Starting phenix.real_space_refine on Thu Feb 15 10:52:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ajn_15485/02_2024/8ajn_15485.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ajn_15485/02_2024/8ajn_15485.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ajn_15485/02_2024/8ajn_15485.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ajn_15485/02_2024/8ajn_15485.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ajn_15485/02_2024/8ajn_15485.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ajn_15485/02_2024/8ajn_15485.pdb" } resolution = 3.0 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= 0.001 sd= 0.014 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 60 5.16 5 C 7603 2.51 5 N 2048 2.21 5 O 2298 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 705": "OD1" <-> "OD2" Residue "A PHE 1030": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 12009 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1140, 8918 Classifications: {'peptide': 1140} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 37, 'TRANS': 1098} Chain: "B" Number of atoms: 3091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3091 Classifications: {'peptide': 390} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 373} Chain breaks: 2 Time building chain proxies: 6.62, per 1000 atoms: 0.55 Number of scatterers: 12009 At special positions: 0 Unit cell: (92.105, 111.54, 147.875, 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 60 16.00 O 2298 8.00 N 2048 7.00 C 7603 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 313 " 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 Time building additional restraints: 4.69 Conformation dependent library (CDL) restraints added in 2.2 seconds 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2840 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 32 sheets defined 9.2% alpha, 43.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 381 through 384 Processing helix chain 'A' and resid 755 through 760 Processing helix chain 'A' and resid 769 through 773 removed outlier: 3.786A pdb=" N SER A 772 " --> pdb=" O LYS A 769 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SER A 773 " --> pdb=" O LEU A 770 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 769 through 773' Processing helix chain 'A' and resid 985 through 990 Processing helix chain 'A' and resid 1044 through 1062 removed outlier: 4.189A pdb=" N ASP A1053 " --> pdb=" O ASN A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1075 Processing helix chain 'A' and resid 1090 through 1097 Processing helix chain 'A' and resid 1098 through 1100 No H-bonds generated for 'chain 'A' and resid 1098 through 1100' Processing helix chain 'A' and resid 1101 through 1110 Processing helix chain 'A' and resid 1125 through 1138 Processing helix chain 'B' and resid 45 through 56 Processing helix chain 'B' and resid 60 through 62 No H-bonds generated for 'chain 'B' and resid 60 through 62' Processing helix chain 'B' and resid 63 through 75 Processing helix chain 'B' and resid 76 through 78 No H-bonds generated for 'chain 'B' and resid 76 through 78' Processing helix chain 'B' and resid 213 through 227 Processing helix chain 'B' and resid 327 through 331 removed outlier: 3.654A pdb=" N VAL B 331 " --> pdb=" O SER B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 411 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 10 removed outlier: 6.341A pdb=" N ILE A1037 " --> pdb=" O ALA A 9 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N SER A1042 " --> pdb=" O GLY A1026 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N GLY A1026 " --> pdb=" O SER A1042 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A1006 " --> pdb=" O GLY A1031 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 21 removed outlier: 6.195A pdb=" N VAL A 43 " --> pdb=" O PRO A 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 67 removed outlier: 4.110A pdb=" N ASN A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ALA A 86 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N HIS A 105 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE A 88 " --> pdb=" O ARG A 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 124 removed outlier: 3.560A pdb=" N ILE A 121 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU A 135 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N LEU A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 163 through 169 removed outlier: 5.789A pdb=" N VAL A 164 " --> pdb=" O GLN A 183 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLN A 183 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR A 192 " --> pdb=" O TRP A 207 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N TRP A 207 " --> pdb=" O THR A 192 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N GLU A 194 " --> pdb=" O GLY A 205 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N GLY A 205 " --> pdb=" O GLU A 194 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N SER A 196 " --> pdb=" O ASN A 203 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ASN A 203 " --> pdb=" O SER A 196 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 217 through 221 removed outlier: 4.251A pdb=" N MET A 218 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE A 232 " --> pdb=" O MET A 218 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 258 through 263 removed outlier: 6.829A pdb=" N GLY A 274 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N HIS A 261 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU A 272 " --> pdb=" O HIS A 261 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ARG A 263 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ARG A 270 " --> pdb=" O ARG A 263 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ARG A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU A 280 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP A 299 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N GLU A 288 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LEU A 297 " --> pdb=" O GLU A 288 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 313 through 316 removed outlier: 6.642A pdb=" N SER A 331 " --> pdb=" O THR A 352 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N THR A 352 " --> pdb=" O SER A 331 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU A 333 " --> pdb=" O MET A 350 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 365 removed outlier: 3.968A pdb=" N ASP A 361 " --> pdb=" O CYS A 378 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 396 through 402 removed outlier: 5.552A pdb=" N GLU A 398 " --> pdb=" O THR A 703 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR A 703 " --> pdb=" O GLU A 398 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 409 through 413 removed outlier: 3.896A pdb=" N GLY A 409 " --> pdb=" O SER A 428 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A 435 " --> pdb=" O THR A 446 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 457 through 463 removed outlier: 3.566A pdb=" N PHE A 459 " --> pdb=" O ILE A 471 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N SER A 480 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU A 486 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 500 through 503 removed outlier: 3.594A pdb=" N VAL A 500 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU A 516 " --> pdb=" O HIS A 531 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N HIS A 531 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N TYR A 518 " --> pdb=" O ILE A 529 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 538 through 542 removed outlier: 4.390A pdb=" N SER A 565 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LYS A 570 " --> pdb=" O LEU A 576 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU A 576 " --> pdb=" O LYS A 570 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 588 through 596 removed outlier: 4.714A pdb=" N HIS A 600 " --> pdb=" O LEU A 616 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA A 610 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU A 611 " --> pdb=" O LYS A 628 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LYS A 628 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N TYR A 613 " --> pdb=" O ARG A 626 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ARG A 626 " --> pdb=" O TYR A 613 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 637 through 643 removed outlier: 9.147A pdb=" N THR A 647 " --> pdb=" O SER A 661 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N SER A 661 " --> pdb=" O THR A 647 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 720 through 727 removed outlier: 6.469A pdb=" N LEU A 736 " --> pdb=" O ARG A 722 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE A 724 " --> pdb=" O GLY A 734 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLY A 734 " --> pdb=" O ILE A 724 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N TYR A 726 " --> pdb=" O CYS A 732 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N CYS A 732 " --> pdb=" O TYR A 726 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 720 through 727 removed outlier: 6.469A pdb=" N LEU A 736 " --> pdb=" O ARG A 722 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE A 724 " --> pdb=" O GLY A 734 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLY A 734 " --> pdb=" O ILE A 724 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N TYR A 726 " --> pdb=" O CYS A 732 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N CYS A 732 " --> pdb=" O TYR A 726 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU A 784 " --> pdb=" O GLN A 743 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASP A 795 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL A 801 " --> pdb=" O ASP A 795 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N SER A 764 " --> pdb=" O GLN A 806 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 811 through 820 removed outlier: 4.983A pdb=" N ALA A 813 " --> pdb=" O ALA A 834 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ALA A 834 " --> pdb=" O ALA A 813 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N THR A 827 " --> pdb=" O TYR A 853 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N TYR A 853 " --> pdb=" O THR A 827 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG A 847 " --> pdb=" O THR A 833 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLN A 852 " --> pdb=" O THR A 860 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N THR A 860 " --> pdb=" O GLN A 852 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N SER A 854 " --> pdb=" O LEU A 858 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N LEU A 858 " --> pdb=" O SER A 854 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 870 through 876 removed outlier: 3.827A pdb=" N SER A 872 " --> pdb=" O SER A 883 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N GLU A 892 " --> pdb=" O THR A 901 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N THR A 901 " --> pdb=" O GLU A 892 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 911 through 917 removed outlier: 6.236A pdb=" N ALA A 934 " --> pdb=" O GLU A 944 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N GLU A 944 " --> pdb=" O ALA A 934 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 954 through 959 removed outlier: 3.641A pdb=" N ASN A 973 " --> pdb=" O GLU A 969 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLN A 978 " --> pdb=" O GLU A 994 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N GLU A 994 " --> pdb=" O GLN A 978 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1076 through 1077 Processing sheet with id=AC6, first strand: chain 'A' and resid 1113 through 1115 Processing sheet with id=AC7, first strand: chain 'B' and resid 80 through 83 removed outlier: 7.436A pdb=" N GLY B 438 " --> pdb=" O VAL B 421 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL B 421 " --> pdb=" O GLY B 438 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 92 through 99 removed outlier: 6.575A pdb=" N GLN B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU B 112 " --> pdb=" O ILE B 125 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 146 through 148 removed outlier: 7.028A pdb=" N ILE B 167 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP B 174 " --> pdb=" O ARG B 169 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.552A pdb=" N SER B 206 " --> pdb=" O SER B 202 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B 239 " --> pdb=" O LEU B 209 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 255 through 261 removed outlier: 3.872A pdb=" N TYR B 275 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N PHE B 276 " --> pdb=" O SER B 290 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER B 290 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU B 278 " --> pdb=" O LEU B 288 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 302 through 304 removed outlier: 3.595A pdb=" N LYS B 332 " --> pdb=" O PHE B 321 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 343 through 349 removed outlier: 6.646A pdb=" N GLY B 356 " --> pdb=" O ARG B 344 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL B 346 " --> pdb=" O THR B 354 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N THR B 354 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N PHE B 348 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE B 352 " --> pdb=" O PHE B 348 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER B 361 " --> pdb=" O THR B 357 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 343 through 349 removed outlier: 6.646A pdb=" N GLY B 356 " --> pdb=" O ARG B 344 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL B 346 " --> pdb=" O THR B 354 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N THR B 354 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N PHE B 348 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE B 352 " --> pdb=" O PHE B 348 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER B 361 " --> pdb=" O THR B 357 " (cutoff:3.500A) 471 hydrogen bonds defined for protein. 1278 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: 5.40 Time building geometry restraints manager: 5.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3456 1.33 - 1.45: 2058 1.45 - 1.57: 6648 1.57 - 1.69: 0 1.69 - 1.81: 89 Bond restraints: 12251 Sorted by residual: bond pdb=" N ALA B 191 " pdb=" CA ALA B 191 " ideal model delta sigma weight residual 1.458 1.481 -0.024 1.16e-02 7.43e+03 4.26e+00 bond pdb=" CA HIS B 351 " pdb=" C HIS B 351 " ideal model delta sigma weight residual 1.523 1.560 -0.037 1.80e-02 3.09e+03 4.22e+00 bond pdb=" C SER B 189 " pdb=" N ILE B 190 " ideal model delta sigma weight residual 1.332 1.356 -0.023 1.20e-02 6.94e+03 3.76e+00 bond pdb=" C ILE B 190 " pdb=" N ALA B 191 " ideal model delta sigma weight residual 1.332 1.354 -0.022 1.25e-02 6.40e+03 3.11e+00 bond pdb=" CB PHE A 771 " pdb=" CG PHE A 771 " ideal model delta sigma weight residual 1.502 1.543 -0.041 2.30e-02 1.89e+03 3.10e+00 ... (remaining 12246 not shown) Histogram of bond angle deviations from ideal: 98.20 - 105.42: 239 105.42 - 112.63: 6360 112.63 - 119.85: 4233 119.85 - 127.06: 5660 127.06 - 134.28: 118 Bond angle restraints: 16610 Sorted by residual: angle pdb=" CA TYR B 48 " pdb=" CB TYR B 48 " pdb=" CG TYR B 48 " ideal model delta sigma weight residual 113.90 121.27 -7.37 1.80e+00 3.09e-01 1.68e+01 angle pdb=" N ASN A 36 " pdb=" CA ASN A 36 " pdb=" C ASN A 36 " ideal model delta sigma weight residual 111.37 118.09 -6.72 1.65e+00 3.67e-01 1.66e+01 angle pdb=" N GLU A 779 " pdb=" CA GLU A 779 " pdb=" C GLU A 779 " ideal model delta sigma weight residual 111.82 116.12 -4.30 1.16e+00 7.43e-01 1.38e+01 angle pdb=" N ASP A 542 " pdb=" CA ASP A 542 " pdb=" C ASP A 542 " ideal model delta sigma weight residual 108.99 114.40 -5.41 1.57e+00 4.06e-01 1.19e+01 angle pdb=" CA TYR B 168 " pdb=" CB TYR B 168 " pdb=" CG TYR B 168 " ideal model delta sigma weight residual 113.90 119.89 -5.99 1.80e+00 3.09e-01 1.11e+01 ... (remaining 16605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 6869 17.86 - 35.72: 379 35.72 - 53.58: 67 53.58 - 71.44: 24 71.44 - 89.30: 9 Dihedral angle restraints: 7348 sinusoidal: 2930 harmonic: 4418 Sorted by residual: dihedral pdb=" CA LEU B 322 " pdb=" C LEU B 322 " pdb=" N ASP B 323 " pdb=" CA ASP B 323 " ideal model delta harmonic sigma weight residual 180.00 150.10 29.90 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA GLU A 779 " pdb=" C GLU A 779 " pdb=" N THR A 780 " pdb=" CA THR A 780 " ideal model delta harmonic sigma weight residual -180.00 -151.35 -28.65 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA PRO B 418 " pdb=" C PRO B 418 " pdb=" N ASN B 419 " pdb=" CA ASN B 419 " ideal model delta harmonic sigma weight residual -180.00 -151.91 -28.09 0 5.00e+00 4.00e-02 3.16e+01 ... (remaining 7345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1158 0.040 - 0.080: 476 0.080 - 0.120: 179 0.120 - 0.160: 60 0.160 - 0.200: 15 Chirality restraints: 1888 Sorted by residual: chirality pdb=" CA ILE A1089 " pdb=" N ILE A1089 " pdb=" C ILE A1089 " pdb=" CB ILE A1089 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.97e-01 chirality pdb=" CB THR B 213 " pdb=" CA THR B 213 " pdb=" OG1 THR B 213 " pdb=" CG2 THR B 213 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.95e-01 chirality pdb=" CA VAL A 167 " pdb=" N VAL A 167 " pdb=" C VAL A 167 " pdb=" CB VAL A 167 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.38e-01 ... (remaining 1885 not shown) Planarity restraints: 2143 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 210 " -0.054 2.00e-02 2.50e+03 2.59e-02 1.67e+01 pdb=" CG TRP B 210 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP B 210 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP B 210 " 0.013 2.00e-02 2.50e+03 pdb=" NE1 TRP B 210 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B 210 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 210 " 0.027 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 210 " -0.018 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 210 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP B 210 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 295 " -0.045 2.00e-02 2.50e+03 2.32e-02 1.07e+01 pdb=" CG TYR B 295 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR B 295 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR B 295 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR B 295 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 295 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 295 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 295 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 965 " -0.039 2.00e-02 2.50e+03 2.45e-02 1.05e+01 pdb=" CG PHE A 965 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 965 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE A 965 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 965 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 965 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 965 " -0.024 2.00e-02 2.50e+03 ... (remaining 2140 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 3893 2.85 - 3.36: 10936 3.36 - 3.87: 21319 3.87 - 4.39: 24659 4.39 - 4.90: 41835 Nonbonded interactions: 102642 Sorted by model distance: nonbonded pdb=" O ARG A 134 " pdb=" NH1 ARG A 134 " model vdw 2.334 2.520 nonbonded pdb=" NZ LYS B 51 " pdb=" OE1 GLU B 54 " model vdw 2.338 2.520 nonbonded pdb=" N PHE A 382 " pdb=" OG SER A 720 " model vdw 2.406 2.520 nonbonded pdb=" OE2 GLU A 969 " pdb=" N ASN A 973 " model vdw 2.436 2.520 nonbonded pdb=" O LEU A1093 " pdb=" OG SER A1096 " model vdw 2.440 2.440 ... (remaining 102637 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=0.00 max=1.00 mean=0.85 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.600 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: 10.050 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 35.750 Find NCS groups from input model: 0.440 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: 0.020 Load rotamer database and sin/cos tables:12.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5830 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 : 0.006 0.058 12251 Z= 0.398 Angle : 0.940 7.553 16610 Z= 0.564 Chirality : 0.053 0.200 1888 Planarity : 0.008 0.117 2143 Dihedral : 12.629 89.298 4505 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.60 % Allowed : 3.29 % Favored : 96.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.20), residues: 1522 helix: -1.34 (0.40), residues: 110 sheet: -0.44 (0.20), residues: 626 loop : -0.81 (0.20), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.006 TRP B 210 HIS 0.010 0.002 HIS A 189 PHE 0.049 0.005 PHE A 851 TYR 0.045 0.006 TYR B 295 ARG 0.009 0.001 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 227 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ASP cc_start: 0.8409 (m-30) cc_final: 0.8038 (p0) REVERT: A 218 MET cc_start: 0.5572 (mtp) cc_final: 0.5241 (mtp) REVERT: A 900 ARG cc_start: 0.7993 (ttp-170) cc_final: 0.7596 (mmt90) REVERT: A 969 GLU cc_start: 0.5940 (OUTLIER) cc_final: 0.5650 (pp20) REVERT: A 1036 MET cc_start: 0.5883 (tmt) cc_final: 0.5494 (tmt) REVERT: A 1105 MET cc_start: 0.5906 (mtt) cc_final: 0.5572 (mtt) REVERT: B 197 MET cc_start: 0.3753 (mtm) cc_final: 0.3491 (tpp) REVERT: B 390 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8668 (tp30) outliers start: 8 outliers final: 4 residues processed: 234 average time/residue: 1.3227 time to fit residues: 333.9778 Evaluate side-chains 104 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 99 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 1062 ILE Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 188 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 39 optimal weight: 0.4980 chunk 78 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 119 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 ASN ** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 809 GLN A 826 ASN ** A 905 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 GLN ** B 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6039 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 12251 Z= 0.395 Angle : 0.781 9.028 16610 Z= 0.413 Chirality : 0.051 0.220 1888 Planarity : 0.005 0.055 2143 Dihedral : 6.954 87.924 1662 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.44 % Allowed : 11.58 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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 (0.20), residues: 1522 helix: -0.53 (0.47), residues: 116 sheet: -0.44 (0.19), residues: 678 loop : -0.96 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 308 HIS 0.009 0.001 HIS A 600 PHE 0.035 0.003 PHE A 851 TYR 0.020 0.002 TYR A 891 ARG 0.005 0.001 ARG B 337 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 113 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.5656 (mtp) cc_final: 0.5423 (mtp) REVERT: A 900 ARG cc_start: 0.8063 (ttp-170) cc_final: 0.7674 (mpt-90) outliers start: 46 outliers final: 14 residues processed: 147 average time/residue: 0.9880 time to fit residues: 161.7242 Evaluate side-chains 104 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 90 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 981 SER Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 273 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 77 optimal weight: 4.9990 chunk 43 optimal weight: 20.0000 chunk 115 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 150 optimal weight: 0.6980 chunk 123 optimal weight: 10.0000 chunk 138 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 111 optimal weight: 0.5980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS A 789 HIS ** A 905 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 HIS ** B 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5986 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 12251 Z= 0.271 Angle : 0.678 8.763 16610 Z= 0.353 Chirality : 0.047 0.181 1888 Planarity : 0.004 0.044 2143 Dihedral : 6.119 88.304 1652 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.21 % Allowed : 13.89 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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 (0.21), residues: 1522 helix: -0.32 (0.46), residues: 124 sheet: -0.41 (0.19), residues: 689 loop : -0.92 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 97 HIS 0.005 0.001 HIS A 905 PHE 0.026 0.002 PHE A 851 TYR 0.016 0.002 TYR A 678 ARG 0.005 0.001 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 96 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASP cc_start: 0.3650 (t0) cc_final: 0.3286 (t0) REVERT: A 218 MET cc_start: 0.5461 (mtp) cc_final: 0.5165 (mtp) REVERT: A 900 ARG cc_start: 0.8020 (ttp-170) cc_final: 0.7578 (mmt90) outliers start: 43 outliers final: 16 residues processed: 126 average time/residue: 0.9274 time to fit residues: 131.3807 Evaluate side-chains 100 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 84 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 962 ASP Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 411 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 66 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 39 optimal weight: 0.6980 chunk 123 optimal weight: 9.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 826 ASN ** A 905 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5949 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12251 Z= 0.223 Angle : 0.635 10.513 16610 Z= 0.329 Chirality : 0.046 0.187 1888 Planarity : 0.004 0.046 2143 Dihedral : 5.780 87.811 1652 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.21 % Allowed : 14.56 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: -1.01 (0.21), residues: 1522 helix: 0.02 (0.48), residues: 124 sheet: -0.36 (0.20), residues: 652 loop : -1.00 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 210 HIS 0.006 0.001 HIS A 905 PHE 0.027 0.002 PHE A 67 TYR 0.018 0.002 TYR A 678 ARG 0.003 0.000 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 101 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASP cc_start: 0.3833 (t0) cc_final: 0.3543 (t0) REVERT: A 839 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6884 (pm20) REVERT: A 877 ASN cc_start: 0.7911 (p0) cc_final: 0.7362 (p0) REVERT: A 900 ARG cc_start: 0.7987 (ttp-170) cc_final: 0.7597 (mpt90) outliers start: 43 outliers final: 16 residues processed: 135 average time/residue: 0.9820 time to fit residues: 147.7130 Evaluate side-chains 104 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 839 GLU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 411 PHE Chi-restraints excluded: chain B residue 413 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 61 optimal weight: 8.9990 chunk 126 optimal weight: 20.0000 chunk 102 optimal weight: 0.0060 chunk 0 optimal weight: 7.9990 chunk 75 optimal weight: 0.0470 chunk 132 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 overall best weight: 1.1898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5971 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12251 Z= 0.234 Angle : 0.638 10.483 16610 Z= 0.331 Chirality : 0.046 0.177 1888 Planarity : 0.004 0.047 2143 Dihedral : 5.708 87.570 1652 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.91 % Allowed : 16.43 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: -1.07 (0.21), residues: 1522 helix: 0.06 (0.50), residues: 122 sheet: -0.49 (0.19), residues: 673 loop : -0.96 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 210 HIS 0.007 0.001 HIS A 905 PHE 0.029 0.002 PHE A 67 TYR 0.017 0.002 TYR A 678 ARG 0.004 0.000 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 98 time to evaluate : 1.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASP cc_start: 0.3700 (t0) cc_final: 0.3474 (t0) REVERT: A 877 ASN cc_start: 0.7958 (p0) cc_final: 0.7404 (p0) REVERT: A 894 THR cc_start: 0.6979 (p) cc_final: 0.6774 (t) REVERT: A 900 ARG cc_start: 0.7922 (ttp-170) cc_final: 0.7536 (mpt90) outliers start: 39 outliers final: 18 residues processed: 131 average time/residue: 1.0426 time to fit residues: 152.7129 Evaluate side-chains 105 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 87 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1074 ARG Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 413 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 148 optimal weight: 4.9990 chunk 122 optimal weight: 8.9990 chunk 68 optimal weight: 7.9990 chunk 12 optimal weight: 0.5980 chunk 48 optimal weight: 0.0770 chunk 77 optimal weight: 0.9980 chunk 142 optimal weight: 0.3980 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 826 ASN B 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5898 moved from start: 0.4930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12251 Z= 0.183 Angle : 0.610 10.306 16610 Z= 0.316 Chirality : 0.046 0.183 1888 Planarity : 0.004 0.058 2143 Dihedral : 5.513 86.225 1652 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.61 % Allowed : 16.80 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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 (0.21), residues: 1522 helix: 0.14 (0.50), residues: 124 sheet: -0.47 (0.20), residues: 674 loop : -0.87 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 97 HIS 0.006 0.001 HIS A 905 PHE 0.029 0.002 PHE A 67 TYR 0.021 0.002 TYR A 678 ARG 0.009 0.000 ARG A1080 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 95 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASP cc_start: 0.3785 (t0) cc_final: 0.3557 (t0) REVERT: A 859 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8302 (mp10) REVERT: A 877 ASN cc_start: 0.7922 (p0) cc_final: 0.7328 (p0) REVERT: A 900 ARG cc_start: 0.8040 (ttp-170) cc_final: 0.7664 (mpt90) outliers start: 35 outliers final: 12 residues processed: 124 average time/residue: 1.0497 time to fit residues: 145.1641 Evaluate side-chains 95 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 82 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 859 GLN Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 391 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 16 optimal weight: 0.0570 chunk 84 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 chunk 82 optimal weight: 0.6980 chunk 147 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5899 moved from start: 0.5071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12251 Z= 0.188 Angle : 0.616 9.435 16610 Z= 0.315 Chirality : 0.046 0.165 1888 Planarity : 0.004 0.047 2143 Dihedral : 5.419 85.686 1652 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.54 % Allowed : 17.77 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: -1.02 (0.21), residues: 1522 helix: 0.20 (0.50), residues: 122 sheet: -0.50 (0.20), residues: 682 loop : -0.89 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 97 HIS 0.005 0.001 HIS A 905 PHE 0.027 0.002 PHE A 67 TYR 0.015 0.002 TYR A 171 ARG 0.007 0.000 ARG A1080 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 84 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 362 MET cc_start: 0.5943 (pmt) cc_final: 0.5684 (ptp) REVERT: A 840 GLU cc_start: 0.6313 (OUTLIER) cc_final: 0.6074 (mp0) REVERT: A 859 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8338 (mp10) REVERT: A 877 ASN cc_start: 0.7932 (p0) cc_final: 0.7342 (p0) REVERT: A 900 ARG cc_start: 0.8053 (ttp-170) cc_final: 0.7677 (mpt90) REVERT: B 425 CYS cc_start: 0.6931 (OUTLIER) cc_final: 0.6569 (p) outliers start: 34 outliers final: 16 residues processed: 113 average time/residue: 0.9739 time to fit residues: 123.5953 Evaluate side-chains 100 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 81 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 840 GLU Chi-restraints excluded: chain A residue 859 GLN Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 1074 ARG Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 425 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 0.0000 chunk 88 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 93 optimal weight: 0.1980 chunk 100 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 134 optimal weight: 8.9990 chunk 141 optimal weight: 6.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 ASN ** A 905 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5903 moved from start: 0.5238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12251 Z= 0.193 Angle : 0.626 12.186 16610 Z= 0.318 Chirality : 0.046 0.171 1888 Planarity : 0.004 0.047 2143 Dihedral : 5.402 85.597 1652 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.32 % Allowed : 18.00 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: -1.00 (0.21), residues: 1522 helix: 0.33 (0.51), residues: 118 sheet: -0.52 (0.19), residues: 694 loop : -0.86 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 97 HIS 0.004 0.001 HIS B 318 PHE 0.029 0.002 PHE A1097 TYR 0.013 0.002 TYR A 678 ARG 0.005 0.000 ARG A1080 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 80 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 362 MET cc_start: 0.5917 (pmt) cc_final: 0.5681 (ptp) REVERT: A 840 GLU cc_start: 0.6318 (OUTLIER) cc_final: 0.5998 (mp0) REVERT: A 859 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8368 (mp10) REVERT: A 877 ASN cc_start: 0.7939 (p0) cc_final: 0.7347 (p0) REVERT: A 900 ARG cc_start: 0.8057 (ttp-170) cc_final: 0.7680 (mpt90) REVERT: B 231 VAL cc_start: 0.6799 (t) cc_final: 0.6589 (m) REVERT: B 425 CYS cc_start: 0.6933 (OUTLIER) cc_final: 0.6583 (p) outliers start: 31 outliers final: 15 residues processed: 106 average time/residue: 1.0010 time to fit residues: 118.8445 Evaluate side-chains 98 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 840 GLU Chi-restraints excluded: chain A residue 859 GLN Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 1074 ARG Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 425 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 0.8980 chunk 137 optimal weight: 0.6980 chunk 141 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 59 optimal weight: 20.0000 chunk 107 optimal weight: 0.1980 chunk 42 optimal weight: 30.0000 chunk 124 optimal weight: 0.9990 chunk 129 optimal weight: 9.9990 chunk 136 optimal weight: 0.0770 chunk 90 optimal weight: 0.9990 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 ASN ** A 905 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5874 moved from start: 0.5346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12251 Z= 0.183 Angle : 0.640 11.059 16610 Z= 0.325 Chirality : 0.046 0.174 1888 Planarity : 0.004 0.047 2143 Dihedral : 5.409 85.433 1652 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.87 % Allowed : 18.60 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: -1.00 (0.21), residues: 1522 helix: 0.33 (0.51), residues: 118 sheet: -0.46 (0.20), residues: 671 loop : -0.92 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 97 HIS 0.003 0.001 HIS B 318 PHE 0.027 0.002 PHE A 67 TYR 0.011 0.001 TYR A 5 ARG 0.004 0.000 ARG A1080 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 86 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 840 GLU cc_start: 0.6287 (OUTLIER) cc_final: 0.5953 (mp0) REVERT: A 859 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8339 (mp10) REVERT: A 877 ASN cc_start: 0.7879 (p0) cc_final: 0.7256 (p0) REVERT: A 900 ARG cc_start: 0.8044 (ttp-170) cc_final: 0.7665 (mpt90) REVERT: B 231 VAL cc_start: 0.6817 (t) cc_final: 0.6610 (m) REVERT: B 425 CYS cc_start: 0.6866 (OUTLIER) cc_final: 0.6531 (p) outliers start: 25 outliers final: 15 residues processed: 106 average time/residue: 1.0241 time to fit residues: 121.0599 Evaluate side-chains 97 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 79 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 840 GLU Chi-restraints excluded: chain A residue 859 GLN Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 1074 ARG Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 425 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 145 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 152 optimal weight: 7.9990 chunk 140 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 905 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 ASN ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5964 moved from start: 0.5528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12251 Z= 0.248 Angle : 0.675 10.429 16610 Z= 0.345 Chirality : 0.047 0.164 1888 Planarity : 0.004 0.048 2143 Dihedral : 5.625 86.741 1652 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 19.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.79 % Allowed : 19.04 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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 (0.21), residues: 1522 helix: 0.20 (0.51), residues: 118 sheet: -0.41 (0.20), residues: 648 loop : -1.10 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 893 HIS 0.004 0.001 HIS B 318 PHE 0.037 0.002 PHE A1097 TYR 0.013 0.002 TYR B 304 ARG 0.006 0.000 ARG B 256 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 78 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 859 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8436 (mp10) REVERT: A 877 ASN cc_start: 0.8034 (p0) cc_final: 0.7509 (p0) REVERT: A 900 ARG cc_start: 0.7948 (ttp-170) cc_final: 0.7594 (mpt90) REVERT: B 425 CYS cc_start: 0.7000 (OUTLIER) cc_final: 0.6584 (p) outliers start: 24 outliers final: 15 residues processed: 99 average time/residue: 0.9870 time to fit residues: 109.4144 Evaluate side-chains 92 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 75 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 859 GLN Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 425 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 121 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 GLN ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 ASN ** A 905 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.116186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.100559 restraints weight = 45011.675| |-----------------------------------------------------------------------------| r_work (start): 0.4425 rms_B_bonded: 4.33 r_work (final): 0.4425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5983 moved from start: 0.5714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 12251 Z= 0.292 Angle : 0.708 10.239 16610 Z= 0.362 Chirality : 0.048 0.184 1888 Planarity : 0.004 0.048 2143 Dihedral : 5.952 89.763 1652 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 22.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.72 % Allowed : 19.19 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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 (0.21), residues: 1522 helix: 0.07 (0.50), residues: 118 sheet: -0.55 (0.20), residues: 636 loop : -1.20 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 893 HIS 0.005 0.001 HIS B 318 PHE 0.024 0.002 PHE B 188 TYR 0.016 0.002 TYR B 304 ARG 0.008 0.001 ARG B 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3783.92 seconds wall clock time: 68 minutes 39.64 seconds (4119.64 seconds total)