Starting phenix.real_space_refine on Wed Feb 14 17:36:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3f_21035/02_2024/6v3f_21035_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3f_21035/02_2024/6v3f_21035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3f_21035/02_2024/6v3f_21035.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3f_21035/02_2024/6v3f_21035.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3f_21035/02_2024/6v3f_21035_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3f_21035/02_2024/6v3f_21035_updated.pdb" } resolution = 3.7 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= 0.002 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: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 6351 2.51 5 N 1603 2.21 5 O 1838 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 28": "OE1" <-> "OE2" Residue "A GLU 100": "OE1" <-> "OE2" Residue "A GLU 149": "OE1" <-> "OE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A GLU 270": "OE1" <-> "OE2" Residue "A GLU 374": "OE1" <-> "OE2" Residue "A GLU 381": "OE1" <-> "OE2" Residue "A GLU 663": "OE1" <-> "OE2" Residue "A GLU 730": "OE1" <-> "OE2" Residue "A GLU 803": "OE1" <-> "OE2" Residue "A PHE 1094": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1112": "OE1" <-> "OE2" Residue "A GLU 1200": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9855 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1234, 9575 Classifications: {'peptide': 1234} Link IDs: {'PTRANS': 68, 'TRANS': 1165} Chain breaks: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 168 Unusual residues: {'CLR': 1, 'NAG': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 6.10, per 1000 atoms: 0.62 Number of scatterers: 9855 At special positions: 0 Unit cell: (99.992, 149.126, 104.302, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 1838 8.00 N 1603 7.00 C 6351 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 32 " - pdb=" SG CYS A 90 " distance=2.02 Simple disulfide: pdb=" SG CYS A 38 " - pdb=" SG CYS A 56 " distance=2.03 Simple disulfide: pdb=" SG CYS A 77 " - pdb=" SG CYS A 125 " distance=2.05 Simple disulfide: pdb=" SG CYS A 91 " - pdb=" SG CYS A 129 " distance=2.05 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 254 " distance=2.04 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 172 " distance=2.04 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 197 " distance=2.02 Simple disulfide: pdb=" SG CYS A 243 " - pdb=" SG CYS A 259 " distance=2.04 Simple disulfide: pdb=" SG CYS A 256 " - pdb=" SG CYS A 263 " distance=2.04 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 525 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS A1025 " distance=2.03 Simple disulfide: pdb=" SG CYS A 968 " - pdb=" SG CYS A 994 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1401 " - " ASN A 53 " " NAG A1402 " - " ASN A 138 " " NAG A1403 " - " ASN A 244 " " NAG A1404 " - " ASN A 416 " " NAG A1405 " - " ASN A 431 " " NAG A1406 " - " ASN A 464 " " NAG A1411 " - " ASN A 606 " " NAG A1414 " - " ASN A 917 " " NAG A1415 " - " ASN A 996 " " NAG A1418 " - " ASN A1076 " " NAG B 1 " - " ASN A 497 " " NAG C 1 " - " ASN A 506 " " NAG D 1 " - " ASN A 909 " " NAG E 1 " - " ASN A1038 " Time building additional restraints: 4.18 Conformation dependent library (CDL) restraints added in 2.0 seconds 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2326 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 6 sheets defined 53.6% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.92 Creating SS restraints... Processing helix chain 'A' and resid 67 through 76 Processing helix chain 'A' and resid 78 through 80 No H-bonds generated for 'chain 'A' and resid 78 through 80' Processing helix chain 'A' and resid 93 through 109 removed outlier: 4.640A pdb=" N ILE A 105 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N THR A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 129 Proline residue: A 114 - end of helix removed outlier: 4.232A pdb=" N ASP A 118 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N HIS A 126 " --> pdb=" O LEU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 162 through 171 Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 199 through 206 Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 256 through 259 No H-bonds generated for 'chain 'A' and resid 256 through 259' Processing helix chain 'A' and resid 283 through 312 removed outlier: 3.770A pdb=" N VAL A 294 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 299 " --> pdb=" O PHE A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 372 removed outlier: 3.654A pdb=" N TRP A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Proline residue: A 352 - end of helix removed outlier: 3.658A pdb=" N VAL A 355 " --> pdb=" O TRP A 351 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N GLY A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N LEU A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N THR A 371 " --> pdb=" O ALA A 367 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N PHE A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 382 No H-bonds generated for 'chain 'A' and resid 379 through 382' Processing helix chain 'A' and resid 389 through 401 Processing helix chain 'A' and resid 434 through 436 No H-bonds generated for 'chain 'A' and resid 434 through 436' Processing helix chain 'A' and resid 438 through 453 removed outlier: 3.747A pdb=" N LEU A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A 443 " --> pdb=" O ASP A 439 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS A 453 " --> pdb=" O GLU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 469 No H-bonds generated for 'chain 'A' and resid 467 through 469' Processing helix chain 'A' and resid 482 through 484 No H-bonds generated for 'chain 'A' and resid 482 through 484' Processing helix chain 'A' and resid 490 through 494 Processing helix chain 'A' and resid 498 through 502 removed outlier: 3.533A pdb=" N MET A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 498 through 502' Processing helix chain 'A' and resid 518 through 527 removed outlier: 3.679A pdb=" N ASN A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 554 No H-bonds generated for 'chain 'A' and resid 552 through 554' Processing helix chain 'A' and resid 564 through 566 No H-bonds generated for 'chain 'A' and resid 564 through 566' Processing helix chain 'A' and resid 584 through 606 Processing helix chain 'A' and resid 620 through 650 removed outlier: 3.818A pdb=" N ASN A 626 " --> pdb=" O GLU A 622 " (cutoff:3.500A) Proline residue: A 634 - end of helix removed outlier: 3.613A pdb=" N ILE A 641 " --> pdb=" O ALA A 637 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL A 643 " --> pdb=" O SER A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 663 No H-bonds generated for 'chain 'A' and resid 660 through 663' Processing helix chain 'A' and resid 666 through 690 Processing helix chain 'A' and resid 696 through 723 Proline residue: A 703 - end of helix removed outlier: 3.962A pdb=" N VAL A 709 " --> pdb=" O LEU A 705 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ASP A 712 " --> pdb=" O ALA A 708 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASN A 713 " --> pdb=" O VAL A 709 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ILE A 714 " --> pdb=" O GLY A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 761 Proline residue: A 745 - end of helix Processing helix chain 'A' and resid 767 through 787 removed outlier: 3.685A pdb=" N ILE A 781 " --> pdb=" O GLY A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 803 Processing helix chain 'A' and resid 827 through 834 Processing helix chain 'A' and resid 836 through 840 Processing helix chain 'A' and resid 846 through 865 removed outlier: 4.767A pdb=" N CYS A 865 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 876 Processing helix chain 'A' and resid 882 through 893 Processing helix chain 'A' and resid 913 through 917 Processing helix chain 'A' and resid 930 through 939 removed outlier: 3.572A pdb=" N GLU A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 961 Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 1006 through 1018 Proline residue: A1014 - end of helix removed outlier: 3.821A pdb=" N ASN A1018 " --> pdb=" O PRO A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1060 through 1083 removed outlier: 4.582A pdb=" N LYS A1083 " --> pdb=" O ALA A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1106 removed outlier: 4.236A pdb=" N VAL A1101 " --> pdb=" O ILE A1098 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE A1102 " --> pdb=" O SER A1099 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLN A1104 " --> pdb=" O VAL A1101 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN A1105 " --> pdb=" O PHE A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1131 removed outlier: 4.025A pdb=" N PHE A1121 " --> pdb=" O LEU A1117 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N VAL A1122 " --> pdb=" O ALA A1118 " (cutoff:3.500A) Proline residue: A1123 - end of helix Processing helix chain 'A' and resid 1136 through 1159 Processing helix chain 'A' and resid 1166 through 1191 removed outlier: 4.126A pdb=" N VAL A1180 " --> pdb=" O VAL A1176 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLU A1181 " --> pdb=" O GLY A1177 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE A1182 " --> pdb=" O MET A1178 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N HIS A1185 " --> pdb=" O GLU A1181 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ILE A1186 " --> pdb=" O PHE A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1230 removed outlier: 3.652A pdb=" N LYS A1203 " --> pdb=" O LEU A1199 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP A1204 " --> pdb=" O GLU A1200 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A1205 " --> pdb=" O ARG A1201 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N MET A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) Proline residue: A1223 - end of helix removed outlier: 3.780A pdb=" N ILE A1227 " --> pdb=" O PRO A1223 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU A1228 " --> pdb=" O GLY A1224 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY A1229 " --> pdb=" O ILE A1225 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N PHE A1230 " --> pdb=" O LEU A1226 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1239 Processing helix chain 'A' and resid 1241 through 1256 Processing helix chain 'A' and resid 1258 through 1266 Processing helix chain 'A' and resid 1272 through 1280 Processing sheet with id= A, first strand: chain 'A' and resid 137 through 139 removed outlier: 6.275A pdb=" N ASP A 217 " --> pdb=" O TYR A 156 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ALA A 158 " --> pdb=" O ASP A 217 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N THR A 219 " --> pdb=" O ALA A 158 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N TYR A 160 " --> pdb=" O THR A 219 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N HIS A 221 " --> pdb=" O TYR A 160 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 569 through 576 Processing sheet with id= C, first strand: chain 'A' and resid 420 through 424 Processing sheet with id= D, first strand: chain 'A' and resid 456 through 458 Processing sheet with id= E, first strand: chain 'A' and resid 505 through 509 Processing sheet with id= F, first strand: chain 'A' and resid 1093 through 1096 removed outlier: 6.993A pdb=" N ASN A1038 " --> pdb=" O ILE A1046 " (cutoff:3.500A) 440 hydrogen bonds defined for protein. 1191 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: 3.06 Time building geometry restraints manager: 4.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3080 1.35 - 1.47: 2555 1.47 - 1.60: 4364 1.60 - 1.72: 0 1.72 - 1.85: 87 Bond restraints: 10086 Sorted by residual: bond pdb=" C1 NAG A1404 " pdb=" O5 NAG A1404 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.73e+00 bond pdb=" C17 CLR A1419 " pdb=" C20 CLR A1419 " ideal model delta sigma weight residual 1.535 1.590 -0.055 2.00e-02 2.50e+03 7.52e+00 bond pdb=" C1 NAG A1403 " pdb=" O5 NAG A1403 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.64e+00 bond pdb=" C1 NAG A1405 " pdb=" O5 NAG A1405 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.54e+00 bond pdb=" C1 NAG A1411 " pdb=" O5 NAG A1411 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.34e+00 ... (remaining 10081 not shown) Histogram of bond angle deviations from ideal: 98.65 - 105.92: 273 105.92 - 113.19: 5366 113.19 - 120.47: 4304 120.47 - 127.74: 3701 127.74 - 135.02: 92 Bond angle restraints: 13736 Sorted by residual: angle pdb=" CA CYS A 113 " pdb=" CB CYS A 113 " pdb=" SG CYS A 113 " ideal model delta sigma weight residual 114.40 127.59 -13.19 2.30e+00 1.89e-01 3.29e+01 angle pdb=" CA LEU A 48 " pdb=" CB LEU A 48 " pdb=" CG LEU A 48 " ideal model delta sigma weight residual 116.30 134.32 -18.02 3.50e+00 8.16e-02 2.65e+01 angle pdb=" C HIS A 453 " pdb=" N LEU A 454 " pdb=" CA LEU A 454 " ideal model delta sigma weight residual 121.31 128.66 -7.35 1.49e+00 4.50e-01 2.44e+01 angle pdb=" C SER A 655 " pdb=" N ARG A 656 " pdb=" CA ARG A 656 " ideal model delta sigma weight residual 121.54 130.89 -9.35 1.91e+00 2.74e-01 2.40e+01 angle pdb=" C ALA A 228 " pdb=" N LEU A 229 " pdb=" CA LEU A 229 " ideal model delta sigma weight residual 121.80 133.55 -11.75 2.44e+00 1.68e-01 2.32e+01 ... (remaining 13731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 5933 17.21 - 34.42: 288 34.42 - 51.62: 73 51.62 - 68.83: 26 68.83 - 86.04: 5 Dihedral angle restraints: 6325 sinusoidal: 2726 harmonic: 3599 Sorted by residual: dihedral pdb=" CB CYS A 38 " pdb=" SG CYS A 38 " pdb=" SG CYS A 56 " pdb=" CB CYS A 56 " ideal model delta sinusoidal sigma weight residual -86.00 -171.22 85.22 1 1.00e+01 1.00e-02 8.80e+01 dihedral pdb=" CB CYS A 243 " pdb=" SG CYS A 243 " pdb=" SG CYS A 259 " pdb=" CB CYS A 259 " ideal model delta sinusoidal sigma weight residual 93.00 158.01 -65.01 1 1.00e+01 1.00e-02 5.54e+01 dihedral pdb=" CB CYS A 77 " pdb=" SG CYS A 77 " pdb=" SG CYS A 125 " pdb=" CB CYS A 125 " ideal model delta sinusoidal sigma weight residual 93.00 140.19 -47.19 1 1.00e+01 1.00e-02 3.08e+01 ... (remaining 6322 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 1541 0.124 - 0.248: 93 0.248 - 0.372: 5 0.372 - 0.496: 1 0.496 - 0.620: 1 Chirality restraints: 1641 Sorted by residual: chirality pdb=" C1 NAG A1404 " pdb=" ND2 ASN A 416 " pdb=" C2 NAG A1404 " pdb=" O5 NAG A1404 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.60e+00 chirality pdb=" C1 NAG A1405 " pdb=" ND2 ASN A 431 " pdb=" C2 NAG A1405 " pdb=" O5 NAG A1405 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.19e+00 chirality pdb=" C2 NAG D 2 " pdb=" C1 NAG D 2 " pdb=" C3 NAG D 2 " pdb=" N2 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.13 -0.36 2.00e-01 2.50e+01 3.20e+00 ... (remaining 1638 not shown) Planarity restraints: 1738 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 113 " -0.019 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C CYS A 113 " 0.064 2.00e-02 2.50e+03 pdb=" O CYS A 113 " -0.024 2.00e-02 2.50e+03 pdb=" N PRO A 114 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 126 " -0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C HIS A 126 " 0.060 2.00e-02 2.50e+03 pdb=" O HIS A 126 " -0.023 2.00e-02 2.50e+03 pdb=" N ASN A 127 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 286 " -0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C ALA A 286 " 0.059 2.00e-02 2.50e+03 pdb=" O ALA A 286 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU A 287 " -0.020 2.00e-02 2.50e+03 ... (remaining 1735 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2381 2.81 - 3.33: 9317 3.33 - 3.85: 15481 3.85 - 4.38: 16772 4.38 - 4.90: 30104 Nonbonded interactions: 74055 Sorted by model distance: nonbonded pdb=" O ALA A 108 " pdb=" OG1 THR A 111 " model vdw 2.285 2.440 nonbonded pdb=" O ASN A 119 " pdb=" OG SER A 122 " model vdw 2.288 2.440 nonbonded pdb=" N ASP A 872 " pdb=" OD1 ASP A 872 " model vdw 2.297 2.520 nonbonded pdb=" OG SER A 437 " pdb=" OD1 ASP A 439 " model vdw 2.316 2.440 nonbonded pdb=" OD2 ASP A 956 " pdb=" OH TYR A1033 " model vdw 2.319 2.440 ... (remaining 74050 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 2.080 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: 7.400 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 30.480 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 10086 Z= 0.436 Angle : 1.177 18.024 13736 Z= 0.653 Chirality : 0.067 0.620 1641 Planarity : 0.008 0.044 1724 Dihedral : 11.527 86.038 3960 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.44 % Favored : 97.31 % Rotamer: Outliers : 1.04 % Allowed : 4.16 % Favored : 94.80 % 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: 1.13 (0.23), residues: 1228 helix: 1.42 (0.19), residues: 628 sheet: 0.70 (0.57), residues: 80 loop : 0.04 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP A 202 HIS 0.010 0.003 HIS A 453 PHE 0.022 0.003 PHE A 411 TYR 0.031 0.003 TYR A 689 ARG 0.011 0.001 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 136 time to evaluate : 1.104 Fit side-chains revert: symmetry clash REVERT: A 124 HIS cc_start: 0.7794 (m-70) cc_final: 0.7578 (m-70) REVERT: A 156 TYR cc_start: 0.8362 (p90) cc_final: 0.7938 (p90) REVERT: A 290 ILE cc_start: 0.8637 (mm) cc_final: 0.8431 (mt) REVERT: A 1144 LEU cc_start: 0.9009 (mt) cc_final: 0.8795 (mt) REVERT: A 1148 MET cc_start: 0.8534 (mtp) cc_final: 0.8314 (mtp) outliers start: 11 outliers final: 8 residues processed: 146 average time/residue: 0.2401 time to fit residues: 47.8229 Evaluate side-chains 83 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 75 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 872 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 96 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 111 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 GLN A 860 ASN A1010 HIS A1142 ASN A1234 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10086 Z= 0.240 Angle : 0.692 10.722 13736 Z= 0.342 Chirality : 0.044 0.281 1641 Planarity : 0.005 0.041 1724 Dihedral : 7.424 58.682 1783 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.44 % Favored : 97.48 % Rotamer: Outliers : 1.89 % Allowed : 8.99 % Favored : 89.12 % 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: 1.41 (0.24), residues: 1228 helix: 1.78 (0.20), residues: 621 sheet: 0.43 (0.55), residues: 82 loop : 0.07 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 202 HIS 0.005 0.001 HIS A 124 PHE 0.018 0.002 PHE A 411 TYR 0.016 0.001 TYR A 646 ARG 0.005 0.001 ARG A 726 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 85 time to evaluate : 1.160 Fit side-chains revert: symmetry clash REVERT: A 1144 LEU cc_start: 0.9013 (mt) cc_final: 0.8790 (mt) REVERT: A 1148 MET cc_start: 0.8462 (mtp) cc_final: 0.8129 (mtp) REVERT: A 1152 ASP cc_start: 0.8256 (m-30) cc_final: 0.7991 (m-30) outliers start: 20 outliers final: 13 residues processed: 100 average time/residue: 0.1757 time to fit residues: 27.3225 Evaluate side-chains 80 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 67 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 868 ASN Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 1130 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 0.5980 chunk 34 optimal weight: 6.9990 chunk 92 optimal weight: 0.1980 chunk 76 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 631 GLN A 860 ASN A1010 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10086 Z= 0.155 Angle : 0.595 12.222 13736 Z= 0.291 Chirality : 0.041 0.257 1641 Planarity : 0.004 0.037 1724 Dihedral : 6.601 57.539 1780 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.01 % Favored : 96.91 % Rotamer: Outliers : 1.89 % Allowed : 9.56 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.24), residues: 1228 helix: 1.79 (0.20), residues: 619 sheet: 0.45 (0.56), residues: 82 loop : 0.10 (0.28), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 202 HIS 0.012 0.001 HIS A 124 PHE 0.013 0.001 PHE A 205 TYR 0.021 0.001 TYR A 936 ARG 0.006 0.000 ARG A 726 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 80 time to evaluate : 1.156 Fit side-chains revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8473 (mmmt) cc_final: 0.7689 (tmtt) REVERT: A 1144 LEU cc_start: 0.8990 (mt) cc_final: 0.8786 (mt) REVERT: A 1148 MET cc_start: 0.8436 (mtp) cc_final: 0.7849 (mtp) REVERT: A 1152 ASP cc_start: 0.8252 (m-30) cc_final: 0.7937 (m-30) outliers start: 20 outliers final: 10 residues processed: 95 average time/residue: 0.1728 time to fit residues: 26.0114 Evaluate side-chains 81 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 71 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 1130 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 12 optimal weight: 20.0000 chunk 53 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 ASN A1010 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10086 Z= 0.253 Angle : 0.621 9.638 13736 Z= 0.306 Chirality : 0.043 0.270 1641 Planarity : 0.004 0.039 1724 Dihedral : 6.385 57.077 1777 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.26 % Favored : 96.66 % Rotamer: Outliers : 2.84 % Allowed : 10.31 % Favored : 86.85 % 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: 1.12 (0.24), residues: 1228 helix: 1.56 (0.21), residues: 629 sheet: 0.25 (0.55), residues: 82 loop : -0.11 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 202 HIS 0.005 0.001 HIS A1054 PHE 0.016 0.002 PHE A 411 TYR 0.014 0.002 TYR A 689 ARG 0.002 0.000 ARG A 973 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 79 time to evaluate : 1.137 Fit side-chains revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8477 (mmmt) cc_final: 0.7719 (tmtt) REVERT: A 1144 LEU cc_start: 0.9038 (mt) cc_final: 0.8765 (mt) REVERT: A 1148 MET cc_start: 0.8496 (mtp) cc_final: 0.8025 (mtm) REVERT: A 1152 ASP cc_start: 0.8308 (m-30) cc_final: 0.8074 (m-30) outliers start: 30 outliers final: 20 residues processed: 101 average time/residue: 0.1674 time to fit residues: 26.6317 Evaluate side-chains 92 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 72 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 868 ASN Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1253 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 60 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 860 ASN A1010 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10086 Z= 0.209 Angle : 0.585 9.930 13736 Z= 0.286 Chirality : 0.042 0.263 1641 Planarity : 0.004 0.042 1724 Dihedral : 6.210 56.589 1777 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.26 % Favored : 96.66 % Rotamer: Outliers : 2.37 % Allowed : 11.92 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.24), residues: 1228 helix: 1.53 (0.21), residues: 632 sheet: 0.43 (0.56), residues: 80 loop : -0.25 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 202 HIS 0.003 0.001 HIS A1054 PHE 0.013 0.001 PHE A 411 TYR 0.014 0.001 TYR A 646 ARG 0.002 0.000 ARG A 75 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 71 time to evaluate : 1.189 Fit side-chains revert: symmetry clash REVERT: A 1144 LEU cc_start: 0.9012 (mt) cc_final: 0.8747 (mt) REVERT: A 1148 MET cc_start: 0.8494 (mtp) cc_final: 0.8000 (mtm) REVERT: A 1152 ASP cc_start: 0.8259 (m-30) cc_final: 0.8040 (m-30) outliers start: 25 outliers final: 21 residues processed: 91 average time/residue: 0.1630 time to fit residues: 23.6538 Evaluate side-chains 89 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 68 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 1051 MET Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1253 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 119 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 9 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 62 optimal weight: 0.0770 chunk 114 optimal weight: 0.4980 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 257 GLN A 527 ASN A1010 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10086 Z= 0.130 Angle : 0.567 11.837 13736 Z= 0.268 Chirality : 0.040 0.247 1641 Planarity : 0.004 0.043 1724 Dihedral : 5.896 56.938 1777 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.34 % Favored : 96.58 % Rotamer: Outliers : 2.18 % Allowed : 12.58 % Favored : 85.24 % 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: 1.27 (0.24), residues: 1228 helix: 1.73 (0.21), residues: 625 sheet: 0.60 (0.57), residues: 80 loop : -0.15 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 202 HIS 0.004 0.001 HIS A 126 PHE 0.011 0.001 PHE A 411 TYR 0.020 0.001 TYR A 862 ARG 0.002 0.000 ARG A 997 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 76 time to evaluate : 1.037 Fit side-chains REVERT: A 1148 MET cc_start: 0.8445 (mtp) cc_final: 0.8057 (mtm) outliers start: 23 outliers final: 15 residues processed: 95 average time/residue: 0.1732 time to fit residues: 25.9409 Evaluate side-chains 83 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 68 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1253 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN A 860 ASN A1010 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10086 Z= 0.149 Angle : 0.565 10.480 13736 Z= 0.269 Chirality : 0.040 0.250 1641 Planarity : 0.004 0.044 1724 Dihedral : 5.827 56.590 1777 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.34 % Favored : 96.58 % Rotamer: Outliers : 1.70 % Allowed : 13.72 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.24), residues: 1228 helix: 1.76 (0.21), residues: 622 sheet: 0.63 (0.57), residues: 80 loop : -0.16 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 202 HIS 0.003 0.001 HIS A 126 PHE 0.026 0.001 PHE A 717 TYR 0.016 0.001 TYR A 646 ARG 0.004 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 74 time to evaluate : 1.081 Fit side-chains REVERT: A 1148 MET cc_start: 0.8336 (mtp) cc_final: 0.8116 (mtp) outliers start: 18 outliers final: 16 residues processed: 89 average time/residue: 0.1611 time to fit residues: 23.8103 Evaluate side-chains 89 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 73 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1253 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 23 optimal weight: 0.3980 chunk 22 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 58 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10086 Z= 0.218 Angle : 0.598 9.649 13736 Z= 0.288 Chirality : 0.042 0.263 1641 Planarity : 0.004 0.046 1724 Dihedral : 5.950 56.859 1775 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.34 % Favored : 96.58 % Rotamer: Outliers : 2.08 % Allowed : 13.53 % Favored : 84.39 % 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: 1.08 (0.24), residues: 1228 helix: 1.62 (0.21), residues: 631 sheet: 0.63 (0.56), residues: 80 loop : -0.35 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 202 HIS 0.004 0.001 HIS A1054 PHE 0.016 0.001 PHE A 717 TYR 0.015 0.001 TYR A 646 ARG 0.002 0.000 ARG A 417 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 69 time to evaluate : 1.203 Fit side-chains outliers start: 22 outliers final: 20 residues processed: 86 average time/residue: 0.1553 time to fit residues: 22.0426 Evaluate side-chains 86 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 66 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 811 CYS Chi-restraints excluded: chain A residue 868 ASN Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1253 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10086 Z= 0.177 Angle : 0.578 10.090 13736 Z= 0.276 Chirality : 0.041 0.256 1641 Planarity : 0.004 0.048 1724 Dihedral : 5.818 56.551 1772 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.34 % Favored : 96.58 % Rotamer: Outliers : 1.99 % Allowed : 13.81 % Favored : 84.20 % 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 (0.24), residues: 1228 helix: 1.66 (0.21), residues: 629 sheet: 0.67 (0.57), residues: 80 loop : -0.39 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 202 HIS 0.003 0.001 HIS A1054 PHE 0.016 0.001 PHE A 717 TYR 0.015 0.001 TYR A 646 ARG 0.002 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 67 time to evaluate : 1.291 Fit side-chains REVERT: A 94 LYS cc_start: 0.8556 (mmmt) cc_final: 0.7817 (tmtt) REVERT: A 281 MET cc_start: 0.5490 (mmm) cc_final: 0.5247 (mmm) REVERT: A 649 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.7927 (tt) outliers start: 21 outliers final: 20 residues processed: 84 average time/residue: 0.1635 time to fit residues: 22.3995 Evaluate side-chains 86 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 65 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 811 CYS Chi-restraints excluded: chain A residue 864 MET Chi-restraints excluded: chain A residue 868 ASN Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1253 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 81 optimal weight: 0.0040 chunk 122 optimal weight: 0.1980 chunk 112 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 59 optimal weight: 0.5980 chunk 77 optimal weight: 0.4980 chunk 103 optimal weight: 3.9990 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 860 ASN A1010 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10086 Z= 0.125 Angle : 0.560 10.353 13736 Z= 0.262 Chirality : 0.040 0.241 1641 Planarity : 0.004 0.047 1724 Dihedral : 5.571 57.141 1772 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.42 % Favored : 96.50 % Rotamer: Outliers : 1.80 % Allowed : 14.10 % Favored : 84.11 % 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: 1.27 (0.24), residues: 1228 helix: 1.78 (0.21), residues: 623 sheet: 0.72 (0.58), residues: 80 loop : -0.24 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 202 HIS 0.002 0.001 HIS A 126 PHE 0.016 0.001 PHE A 717 TYR 0.016 0.001 TYR A 646 ARG 0.002 0.000 ARG A 997 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 75 time to evaluate : 1.082 Fit side-chains revert: symmetry clash REVERT: A 281 MET cc_start: 0.5567 (mmm) cc_final: 0.5287 (mmm) REVERT: A 543 MET cc_start: 0.8990 (mmm) cc_final: 0.8779 (mtp) REVERT: A 649 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7870 (tt) outliers start: 19 outliers final: 17 residues processed: 93 average time/residue: 0.1633 time to fit residues: 24.3539 Evaluate side-chains 84 residues out of total 1057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 66 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 811 CYS Chi-restraints excluded: chain A residue 864 MET Chi-restraints excluded: chain A residue 868 ASN Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1253 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 10.0000 chunk 89 optimal weight: 0.0050 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.116126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.084594 restraints weight = 19072.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.084358 restraints weight = 15205.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.085069 restraints weight = 15451.253| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10086 Z= 0.165 Angle : 0.578 10.859 13736 Z= 0.271 Chirality : 0.041 0.250 1641 Planarity : 0.004 0.047 1724 Dihedral : 5.581 56.553 1772 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.09 % Favored : 96.82 % Rotamer: Outliers : 1.70 % Allowed : 14.47 % Favored : 83.82 % 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: 1.21 (0.24), residues: 1228 helix: 1.76 (0.21), residues: 629 sheet: 0.74 (0.58), residues: 80 loop : -0.34 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 202 HIS 0.003 0.001 HIS A 842 PHE 0.015 0.001 PHE A 717 TYR 0.017 0.001 TYR A 646 ARG 0.003 0.000 ARG A 843 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1824.48 seconds wall clock time: 34 minutes 0.99 seconds (2040.99 seconds total)