Starting phenix.real_space_refine on Thu Feb 13 13:18:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7op8_13014/02_2025/7op8_13014.cif Found real_map, /net/cci-nas-00/data/ceres_data/7op8_13014/02_2025/7op8_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_13014/02_2025/7op8_13014.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7op8_13014/02_2025/7op8_13014.map" model { file = "/net/cci-nas-00/data/ceres_data/7op8_13014/02_2025/7op8_13014.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7op8_13014/02_2025/7op8_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-5592/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: 5.95, per 1000 atoms: 0.67 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: 2.25 Conformation dependent library (CDL) restraints added in 958.2 milliseconds 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: 1.18 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: 3.18 Time building geometry restraints manager: 2.55 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.030 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.410 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.070 ------------------------------------------------------------------------------- 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 : 0.972 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: 0.1910 time to fit residues: 45.7803 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 : 0.919 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.200235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.161979 restraints weight = 13149.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.161734 restraints weight = 8502.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.164013 restraints weight = 8478.065| |-----------------------------------------------------------------------------| r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 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 : 0.944 Fit side-chains REVERT: A 221 SER cc_start: 0.7212 (t) cc_final: 0.6864 (t) REVERT: A 223 PHE cc_start: 0.7035 (m-80) cc_final: 0.6597 (m-80) REVERT: A 530 HIS cc_start: 0.6955 (OUTLIER) cc_final: 0.6448 (t-90) REVERT: A 975 GLU cc_start: 0.7199 (tm-30) cc_final: 0.6781 (tm-30) REVERT: A 1129 ASP cc_start: 0.7398 (p0) cc_final: 0.6859 (p0) REVERT: A 1231 MET cc_start: 0.7171 (mmm) cc_final: 0.6786 (mmm) outliers start: 17 outliers final: 12 residues processed: 149 average time/residue: 0.1691 time to fit residues: 38.2912 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 : 1.380 ------------------------------------------------------------------------------- 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 57 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 70 optimal weight: 0.0060 chunk 28 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 109 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 overall best weight: 1.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 ASN A1225 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.194477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.154822 restraints weight = 13457.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.157442 restraints weight = 7981.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.158520 restraints weight = 7340.892| |-----------------------------------------------------------------------------| r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9090 Z= 0.246 Angle : 0.591 7.387 12349 Z= 0.302 Chirality : 0.044 0.209 1408 Planarity : 0.004 0.045 1546 Dihedral : 4.717 21.573 1213 Min Nonbonded Distance : 1.328 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.46 % Allowed : 13.24 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.25), residues: 1100 helix: 0.61 (0.25), residues: 437 sheet: -1.35 (0.45), residues: 130 loop : -1.56 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 270 HIS 0.018 0.001 HIS A1225 PHE 0.027 0.001 PHE A1339 TYR 0.027 0.001 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 150 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.993 Fit side-chains REVERT: A 221 SER cc_start: 0.7266 (t) cc_final: 0.6872 (t) REVERT: A 223 PHE cc_start: 0.7135 (m-80) cc_final: 0.6724 (m-80) REVERT: A 530 HIS cc_start: 0.6915 (OUTLIER) cc_final: 0.6416 (t-90) REVERT: A 975 GLU cc_start: 0.7363 (tm-30) cc_final: 0.6964 (tm-30) REVERT: A 1129 ASP cc_start: 0.7511 (p0) cc_final: 0.6948 (p0) REVERT: A 1225 HIS cc_start: 0.8074 (OUTLIER) cc_final: 0.7314 (t70) REVERT: A 1231 MET cc_start: 0.7209 (mmm) cc_final: 0.6810 (mmm) REVERT: A 1344 PHE cc_start: 0.8507 (t80) cc_final: 0.8183 (t80) outliers start: 24 outliers final: 18 residues processed: 141 average time/residue: 0.1476 time to fit residues: 32.3987 Evaluate side-chains 145 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 527 THR Chi-restraints excluded: chain A residue 530 HIS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 676 LEU 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 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 98 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1225 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.193962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.155185 restraints weight = 13248.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.154750 restraints weight = 8764.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.156751 restraints weight = 7707.343| |-----------------------------------------------------------------------------| r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9090 Z= 0.206 Angle : 0.573 7.972 12349 Z= 0.291 Chirality : 0.043 0.197 1408 Planarity : 0.004 0.042 1546 Dihedral : 4.586 21.184 1213 Min Nonbonded Distance : 1.344 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.87 % Allowed : 15.30 % Favored : 81.83 % 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: 1100 helix: 0.76 (0.25), residues: 433 sheet: -1.35 (0.45), residues: 130 loop : -1.55 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 270 HIS 0.008 0.001 HIS A1225 PHE 0.020 0.001 PHE A1339 TYR 0.024 0.001 TYR A1088 ARG 0.006 0.000 ARG A1241 *********************** 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 156 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.944 Fit side-chains REVERT: A 221 SER cc_start: 0.7273 (t) cc_final: 0.6855 (t) REVERT: A 223 PHE cc_start: 0.7097 (m-80) cc_final: 0.6656 (m-80) REVERT: A 530 HIS cc_start: 0.6894 (OUTLIER) cc_final: 0.6404 (t-90) REVERT: A 975 GLU cc_start: 0.7375 (tm-30) cc_final: 0.7135 (tm-30) REVERT: A 1129 ASP cc_start: 0.7523 (p0) cc_final: 0.6976 (p0) REVERT: A 1135 GLU cc_start: 0.6109 (OUTLIER) cc_final: 0.5658 (mp0) REVERT: A 1225 HIS cc_start: 0.8048 (OUTLIER) cc_final: 0.7187 (t70) REVERT: A 1231 MET cc_start: 0.7214 (mmm) cc_final: 0.6787 (mmm) REVERT: A 1344 PHE cc_start: 0.8512 (t80) cc_final: 0.8302 (t80) outliers start: 28 outliers final: 20 residues processed: 147 average time/residue: 0.1548 time to fit residues: 35.0892 Evaluate side-chains 141 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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 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 1133 VAL Chi-restraints excluded: chain A residue 1135 GLU 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 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 90 optimal weight: 0.0570 chunk 101 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 chunk 97 optimal weight: 0.4980 chunk 43 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.3104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 HIS A1225 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.190043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.150958 restraints weight = 13328.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.150592 restraints weight = 9149.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.152210 restraints weight = 7914.647| |-----------------------------------------------------------------------------| r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 9090 Z= 0.282 Angle : 0.607 9.355 12349 Z= 0.309 Chirality : 0.045 0.212 1408 Planarity : 0.004 0.051 1546 Dihedral : 4.695 22.440 1213 Min Nonbonded Distance : 1.304 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 3.08 % Allowed : 16.53 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.25), residues: 1100 helix: 0.72 (0.25), residues: 434 sheet: -1.54 (0.44), residues: 132 loop : -1.56 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 785 HIS 0.023 0.002 HIS A1225 PHE 0.016 0.001 PHE A1339 TYR 0.035 0.002 TYR A1088 ARG 0.002 0.000 ARG A1288 *********************** 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 155 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.945 Fit side-chains REVERT: A 221 SER cc_start: 0.7427 (t) cc_final: 0.7011 (t) REVERT: A 223 PHE cc_start: 0.7214 (m-80) cc_final: 0.6802 (m-80) REVERT: A 530 HIS cc_start: 0.6868 (OUTLIER) cc_final: 0.6387 (t-90) REVERT: A 975 GLU cc_start: 0.7494 (tm-30) cc_final: 0.7226 (tm-30) REVERT: A 1135 GLU cc_start: 0.6228 (OUTLIER) cc_final: 0.5710 (mp0) REVERT: A 1231 MET cc_start: 0.7377 (mmm) cc_final: 0.6952 (mmm) outliers start: 30 outliers final: 23 residues processed: 143 average time/residue: 0.1717 time to fit residues: 37.4181 Evaluate side-chains 142 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 TRP 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 5 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 14 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4395 r_free = 0.4395 target = 0.192059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.153653 restraints weight = 13288.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.156812 restraints weight = 7873.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.157593 restraints weight = 7092.513| |-----------------------------------------------------------------------------| r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2243 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= 0.185 Angle : 0.571 7.359 12349 Z= 0.289 Chirality : 0.043 0.189 1408 Planarity : 0.004 0.038 1546 Dihedral : 4.549 21.421 1213 Min Nonbonded Distance : 1.367 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.46 % Allowed : 18.38 % Favored : 79.16 % 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: 0.87 (0.25), residues: 433 sheet: -1.54 (0.44), residues: 132 loop : -1.47 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 785 HIS 0.016 0.001 HIS A 367 PHE 0.024 0.001 PHE A1344 TYR 0.024 0.001 TYR A1088 ARG 0.002 0.000 ARG A 696 *********************** 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 151 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.924 Fit side-chains REVERT: A 221 SER cc_start: 0.7338 (t) cc_final: 0.6897 (t) REVERT: A 223 PHE cc_start: 0.7103 (m-80) cc_final: 0.6680 (m-80) REVERT: A 903 ILE cc_start: 0.7843 (mm) cc_final: 0.7604 (mm) REVERT: A 975 GLU cc_start: 0.7462 (tm-30) cc_final: 0.7223 (tm-30) REVERT: A 1135 GLU cc_start: 0.6132 (OUTLIER) cc_final: 0.5622 (mp0) REVERT: A 1225 HIS cc_start: 0.7977 (OUTLIER) cc_final: 0.7353 (t70) REVERT: A 1231 MET cc_start: 0.7272 (mmm) cc_final: 0.6841 (mmm) REVERT: A 1348 TRP cc_start: 0.7668 (t60) cc_final: 0.7437 (t60) outliers start: 24 outliers final: 21 residues processed: 141 average time/residue: 0.1563 time to fit residues: 33.6505 Evaluate side-chains 143 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.995 ------------------------------------------------------------------------------- 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 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 1071 MET 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 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 24 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 98 optimal weight: 0.0170 chunk 53 optimal weight: 5.9990 chunk 7 optimal weight: 0.0030 chunk 33 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 50 optimal weight: 0.0770 chunk 91 optimal weight: 5.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.192323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.154650 restraints weight = 13390.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.154161 restraints weight = 8721.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.156257 restraints weight = 7708.009| |-----------------------------------------------------------------------------| r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9090 Z= 0.184 Angle : 0.583 10.245 12349 Z= 0.292 Chirality : 0.042 0.188 1408 Planarity : 0.004 0.037 1546 Dihedral : 4.463 21.530 1213 Min Nonbonded Distance : 1.384 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.57 % Allowed : 19.40 % Favored : 78.03 % 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: -0.80 (0.25), residues: 1100 helix: 0.89 (0.25), residues: 435 sheet: -1.50 (0.44), residues: 132 loop : -1.49 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 785 HIS 0.012 0.001 HIS A 367 PHE 0.016 0.001 PHE A1344 TYR 0.029 0.001 TYR A 397 ARG 0.004 0.000 ARG A 594 *********************** 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 150 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.783 Fit side-chains REVERT: A 221 SER cc_start: 0.7393 (t) cc_final: 0.6944 (t) REVERT: A 223 PHE cc_start: 0.7119 (m-80) cc_final: 0.6680 (m-80) REVERT: A 903 ILE cc_start: 0.7764 (mm) cc_final: 0.7526 (mm) REVERT: A 975 GLU cc_start: 0.7483 (tm-30) cc_final: 0.7234 (tm-30) REVERT: A 1088 TYR cc_start: 0.8526 (OUTLIER) cc_final: 0.6611 (t80) REVERT: A 1135 GLU cc_start: 0.6051 (OUTLIER) cc_final: 0.5600 (mp0) REVERT: A 1225 HIS cc_start: 0.7965 (OUTLIER) cc_final: 0.7200 (t70) REVERT: A 1231 MET cc_start: 0.7277 (mmm) cc_final: 0.6840 (mmm) REVERT: A 1394 GLN cc_start: 0.6583 (mp10) cc_final: 0.6260 (mt0) outliers start: 25 outliers final: 19 residues processed: 141 average time/residue: 0.1586 time to fit residues: 34.3668 Evaluate side-chains 139 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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 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 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 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 82 optimal weight: 0.0470 chunk 10 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 22 optimal weight: 8.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- 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 = 0.4383 r_free = 0.4383 target = 0.190850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.152427 restraints weight = 13534.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.154229 restraints weight = 8017.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.155492 restraints weight = 7865.191| |-----------------------------------------------------------------------------| r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9090 Z= 0.221 Angle : 0.594 8.102 12349 Z= 0.297 Chirality : 0.043 0.197 1408 Planarity : 0.004 0.036 1546 Dihedral : 4.481 21.980 1213 Min Nonbonded Distance : 1.360 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 3.08 % Allowed : 19.92 % 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: -0.79 (0.25), residues: 1100 helix: 0.91 (0.25), residues: 435 sheet: -1.52 (0.44), residues: 132 loop : -1.49 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1245 HIS 0.009 0.001 HIS A1225 PHE 0.026 0.001 PHE A1339 TYR 0.028 0.001 TYR A1088 ARG 0.002 0.000 ARG A 594 *********************** 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: 30 poor density : 125 time to evaluate : 0.978 Fit side-chains REVERT: A 221 SER cc_start: 0.7434 (t) cc_final: 0.7004 (t) REVERT: A 223 PHE cc_start: 0.7117 (m-80) cc_final: 0.6691 (m-80) REVERT: A 903 ILE cc_start: 0.7833 (mm) cc_final: 0.7604 (mm) REVERT: A 1088 TYR cc_start: 0.8610 (OUTLIER) cc_final: 0.6826 (t80) REVERT: A 1135 GLU cc_start: 0.6088 (OUTLIER) cc_final: 0.5622 (mp0) REVERT: A 1225 HIS cc_start: 0.8003 (OUTLIER) cc_final: 0.7196 (t70) REVERT: A 1231 MET cc_start: 0.7294 (mmm) cc_final: 0.6877 (mmm) REVERT: A 1394 GLN cc_start: 0.6688 (mp10) cc_final: 0.6414 (mt0) outliers start: 30 outliers final: 21 residues processed: 144 average time/residue: 0.1633 time to fit residues: 35.7722 Evaluate side-chains 145 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 TRP 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 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 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 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 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 53 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 41 optimal weight: 10.0000 chunk 79 optimal weight: 0.4980 chunk 4 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4397 r_free = 0.4397 target = 0.192374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.153956 restraints weight = 13349.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.155664 restraints weight = 7999.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.156933 restraints weight = 7880.692| |-----------------------------------------------------------------------------| r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2498 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= 0.210 Angle : 0.610 12.668 12349 Z= 0.302 Chirality : 0.043 0.195 1408 Planarity : 0.004 0.036 1546 Dihedral : 4.489 21.968 1213 Min Nonbonded Distance : 1.377 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 2.77 % Allowed : 20.64 % 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: -0.79 (0.25), residues: 1100 helix: 0.91 (0.25), residues: 435 sheet: -1.54 (0.44), residues: 132 loop : -1.48 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1245 HIS 0.002 0.000 HIS A 276 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 150 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.900 Fit side-chains REVERT: A 221 SER cc_start: 0.7427 (t) cc_final: 0.6988 (t) REVERT: A 223 PHE cc_start: 0.7144 (m-80) cc_final: 0.6714 (m-80) REVERT: A 530 HIS cc_start: 0.6872 (OUTLIER) cc_final: 0.6403 (t-90) REVERT: A 903 ILE cc_start: 0.7828 (mm) cc_final: 0.7601 (mm) REVERT: A 1088 TYR cc_start: 0.8565 (OUTLIER) cc_final: 0.6696 (t80) REVERT: A 1135 GLU cc_start: 0.6087 (OUTLIER) cc_final: 0.5627 (mp0) REVERT: A 1225 HIS cc_start: 0.7979 (OUTLIER) cc_final: 0.7186 (t70) REVERT: A 1231 MET cc_start: 0.7292 (mmm) cc_final: 0.6883 (mmm) outliers start: 27 outliers final: 22 residues processed: 140 average time/residue: 0.1627 time to fit residues: 34.9905 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 : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 TRP 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 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 943 ILE Chi-restraints excluded: chain A residue 971 CYS 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 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 74 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 68 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 34 optimal weight: 0.1980 chunk 12 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 29 optimal weight: 0.4980 chunk 9 optimal weight: 0.9980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.192887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.154465 restraints weight = 13425.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.156218 restraints weight = 8088.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.157523 restraints weight = 7787.757| |-----------------------------------------------------------------------------| r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9090 Z= 0.196 Angle : 0.608 11.957 12349 Z= 0.301 Chirality : 0.043 0.192 1408 Planarity : 0.004 0.035 1546 Dihedral : 4.442 21.808 1213 Min Nonbonded Distance : 1.398 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.46 % Allowed : 21.36 % Favored : 76.18 % 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: -0.77 (0.25), residues: 1100 helix: 0.90 (0.25), residues: 436 sheet: -1.53 (0.44), residues: 132 loop : -1.45 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1245 HIS 0.001 0.000 HIS A 276 PHE 0.031 0.001 PHE A1339 TYR 0.025 0.001 TYR A1088 ARG 0.006 0.000 ARG A 594 ********************** 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 148 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 1.079 Fit side-chains REVERT: A 221 SER cc_start: 0.7420 (t) cc_final: 0.6990 (t) REVERT: A 223 PHE cc_start: 0.7132 (m-80) cc_final: 0.6705 (m-80) REVERT: A 530 HIS cc_start: 0.6859 (OUTLIER) cc_final: 0.6391 (t-90) REVERT: A 903 ILE cc_start: 0.7825 (mm) cc_final: 0.7600 (mm) REVERT: A 1088 TYR cc_start: 0.8526 (OUTLIER) cc_final: 0.6660 (t80) REVERT: A 1135 GLU cc_start: 0.6070 (OUTLIER) cc_final: 0.5619 (mp0) REVERT: A 1231 MET cc_start: 0.7239 (mmm) cc_final: 0.6839 (mmm) outliers start: 24 outliers final: 21 residues processed: 139 average time/residue: 0.1624 time to fit residues: 34.6704 Evaluate side-chains 148 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 971 CYS 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 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 24 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 19 optimal weight: 0.0470 chunk 56 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.192613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.154710 restraints weight = 13310.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.156581 restraints weight = 8089.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.157780 restraints weight = 7843.825| |-----------------------------------------------------------------------------| r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9090 Z= 0.182 Angle : 0.601 11.332 12349 Z= 0.297 Chirality : 0.043 0.186 1408 Planarity : 0.004 0.035 1546 Dihedral : 4.373 21.627 1213 Min Nonbonded Distance : 1.424 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.26 % Allowed : 21.77 % Favored : 75.98 % 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: -0.72 (0.25), residues: 1100 helix: 0.95 (0.25), residues: 435 sheet: -1.48 (0.45), residues: 132 loop : -1.43 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1245 HIS 0.002 0.000 HIS A1225 PHE 0.025 0.001 PHE A1339 TYR 0.025 0.001 TYR A 251 ARG 0.006 0.000 ARG A 594 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2595.01 seconds wall clock time: 47 minutes 42.26 seconds (2862.26 seconds total)