Starting phenix.real_space_refine on Sat Dec 28 19:39:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7op8_13014/12_2024/7op8_13014.cif Found real_map, /net/cci-nas-00/data/ceres_data/7op8_13014/12_2024/7op8_13014.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7op8_13014/12_2024/7op8_13014.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7op8_13014/12_2024/7op8_13014.map" model { file = "/net/cci-nas-00/data/ceres_data/7op8_13014/12_2024/7op8_13014.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7op8_13014/12_2024/7op8_13014.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.071 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mg 1 5.21 5 S 53 5.16 5 Be 1 3.05 5 C 5761 2.51 5 N 1472 2.21 5 O 1581 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8872 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1118, 8867 Classifications: {'peptide': 1118} Link IDs: {'PTRANS': 56, 'TRANS': 1061} Chain breaks: 8 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 5 Unusual residues: {' MG': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.78, per 1000 atoms: 0.65 Number of scatterers: 8872 At special positions: 0 Unit cell: (83.2, 97.344, 143.104, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 53 16.00 Mg 1 11.99 F 3 9.00 O 1581 8.00 N 1472 7.00 C 5761 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 1.2 seconds 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 12 sheets defined 44.0% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 228 through 240 removed outlier: 3.824A pdb=" N ILE A 232 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR A 233 " --> pdb=" O GLY A 229 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL A 235 " --> pdb=" O ALA A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 250 removed outlier: 3.550A pdb=" N LEU A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TRP A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 removed outlier: 3.920A pdb=" N LYS A 257 " --> pdb=" O LYS A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 297 removed outlier: 3.585A pdb=" N THR A 296 " --> pdb=" O PRO A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 373 Processing helix chain 'A' and resid 388 through 393 removed outlier: 3.659A pdb=" N ILE A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 408 removed outlier: 3.997A pdb=" N PHE A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 444 removed outlier: 3.519A pdb=" N ALA A 416 " --> pdb=" O TYR A 412 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA A 417 " --> pdb=" O TYR A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 519 Processing helix chain 'A' and resid 529 through 535 removed outlier: 3.821A pdb=" N HIS A 535 " --> pdb=" O ASP A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 568 Processing helix chain 'A' and resid 569 through 579 Processing helix chain 'A' and resid 587 through 591 removed outlier: 3.515A pdb=" N GLU A 590 " --> pdb=" O LYS A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 614 removed outlier: 3.873A pdb=" N GLY A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A 605 " --> pdb=" O CYS A 601 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL A 612 " --> pdb=" O ILE A 608 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN A 613 " --> pdb=" O VAL A 609 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE A 614 " --> pdb=" O SER A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 630 removed outlier: 3.659A pdb=" N LEU A 623 " --> pdb=" O LEU A 619 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE A 624 " --> pdb=" O HIS A 620 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LEU A 625 " --> pdb=" O TRP A 621 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A 626 " --> pdb=" O THR A 622 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG A 627 " --> pdb=" O LEU A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 658 removed outlier: 3.729A pdb=" N THR A 645 " --> pdb=" O PRO A 641 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A 646 " --> pdb=" O ALA A 642 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS A 658 " --> pdb=" O ARG A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 668 removed outlier: 3.586A pdb=" N VAL A 668 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 674 removed outlier: 3.642A pdb=" N GLY A 672 " --> pdb=" O ASN A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 760 Processing helix chain 'A' and resid 773 through 784 Processing helix chain 'A' and resid 880 through 891 removed outlier: 3.567A pdb=" N ALA A 891 " --> pdb=" O TYR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 919 removed outlier: 3.530A pdb=" N GLU A 918 " --> pdb=" O THR A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 949 Processing helix chain 'A' and resid 960 through 971 Processing helix chain 'A' and resid 1042 through 1053 removed outlier: 3.851A pdb=" N ASP A1051 " --> pdb=" O ARG A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1064 Processing helix chain 'A' and resid 1072 through 1086 removed outlier: 3.851A pdb=" N ILE A1086 " --> pdb=" O LYS A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1105 removed outlier: 3.796A pdb=" N LYS A1104 " --> pdb=" O CYS A1100 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA A1105 " --> pdb=" O ALA A1101 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1100 through 1105' Processing helix chain 'A' and resid 1131 through 1143 removed outlier: 4.349A pdb=" N GLU A1135 " --> pdb=" O ARG A1131 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY A1140 " --> pdb=" O VAL A1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1167 removed outlier: 3.683A pdb=" N TYR A1153 " --> pdb=" O SER A1149 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER A1155 " --> pdb=" O PHE A1151 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU A1156 " --> pdb=" O LYS A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1168 through 1170 No H-bonds generated for 'chain 'A' and resid 1168 through 1170' Processing helix chain 'A' and resid 1178 through 1187 removed outlier: 3.514A pdb=" N LEU A1187 " --> pdb=" O ILE A1183 " (cutoff:3.500A) Processing helix chain 'A' and resid 1188 through 1196 removed outlier: 3.912A pdb=" N PHE A1194 " --> pdb=" O PRO A1190 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER A1196 " --> pdb=" O ALA A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1215 through 1243 Proline residue: A1221 - end of helix removed outlier: 3.508A pdb=" N ILE A1232 " --> pdb=" O VAL A1228 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1282 removed outlier: 3.733A pdb=" N ALA A1269 " --> pdb=" O THR A1265 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY A1278 " --> pdb=" O TYR A1274 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL A1279 " --> pdb=" O ILE A1275 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A1280 " --> pdb=" O LEU A1276 " (cutoff:3.500A) Processing helix chain 'A' and resid 1297 through 1313 Processing helix chain 'A' and resid 1316 through 1323 removed outlier: 3.557A pdb=" N PHE A1320 " --> pdb=" O PRO A1316 " (cutoff:3.500A) Processing helix chain 'A' and resid 1329 through 1352 removed outlier: 3.714A pdb=" N HIS A1352 " --> pdb=" O TRP A1348 " (cutoff:3.500A) Processing helix chain 'A' and resid 1354 through 1363 Processing helix chain 'A' and resid 1377 through 1392 removed outlier: 3.605A pdb=" N TYR A1392 " --> pdb=" O PHE A1388 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 209 Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 209 Processing sheet with id=AA3, first strand: chain 'A' and resid 322 through 325 Processing sheet with id=AA4, first strand: chain 'A' and resid 451 through 455 Processing sheet with id=AA5, first strand: chain 'A' and resid 472 through 473 Processing sheet with id=AA6, first strand: chain 'A' and resid 508 through 510 removed outlier: 6.156A pdb=" N ASN A 497 " --> pdb=" O LEU A 543 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N LEU A 543 " --> pdb=" O ASN A 497 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 660 through 662 removed outlier: 6.922A pdb=" N SER A1111 " --> pdb=" O SER A1125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 952 through 955 removed outlier: 7.047A pdb=" N LEU A 676 " --> pdb=" O GLY A1091 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N CYS A1093 " --> pdb=" O LEU A 676 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N CYS A 678 " --> pdb=" O CYS A1093 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 704 through 705 removed outlier: 3.654A pdb=" N ARG A 704 " --> pdb=" O SER A 699 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N VAL A 692 " --> pdb=" O GLU A 932 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N GLU A 932 " --> pdb=" O VAL A 692 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY A 694 " --> pdb=" O ILE A 930 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL A 926 " --> pdb=" O ALA A 698 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N PHE A 925 " --> pdb=" O THR A 900 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N THR A 900 " --> pdb=" O PHE A 925 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY A 927 " --> pdb=" O CYS A 898 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N SER A 846 " --> pdb=" O ALA A 835 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ALA A 835 " --> pdb=" O SER A 846 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE A 848 " --> pdb=" O LEU A 833 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 764 through 765 removed outlier: 3.712A pdb=" N ARG A 764 " --> pdb=" O VAL A 771 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL A 771 " --> pdb=" O ARG A 764 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 981 through 986 removed outlier: 4.143A pdb=" N LYS A 996 " --> pdb=" O ILE A 986 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1039 through 1041 removed outlier: 7.147A pdb=" N ILE A1039 " --> pdb=" O LYS A1066 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N TYR A1068 " --> pdb=" O ILE A1039 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL A1041 " --> pdb=" O TYR A1068 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 363 hydrogen bonds defined for protein. 1029 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.02 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2528 1.34 - 1.46: 1707 1.46 - 1.58: 4778 1.58 - 1.69: 0 1.69 - 1.81: 77 Bond restraints: 9090 Sorted by residual: bond pdb=" F2 BEF A1401 " pdb="BE BEF A1401 " ideal model delta sigma weight residual 1.476 1.560 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" F3 BEF A1401 " pdb="BE BEF A1401 " ideal model delta sigma weight residual 1.476 1.544 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" F1 BEF A1401 " pdb="BE BEF A1401 " ideal model delta sigma weight residual 1.476 1.531 -0.055 2.00e-02 2.50e+03 7.67e+00 bond pdb=" C ASP A1010 " pdb=" N PRO A1011 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.93e+00 bond pdb=" C ARG A1285 " pdb=" N PRO A1286 " ideal model delta sigma weight residual 1.334 1.373 -0.039 2.34e-02 1.83e+03 2.85e+00 ... (remaining 9085 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 12060 2.50 - 5.00: 233 5.00 - 7.50: 47 7.50 - 10.01: 6 10.01 - 12.51: 3 Bond angle restraints: 12349 Sorted by residual: angle pdb=" F2 BEF A1401 " pdb="BE BEF A1401 " pdb=" F3 BEF A1401 " ideal model delta sigma weight residual 119.96 107.45 12.51 3.00e+00 1.11e-01 1.74e+01 angle pdb=" CA LYS A1383 " pdb=" CB LYS A1383 " pdb=" CG LYS A1383 " ideal model delta sigma weight residual 114.10 121.43 -7.33 2.00e+00 2.50e-01 1.34e+01 angle pdb=" C VAL A1251 " pdb=" N ASP A1252 " pdb=" CA ASP A1252 " ideal model delta sigma weight residual 121.70 128.21 -6.51 1.80e+00 3.09e-01 1.31e+01 angle pdb=" C GLU A 975 " pdb=" CA GLU A 975 " pdb=" CB GLU A 975 " ideal model delta sigma weight residual 109.54 116.11 -6.57 1.84e+00 2.95e-01 1.28e+01 angle pdb=" CB GLU A1078 " pdb=" CG GLU A1078 " pdb=" CD GLU A1078 " ideal model delta sigma weight residual 112.60 118.49 -5.89 1.70e+00 3.46e-01 1.20e+01 ... (remaining 12344 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 4763 16.90 - 33.80: 509 33.80 - 50.70: 89 50.70 - 67.61: 10 67.61 - 84.51: 11 Dihedral angle restraints: 5382 sinusoidal: 2120 harmonic: 3262 Sorted by residual: dihedral pdb=" CA TRP A 345 " pdb=" C TRP A 345 " pdb=" N LYS A 346 " pdb=" CA LYS A 346 " ideal model delta harmonic sigma weight residual 180.00 -160.48 -19.52 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA GLU A 866 " pdb=" C GLU A 866 " pdb=" N CYS A 867 " pdb=" CA CYS A 867 " ideal model delta harmonic sigma weight residual 180.00 161.27 18.73 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA PRO A 252 " pdb=" C PRO A 252 " pdb=" N LYS A 253 " pdb=" CA LYS A 253 " ideal model delta harmonic sigma weight residual -180.00 -161.58 -18.42 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 5379 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1159 0.068 - 0.135: 222 0.135 - 0.203: 20 0.203 - 0.271: 5 0.271 - 0.339: 2 Chirality restraints: 1408 Sorted by residual: chirality pdb=" CB VAL A 468 " pdb=" CA VAL A 468 " pdb=" CG1 VAL A 468 " pdb=" CG2 VAL A 468 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CB THR A 429 " pdb=" CA THR A 429 " pdb=" OG1 THR A 429 " pdb=" CG2 THR A 429 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB VAL A 472 " pdb=" CA VAL A 472 " pdb=" CG1 VAL A 472 " pdb=" CG2 VAL A 472 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 1405 not shown) Planarity restraints: 1546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 624 " -0.016 2.00e-02 2.50e+03 3.16e-02 9.96e+00 pdb=" C ILE A 624 " 0.055 2.00e-02 2.50e+03 pdb=" O ILE A 624 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU A 625 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1339 " 0.016 2.00e-02 2.50e+03 2.29e-02 9.21e+00 pdb=" CG PHE A1339 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE A1339 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE A1339 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE A1339 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A1339 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A1339 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A1004 " -0.046 5.00e-02 4.00e+02 7.09e-02 8.05e+00 pdb=" N PRO A1005 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO A1005 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A1005 " -0.039 5.00e-02 4.00e+02 ... (remaining 1543 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 68 2.54 - 3.13: 6591 3.13 - 3.72: 13856 3.72 - 4.31: 18444 4.31 - 4.90: 30770 Nonbonded interactions: 69729 Sorted by model distance: nonbonded pdb="BE BEF A1401 " pdb="MG MG A1402 " model vdw 1.950 1.550 nonbonded pdb=" F3 BEF A1401 " pdb="MG MG A1402 " model vdw 2.002 2.120 nonbonded pdb=" F1 BEF A1401 " pdb="MG MG A1402 " model vdw 2.023 2.120 nonbonded pdb=" F2 BEF A1401 " pdb="MG MG A1402 " model vdw 2.139 2.120 nonbonded pdb=" O THR A 682 " pdb="MG MG A1402 " model vdw 2.181 2.170 ... (remaining 69724 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 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: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.070 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 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 : 0.004 0.084 9090 Z= 0.272 Angle : 0.861 12.507 12349 Z= 0.432 Chirality : 0.054 0.339 1408 Planarity : 0.006 0.071 1546 Dihedral : 14.437 84.507 3270 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: -1.73 (0.23), residues: 1100 helix: -0.34 (0.23), residues: 419 sheet: -1.50 (0.46), residues: 119 loop : -1.69 (0.24), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A1245 HIS 0.009 0.001 HIS A1225 PHE 0.052 0.002 PHE A1339 TYR 0.045 0.002 TYR A1088 ARG 0.006 0.000 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 1.035 Fit side-chains REVERT: A 221 SER cc_start: 0.6503 (t) cc_final: 0.6000 (t) REVERT: A 1129 ASP cc_start: 0.7068 (p0) cc_final: 0.6577 (p0) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1680 time to fit residues: 39.7746 Evaluate side-chains 121 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 56 optimal weight: 0.0770 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 HIS A1225 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9090 Z= 0.227 Angle : 0.613 8.025 12349 Z= 0.313 Chirality : 0.045 0.221 1408 Planarity : 0.005 0.047 1546 Dihedral : 4.817 22.141 1213 Min Nonbonded Distance : 1.223 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.75 % Allowed : 10.57 % Favored : 87.68 % 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: -1.24 (0.24), residues: 1100 helix: 0.32 (0.24), residues: 435 sheet: -1.36 (0.45), residues: 129 loop : -1.65 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1245 HIS 0.002 0.001 HIS A 367 PHE 0.039 0.001 PHE A1339 TYR 0.023 0.002 TYR A1088 ARG 0.003 0.000 ARG A 594 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 1.270 Fit side-chains REVERT: A 221 SER cc_start: 0.6977 (t) cc_final: 0.6687 (t) REVERT: A 223 PHE cc_start: 0.6801 (m-80) cc_final: 0.6438 (m-80) REVERT: A 530 HIS cc_start: 0.6949 (OUTLIER) cc_final: 0.6456 (t-90) REVERT: A 975 GLU cc_start: 0.6999 (tm-30) cc_final: 0.6678 (tm-30) REVERT: A 1129 ASP cc_start: 0.7276 (p0) cc_final: 0.6766 (p0) REVERT: A 1231 MET cc_start: 0.7119 (mmm) cc_final: 0.6735 (mmm) outliers start: 17 outliers final: 12 residues processed: 149 average time/residue: 0.1708 time to fit residues: 38.4087 Evaluate side-chains 134 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 414 TYR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 530 HIS Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 943 ILE Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1225 HIS Chi-restraints excluded: chain A residue 1305 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 HIS A 613 ASN A1225 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 9090 Z= 0.318 Angle : 0.628 7.759 12349 Z= 0.322 Chirality : 0.046 0.224 1408 Planarity : 0.004 0.046 1546 Dihedral : 4.868 22.675 1213 Min Nonbonded Distance : 1.311 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.77 % Allowed : 13.55 % Favored : 83.68 % 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: -1.10 (0.25), residues: 1100 helix: 0.54 (0.25), residues: 435 sheet: -1.46 (0.45), residues: 132 loop : -1.62 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 350 HIS 0.025 0.002 HIS A1225 PHE 0.027 0.001 PHE A1339 TYR 0.037 0.002 TYR A1088 ARG 0.003 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 1.041 Fit side-chains REVERT: A 221 SER cc_start: 0.7140 (t) cc_final: 0.6832 (t) REVERT: A 223 PHE cc_start: 0.6967 (m-80) cc_final: 0.6620 (m-80) REVERT: A 530 HIS cc_start: 0.6926 (OUTLIER) cc_final: 0.6453 (t-90) REVERT: A 1231 MET cc_start: 0.7240 (mmm) cc_final: 0.6842 (mmm) REVERT: A 1344 PHE cc_start: 0.8465 (t80) cc_final: 0.8193 (t80) outliers start: 27 outliers final: 21 residues processed: 147 average time/residue: 0.1626 time to fit residues: 36.8946 Evaluate side-chains 140 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 414 TYR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 530 HIS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 943 ILE Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1095 ASP Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1225 HIS Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1384 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 11 optimal weight: 0.0030 chunk 48 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 28 optimal weight: 0.4980 chunk 89 optimal weight: 0.6980 chunk 60 optimal weight: 9.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 HIS ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1225 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9090 Z= 0.174 Angle : 0.571 7.831 12349 Z= 0.290 Chirality : 0.043 0.186 1408 Planarity : 0.004 0.044 1546 Dihedral : 4.624 21.146 1213 Min Nonbonded Distance : 1.388 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.26 % Allowed : 16.94 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.85 (0.25), residues: 1100 helix: 0.85 (0.25), residues: 427 sheet: -1.37 (0.45), residues: 130 loop : -1.53 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 270 HIS 0.019 0.002 HIS A 367 PHE 0.021 0.001 PHE A1339 TYR 0.022 0.001 TYR A1088 ARG 0.002 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 1.058 Fit side-chains revert: symmetry clash REVERT: A 221 SER cc_start: 0.6991 (t) cc_final: 0.6663 (t) REVERT: A 223 PHE cc_start: 0.6807 (m-80) cc_final: 0.6499 (m-80) REVERT: A 367 HIS cc_start: 0.6131 (m90) cc_final: 0.5028 (m90) REVERT: A 1135 GLU cc_start: 0.6034 (OUTLIER) cc_final: 0.5653 (mp0) REVERT: A 1225 HIS cc_start: 0.7933 (OUTLIER) cc_final: 0.7193 (t70) REVERT: A 1231 MET cc_start: 0.7219 (mmm) cc_final: 0.6811 (mmm) outliers start: 22 outliers final: 16 residues processed: 150 average time/residue: 0.1672 time to fit residues: 38.0356 Evaluate side-chains 142 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 TRP Chi-restraints excluded: chain A residue 414 TYR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 943 ILE Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1095 ASP Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1135 GLU Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1225 HIS Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1384 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.0770 chunk 79 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1225 HIS ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9090 Z= 0.187 Angle : 0.575 9.933 12349 Z= 0.290 Chirality : 0.043 0.180 1408 Planarity : 0.004 0.039 1546 Dihedral : 4.549 21.511 1213 Min Nonbonded Distance : 1.351 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.08 % Allowed : 17.56 % Favored : 79.36 % 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: -0.83 (0.25), residues: 1100 helix: 0.83 (0.25), residues: 433 sheet: -1.41 (0.45), residues: 130 loop : -1.49 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 270 HIS 0.007 0.001 HIS A1225 PHE 0.017 0.001 PHE A1339 TYR 0.022 0.001 TYR A1088 ARG 0.006 0.000 ARG A 292 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.970 Fit side-chains REVERT: A 221 SER cc_start: 0.7001 (t) cc_final: 0.6651 (t) REVERT: A 223 PHE cc_start: 0.6814 (m-80) cc_final: 0.6534 (m-80) REVERT: A 530 HIS cc_start: 0.6838 (OUTLIER) cc_final: 0.6375 (t-90) REVERT: A 1135 GLU cc_start: 0.6048 (OUTLIER) cc_final: 0.5642 (mp0) REVERT: A 1225 HIS cc_start: 0.7841 (OUTLIER) cc_final: 0.7031 (t70) REVERT: A 1231 MET cc_start: 0.7259 (mmm) cc_final: 0.6836 (mmm) REVERT: A 1242 GLN cc_start: 0.8172 (pp30) cc_final: 0.7921 (mp10) outliers start: 30 outliers final: 21 residues processed: 147 average time/residue: 0.1848 time to fit residues: 40.7903 Evaluate side-chains 143 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 TRP Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 414 TYR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 530 HIS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 943 ILE Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1095 ASP Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1135 GLU Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1225 HIS Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1384 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 0.0970 chunk 107 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 12 optimal weight: 8.9990 chunk 61 optimal weight: 0.0770 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1225 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9090 Z= 0.172 Angle : 0.566 7.563 12349 Z= 0.284 Chirality : 0.042 0.177 1408 Planarity : 0.004 0.043 1546 Dihedral : 4.468 20.995 1213 Min Nonbonded Distance : 1.375 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.77 % Allowed : 18.38 % Favored : 78.85 % 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: -0.76 (0.25), residues: 1100 helix: 0.92 (0.25), residues: 435 sheet: -1.43 (0.45), residues: 130 loop : -1.48 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 270 HIS 0.007 0.001 HIS A1225 PHE 0.015 0.001 PHE A1339 TYR 0.020 0.001 TYR A1088 ARG 0.002 0.000 ARG A 292 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 1.085 Fit side-chains revert: symmetry clash REVERT: A 221 SER cc_start: 0.7070 (t) cc_final: 0.6703 (t) REVERT: A 223 PHE cc_start: 0.6770 (m-80) cc_final: 0.6498 (m-80) REVERT: A 530 HIS cc_start: 0.6827 (OUTLIER) cc_final: 0.6366 (t-90) REVERT: A 1135 GLU cc_start: 0.6006 (OUTLIER) cc_final: 0.5616 (mt-10) REVERT: A 1225 HIS cc_start: 0.7836 (OUTLIER) cc_final: 0.7001 (t70) REVERT: A 1231 MET cc_start: 0.7225 (mmm) cc_final: 0.6797 (mmm) outliers start: 27 outliers final: 19 residues processed: 149 average time/residue: 0.1987 time to fit residues: 45.5324 Evaluate side-chains 143 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 TRP Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 414 TYR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 530 HIS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1135 GLU Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1225 HIS Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1384 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.9990 chunk 60 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1225 HIS ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9090 Z= 0.219 Angle : 0.594 11.196 12349 Z= 0.298 Chirality : 0.043 0.189 1408 Planarity : 0.004 0.035 1546 Dihedral : 4.514 21.580 1213 Min Nonbonded Distance : 1.353 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 3.29 % Allowed : 18.79 % Favored : 77.93 % 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: -0.82 (0.25), residues: 1100 helix: 0.88 (0.25), residues: 435 sheet: -1.47 (0.45), residues: 132 loop : -1.52 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A1245 HIS 0.007 0.001 HIS A1225 PHE 0.013 0.001 PHE A1339 TYR 0.031 0.002 TYR A 397 ARG 0.001 0.000 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 1.094 Fit side-chains REVERT: A 221 SER cc_start: 0.7169 (t) cc_final: 0.6799 (t) REVERT: A 223 PHE cc_start: 0.6839 (m-80) cc_final: 0.6506 (m-80) REVERT: A 530 HIS cc_start: 0.6865 (OUTLIER) cc_final: 0.6404 (t-90) REVERT: A 903 ILE cc_start: 0.7917 (mm) cc_final: 0.7660 (mm) REVERT: A 1088 TYR cc_start: 0.8508 (OUTLIER) cc_final: 0.6670 (t80) REVERT: A 1135 GLU cc_start: 0.5990 (OUTLIER) cc_final: 0.5622 (mt-10) REVERT: A 1225 HIS cc_start: 0.7829 (OUTLIER) cc_final: 0.6986 (t70) REVERT: A 1231 MET cc_start: 0.7269 (mmm) cc_final: 0.6855 (mmm) REVERT: A 1242 GLN cc_start: 0.8109 (pp30) cc_final: 0.7783 (mp10) outliers start: 32 outliers final: 22 residues processed: 149 average time/residue: 0.1821 time to fit residues: 41.5159 Evaluate side-chains 143 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 TRP Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 414 TYR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 530 HIS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 943 ILE Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1088 TYR Chi-restraints excluded: chain A residue 1095 ASP Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1135 GLU Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1225 HIS Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1384 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 84 optimal weight: 0.3980 chunk 97 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1225 HIS A1394 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9090 Z= 0.247 Angle : 0.608 9.070 12349 Z= 0.308 Chirality : 0.043 0.197 1408 Planarity : 0.004 0.039 1546 Dihedral : 4.540 21.988 1213 Min Nonbonded Distance : 1.345 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.18 % Allowed : 19.82 % Favored : 77.00 % 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: -0.85 (0.25), residues: 1100 helix: 0.88 (0.25), residues: 435 sheet: -1.54 (0.44), residues: 132 loop : -1.55 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A1245 HIS 0.004 0.001 HIS A1225 PHE 0.027 0.001 PHE A1339 TYR 0.041 0.002 TYR A1392 ARG 0.002 0.000 ARG A1288 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 1.071 Fit side-chains REVERT: A 221 SER cc_start: 0.7201 (t) cc_final: 0.6839 (t) REVERT: A 223 PHE cc_start: 0.6920 (m-80) cc_final: 0.6581 (m-80) REVERT: A 530 HIS cc_start: 0.6893 (OUTLIER) cc_final: 0.6436 (t-90) REVERT: A 903 ILE cc_start: 0.7963 (mm) cc_final: 0.7725 (mm) REVERT: A 1088 TYR cc_start: 0.8611 (OUTLIER) cc_final: 0.6694 (t80) REVERT: A 1135 GLU cc_start: 0.6021 (OUTLIER) cc_final: 0.5650 (mt-10) REVERT: A 1225 HIS cc_start: 0.7817 (OUTLIER) cc_final: 0.6939 (t70) REVERT: A 1231 MET cc_start: 0.7270 (mmm) cc_final: 0.6856 (mmm) REVERT: A 1242 GLN cc_start: 0.8142 (pp30) cc_final: 0.7787 (mp10) outliers start: 31 outliers final: 23 residues processed: 144 average time/residue: 0.1789 time to fit residues: 38.8207 Evaluate side-chains 149 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 TRP Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 414 TYR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 530 HIS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 943 ILE Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1088 TYR Chi-restraints excluded: chain A residue 1095 ASP Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1135 GLU Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1225 HIS Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1303 VAL Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1384 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.4980 chunk 60 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 78 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 94 optimal weight: 0.1980 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 GLN A1225 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9090 Z= 0.199 Angle : 0.608 13.153 12349 Z= 0.303 Chirality : 0.043 0.184 1408 Planarity : 0.004 0.050 1546 Dihedral : 4.508 21.540 1213 Min Nonbonded Distance : 1.393 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 3.08 % Allowed : 20.02 % Favored : 76.90 % 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: -0.81 (0.25), residues: 1100 helix: 0.91 (0.25), residues: 435 sheet: -1.54 (0.44), residues: 132 loop : -1.50 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A1245 HIS 0.006 0.001 HIS A1225 PHE 0.035 0.001 PHE A1339 TYR 0.027 0.001 TYR A1088 ARG 0.005 0.000 ARG A 594 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.996 Fit side-chains REVERT: A 221 SER cc_start: 0.7155 (t) cc_final: 0.6712 (t) REVERT: A 223 PHE cc_start: 0.6874 (m-80) cc_final: 0.6458 (m-10) REVERT: A 530 HIS cc_start: 0.6862 (OUTLIER) cc_final: 0.6412 (t-90) REVERT: A 795 GLU cc_start: 0.7455 (pm20) cc_final: 0.7245 (pp20) REVERT: A 903 ILE cc_start: 0.7940 (mm) cc_final: 0.7702 (mm) REVERT: A 1088 TYR cc_start: 0.8546 (OUTLIER) cc_final: 0.6558 (t80) REVERT: A 1135 GLU cc_start: 0.5964 (OUTLIER) cc_final: 0.5604 (mt-10) REVERT: A 1225 HIS cc_start: 0.7813 (OUTLIER) cc_final: 0.6990 (t70) REVERT: A 1231 MET cc_start: 0.7250 (mmm) cc_final: 0.6843 (mmm) REVERT: A 1242 GLN cc_start: 0.8097 (pp30) cc_final: 0.7801 (mp10) REVERT: A 1392 TYR cc_start: 0.7645 (m-80) cc_final: 0.7182 (m-80) REVERT: A 1393 PHE cc_start: 0.6551 (p90) cc_final: 0.6321 (p90) outliers start: 30 outliers final: 22 residues processed: 145 average time/residue: 0.1781 time to fit residues: 39.1654 Evaluate side-chains 148 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 TRP Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 414 TYR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 530 HIS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 926 VAL Chi-restraints excluded: chain A residue 943 ILE Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1088 TYR Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1135 GLU Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1225 HIS Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1303 VAL Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1384 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1225 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9090 Z= 0.230 Angle : 0.622 12.345 12349 Z= 0.310 Chirality : 0.044 0.195 1408 Planarity : 0.004 0.045 1546 Dihedral : 4.521 22.073 1213 Min Nonbonded Distance : 1.371 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.77 % Allowed : 20.33 % Favored : 76.90 % 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: -0.84 (0.25), residues: 1100 helix: 0.85 (0.25), residues: 436 sheet: -1.55 (0.44), residues: 132 loop : -1.51 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A1245 HIS 0.008 0.001 HIS A1225 PHE 0.030 0.001 PHE A1339 TYR 0.032 0.001 TYR A1088 ARG 0.004 0.000 ARG A 627 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.988 Fit side-chains REVERT: A 221 SER cc_start: 0.7188 (t) cc_final: 0.6754 (t) REVERT: A 223 PHE cc_start: 0.6903 (m-80) cc_final: 0.6507 (m-10) REVERT: A 530 HIS cc_start: 0.6883 (OUTLIER) cc_final: 0.6430 (t-90) REVERT: A 903 ILE cc_start: 0.7958 (mm) cc_final: 0.7722 (mm) REVERT: A 1088 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.6621 (t80) REVERT: A 1135 GLU cc_start: 0.5991 (OUTLIER) cc_final: 0.5624 (mt-10) REVERT: A 1225 HIS cc_start: 0.7813 (OUTLIER) cc_final: 0.6990 (t70) REVERT: A 1231 MET cc_start: 0.7257 (mmm) cc_final: 0.6868 (mmm) REVERT: A 1242 GLN cc_start: 0.8050 (pp30) cc_final: 0.7773 (mp10) outliers start: 27 outliers final: 22 residues processed: 143 average time/residue: 0.1669 time to fit residues: 36.5568 Evaluate side-chains 148 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 TRP Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 414 TYR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 530 HIS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 926 VAL Chi-restraints excluded: chain A residue 943 ILE Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1088 TYR Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1135 GLU Chi-restraints excluded: chain A residue 1155 SER Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1225 HIS Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1303 VAL Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1384 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 90 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 63 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1225 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.188621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.150782 restraints weight = 13265.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.151135 restraints weight = 8384.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.152673 restraints weight = 7722.526| |-----------------------------------------------------------------------------| r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9090 Z= 0.223 Angle : 0.627 11.770 12349 Z= 0.313 Chirality : 0.043 0.196 1408 Planarity : 0.004 0.045 1546 Dihedral : 4.538 22.222 1213 Min Nonbonded Distance : 1.381 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.87 % Allowed : 20.53 % Favored : 76.59 % 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: -0.85 (0.25), residues: 1100 helix: 0.85 (0.25), residues: 436 sheet: -1.59 (0.44), residues: 132 loop : -1.50 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1245 HIS 0.007 0.001 HIS A1225 PHE 0.027 0.001 PHE A1339 TYR 0.032 0.002 TYR A1088 ARG 0.007 0.000 ARG A 594 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1968.58 seconds wall clock time: 36 minutes 55.61 seconds (2215.61 seconds total)