.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.89 (0.25), residues: 1178 helix: 1.46 (0.22), residues: 597 sheet: -0.17 (0.55), residues: 90 loop : -0.26 (0.29), residues: 491 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 76 time to evaluate : 1.447 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: 14 outliers final: 7 residues processed: 86 average time/residue: 0.2482 time to fit residues: 32.5540 Evaluate side-chains 78 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 71 time to evaluate : 1.240 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1144 time to fit residues: 3.1164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 127 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 78 optimal weight: 0.0770 chunk 50 optimal weight: 5.9990 overall best weight: 1.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 13249 Z= 0.172 Angle : 0.530 12.621 18505 Z= 0.277 Chirality : 0.035 0.166 2128 Planarity : 0.003 0.051 1842 Dihedral : 15.509 89.730 2891 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer Outliers : 1.22 % 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: 1.09 (0.25), residues: 1178 helix: 1.60 (0.22), residues: 598 sheet: 0.04 (0.54), residues: 95 loop : -0.16 (0.29), residues: 485 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 1.369 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: 13 outliers final: 7 residues processed: 86 average time/residue: 0.2430 time to fit residues: 32.6896 Evaluate side-chains 75 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 68 time to evaluate : 1.279 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1309 time to fit residues: 3.3869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 86 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 121 optimal weight: 0.0370 chunk 111 optimal weight: 5.9990 overall best weight: 1.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 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: 0.7794 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 13249 Z= 0.165 Angle : 0.529 13.578 18505 Z= 0.275 Chirality : 0.035 0.138 2128 Planarity : 0.003 0.050 1842 Dihedral : 15.477 89.009 2891 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.15 (0.25), residues: 1178 helix: 1.59 (0.22), residues: 599 sheet: 0.17 (0.54), residues: 93 loop : -0.08 (0.29), residues: 486 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 74 time to evaluate : 1.459 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: 6 outliers final: 6 residues processed: 78 average time/residue: 0.2301 time to fit residues: 28.6756 Evaluate side-chains 74 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 1.315 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1201 time to fit residues: 3.0422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 107 optimal weight: 20.0000 chunk 112 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 125 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN ** B 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.5246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.052 13249 Z= 0.357 Angle : 0.672 11.390 18505 Z= 0.356 Chirality : 0.040 0.156 2128 Planarity : 0.005 0.049 1842 Dihedral : 16.020 88.889 2891 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 27.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer Outliers : 1.03 % 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: 0.60 (0.25), residues: 1178 helix: 1.12 (0.21), residues: 598 sheet: -0.26 (0.54), residues: 95 loop : -0.26 (0.30), residues: 485 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 72 average time/residue: 0.2292 time to fit residues: 26.3869 Evaluate side-chains 71 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 63 time to evaluate : 2.049 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1334 time to fit residues: 3.7775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 131 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 83 optimal weight: 0.0970 chunk 111 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1234 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 13249 Z= 0.199 Angle : 0.581 14.170 18505 Z= 0.302 Chirality : 0.036 0.150 2128 Planarity : 0.003 0.050 1842 Dihedral : 15.832 89.893 2891 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 19.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.40 % Favored : 96.52 % Rotamer Outliers : 0.09 % 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: 0.86 (0.25), residues: 1178 helix: 1.34 (0.21), residues: 596 sheet: 0.06 (0.56), residues: 91 loop : -0.18 (0.30), residues: 491 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 73 average time/residue: 0.2207 time to fit residues: 25.7031 Evaluate side-chains 70 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 1.230 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1177 time to fit residues: 1.9221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 107 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 990 ASN ** 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 = 0.3761 r_free = 0.3761 target = 0.068381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.054223 restraints weight = 78566.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.055854 restraints weight = 41199.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.056908 restraints weight = 27280.491| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.5400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 13249 Z= 0.195 Angle : 0.560 13.385 18505 Z= 0.294 Chirality : 0.036 0.137 2128 Planarity : 0.003 0.053 1842 Dihedral : 15.756 88.892 2891 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.74 % Favored : 96.18 % Rotamer Outliers : 0.19 % 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: 0.90 (0.25), residues: 1178 helix: 1.33 (0.21), residues: 604 sheet: 0.03 (0.57), residues: 89 loop : -0.13 (0.30), residues: 485 =============================================================================== Job complete usr+sys time: 2195.86 seconds wall clock time: 42 minutes 9.77 seconds (2529.77 seconds total)