Starting phenix.real_space_refine on Tue Dec 31 22:27:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sl3_25190/12_2024/7sl3_25190_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sl3_25190/12_2024/7sl3_25190.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sl3_25190/12_2024/7sl3_25190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sl3_25190/12_2024/7sl3_25190.map" model { file = "/net/cci-nas-00/data/ceres_data/7sl3_25190/12_2024/7sl3_25190_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sl3_25190/12_2024/7sl3_25190_neut.cif" } resolution = 3.4 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3460 atoms to isotropic. 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 112 5.16 5 C 8898 2.51 5 N 2408 2.21 5 O 2598 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 14016 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 820, 6629 Classifications: {'peptide': 820} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 774} Chain breaks: 6 Chain: "B" Number of atoms: 6629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 820, 6629 Classifications: {'peptide': 820} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 774} Chain breaks: 6 Chain: "C" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 214 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "D" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 214 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "E" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 165 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Chain: "F" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 165 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Time building chain proxies: 9.16, per 1000 atoms: 0.65 Number of scatterers: 14016 At special positions: 0 Unit cell: (139.32, 115.56, 174.96, 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 112 16.00 O 2598 8.00 N 2408 7.00 C 8898 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 159 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 468 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 862 " distance=2.03 Simple disulfide: pdb=" SG CYS A 788 " - pdb=" SG CYS A 797 " distance=2.04 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 26 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 188 " distance=2.03 Simple disulfide: pdb=" SG CYS B 192 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 435 " - pdb=" SG CYS B 468 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 862 " distance=2.03 Simple disulfide: pdb=" SG CYS B 788 " - pdb=" SG CYS B 797 " distance=2.03 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS E 7 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS E 20 " distance=2.03 Simple disulfide: pdb=" SG CYS D 7 " - pdb=" SG CYS F 7 " distance=2.03 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS F 20 " distance=2.03 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 11 " distance=2.03 Simple disulfide: pdb=" SG CYS F 6 " - pdb=" SG CYS F 11 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.23 Conformation dependent library (CDL) restraints added in 1.6 seconds 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3276 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 34 sheets defined 17.2% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.28 Creating SS restraints... Processing helix chain 'A' and resid 18 through 24 removed outlier: 3.977A pdb=" N HIS A 21 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 22 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 23 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU A 24 " --> pdb=" O HIS A 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 18 through 24' Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.733A pdb=" N PHE A 46 " --> pdb=" O PRO A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 221 through 225 removed outlier: 3.817A pdb=" N CYS A 225 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 268 removed outlier: 3.593A pdb=" N CYS A 259 " --> pdb=" O ASN A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 318 removed outlier: 3.801A pdb=" N GLU A 318 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 329 removed outlier: 3.695A pdb=" N GLU A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 358 Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.521A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.502A pdb=" N ARG A 451 " --> pdb=" O THR A 448 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLN A 452 " --> pdb=" O LYS A 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 448 through 452' Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 640 through 645 removed outlier: 3.962A pdb=" N PHE A 644 " --> pdb=" O ASP A 640 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU A 645 " --> pdb=" O SER A 641 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 640 through 645' Processing helix chain 'A' and resid 691 through 716 Processing helix chain 'A' and resid 865 through 872 Processing helix chain 'B' and resid 18 through 24 removed outlier: 4.066A pdb=" N HIS B 21 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU B 22 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B 23 " --> pdb=" O LEU B 20 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU B 24 " --> pdb=" O HIS B 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 18 through 24' Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.719A pdb=" N PHE B 46 " --> pdb=" O PRO B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 221 through 225 removed outlier: 3.837A pdb=" N CYS B 225 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 268 removed outlier: 3.584A pdb=" N CYS B 259 " --> pdb=" O ASN B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 318 removed outlier: 3.807A pdb=" N GLU B 318 " --> pdb=" O LEU B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 329 removed outlier: 3.686A pdb=" N GLU B 329 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 358 Processing helix chain 'B' and resid 435 through 447 removed outlier: 3.511A pdb=" N ILE B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 452 removed outlier: 3.506A pdb=" N ARG B 451 " --> pdb=" O THR B 448 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLN B 452 " --> pdb=" O LYS B 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 448 through 452' Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 640 through 645 removed outlier: 4.028A pdb=" N PHE B 644 " --> pdb=" O ASP B 640 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU B 645 " --> pdb=" O SER B 641 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 640 through 645' Processing helix chain 'B' and resid 690 through 716 removed outlier: 5.283A pdb=" N LYS B 696 " --> pdb=" O SER B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 872 Processing helix chain 'C' and resid 8 through 19 removed outlier: 3.768A pdb=" N VAL C 12 " --> pdb=" O GLY C 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 19 removed outlier: 3.745A pdb=" N VAL D 12 " --> pdb=" O GLY D 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 7 Processing helix chain 'E' and resid 13 through 20 removed outlier: 3.536A pdb=" N GLU E 17 " --> pdb=" O TYR E 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 7 Processing helix chain 'F' and resid 13 through 20 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 14 removed outlier: 3.502A pdb=" N LEU A 36 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N GLN A 34 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU A 63 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU A 36 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG A 65 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU A 61 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N PHE A 96 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU A 63 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU A 93 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N GLU A 120 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE A 95 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ASN A 122 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS A 121 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASN A 148 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 29 Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 173 removed outlier: 3.844A pdb=" N VAL A 179 " --> pdb=" O THR A 172 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 232 through 233 Processing sheet with id=AA5, first strand: chain 'A' and resid 246 through 248 Processing sheet with id=AA6, first strand: chain 'A' and resid 278 through 280 Processing sheet with id=AA7, first strand: chain 'A' and resid 292 through 294 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 312 Processing sheet with id=AA9, first strand: chain 'A' and resid 319 through 321 removed outlier: 3.550A pdb=" N LEU A 368 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N PHE A 427 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TYR A 401 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N HIS A 429 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU A 403 " --> pdb=" O HIS A 429 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 472 through 473 Processing sheet with id=AB2, first strand: chain 'A' and resid 475 through 480 removed outlier: 6.772A pdb=" N ARG A 488 " --> pdb=" O SER A 476 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE A 478 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU A 486 " --> pdb=" O ILE A 478 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 530 through 534 removed outlier: 3.619A pdb=" N GLY A 502 " --> pdb=" O LEU A 571 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 601 through 607 removed outlier: 5.897A pdb=" N ASP A 602 " --> pdb=" O LYS A 618 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LYS A 618 " --> pdb=" O ASP A 602 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 613 " --> pdb=" O ILE A 772 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 770 " --> pdb=" O LEU A 615 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 636 through 637 removed outlier: 4.045A pdb=" N GLY A 780 " --> pdb=" O GLN A 637 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A 630 " --> pdb=" O VAL A 764 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL A 632 " --> pdb=" O GLU A 762 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU A 762 " --> pdb=" O VAL A 632 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 636 through 637 removed outlier: 4.045A pdb=" N GLY A 780 " --> pdb=" O GLN A 637 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 821 through 824 removed outlier: 3.553A pdb=" N VAL A 830 " --> pdb=" O LEU A 876 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 858 through 864 removed outlier: 6.896A pdb=" N THR A 891 " --> pdb=" O VAL A 845 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR A 847 " --> pdb=" O ARG A 889 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG A 889 " --> pdb=" O TYR A 847 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL A 849 " --> pdb=" O ARG A 887 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG A 887 " --> pdb=" O VAL A 849 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR A 851 " --> pdb=" O SER A 885 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N SER A 885 " --> pdb=" O TYR A 851 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ARG A 853 " --> pdb=" O ASN A 883 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ASN A 883 " --> pdb=" O ARG A 853 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY A 882 " --> pdb=" O VAL A 907 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 12 through 13 removed outlier: 3.598A pdb=" N LEU B 36 " --> pdb=" O ILE B 13 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL B 66 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU B 61 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N PHE B 96 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU B 63 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU B 93 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N GLU B 120 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE B 95 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASN B 122 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS B 121 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ASN B 148 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 29 Processing sheet with id=AC2, first strand: chain 'B' and resid 171 through 173 removed outlier: 3.840A pdb=" N VAL B 179 " --> pdb=" O THR B 172 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 182 through 184 removed outlier: 6.580A pdb=" N HIS B 187 " --> pdb=" O TRP B 183 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 231 through 233 removed outlier: 3.718A pdb=" N PHE B 231 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 246 through 248 Processing sheet with id=AC6, first strand: chain 'B' and resid 278 through 280 Processing sheet with id=AC7, first strand: chain 'B' and resid 292 through 294 Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 312 Processing sheet with id=AC9, first strand: chain 'B' and resid 319 through 321 removed outlier: 3.543A pdb=" N LEU B 368 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N PHE B 427 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N TYR B 401 " --> pdb=" O PHE B 427 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N HIS B 429 " --> pdb=" O TYR B 401 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU B 403 " --> pdb=" O HIS B 429 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 472 through 473 Processing sheet with id=AD2, first strand: chain 'B' and resid 475 through 480 removed outlier: 6.735A pdb=" N ARG B 488 " --> pdb=" O SER B 476 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ILE B 478 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU B 486 " --> pdb=" O ILE B 478 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 530 through 534 removed outlier: 3.548A pdb=" N GLY B 502 " --> pdb=" O LEU B 571 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 601 through 606 removed outlier: 5.599A pdb=" N ASP B 602 " --> pdb=" O LYS B 618 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS B 618 " --> pdb=" O ASP B 602 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 761 through 764 removed outlier: 3.509A pdb=" N GLU B 762 " --> pdb=" O VAL B 632 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL B 632 " --> pdb=" O GLU B 762 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 821 through 824 Processing sheet with id=AD7, first strand: chain 'B' and resid 858 through 864 removed outlier: 6.847A pdb=" N THR B 891 " --> pdb=" O VAL B 845 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR B 847 " --> pdb=" O ARG B 889 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG B 889 " --> pdb=" O TYR B 847 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL B 849 " --> pdb=" O ARG B 887 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ARG B 887 " --> pdb=" O VAL B 849 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR B 851 " --> pdb=" O SER B 885 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N SER B 885 " --> pdb=" O TYR B 851 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ARG B 853 " --> pdb=" O ASN B 883 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASN B 883 " --> pdb=" O ARG B 853 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY B 882 " --> pdb=" O VAL B 907 " (cutoff:3.500A) 334 hydrogen bonds defined for protein. 858 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: 5.35 Time building geometry restraints manager: 3.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4591 1.34 - 1.46: 3333 1.46 - 1.58: 6298 1.58 - 1.70: 0 1.70 - 1.82: 136 Bond restraints: 14358 Sorted by residual: bond pdb=" CA THR B 690 " pdb=" CB THR B 690 " ideal model delta sigma weight residual 1.518 1.540 -0.023 2.08e-02 2.31e+03 1.18e+00 bond pdb=" N TYR B 581 " pdb=" CA TYR B 581 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.13e+00 bond pdb=" CA LYS B 559 " pdb=" CB LYS B 559 " ideal model delta sigma weight residual 1.519 1.537 -0.017 1.73e-02 3.34e+03 9.81e-01 bond pdb=" CA CYS B 687 " pdb=" C CYS B 687 " ideal model delta sigma weight residual 1.524 1.516 0.008 8.10e-03 1.52e+04 9.47e-01 bond pdb=" CA LYS A 559 " pdb=" CB LYS A 559 " ideal model delta sigma weight residual 1.519 1.536 -0.016 1.73e-02 3.34e+03 9.03e-01 ... (remaining 14353 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 19248 2.20 - 4.40: 198 4.40 - 6.59: 11 6.59 - 8.79: 1 8.79 - 10.99: 2 Bond angle restraints: 19460 Sorted by residual: angle pdb=" C THR B 580 " pdb=" N TYR B 581 " pdb=" CA TYR B 581 " ideal model delta sigma weight residual 121.54 132.53 -10.99 1.91e+00 2.74e-01 3.31e+01 angle pdb=" C THR A 580 " pdb=" N TYR A 581 " pdb=" CA TYR A 581 " ideal model delta sigma weight residual 121.54 131.73 -10.19 1.91e+00 2.74e-01 2.85e+01 angle pdb=" C THR B 690 " pdb=" CA THR B 690 " pdb=" CB THR B 690 " ideal model delta sigma weight residual 115.79 109.56 6.23 1.19e+00 7.06e-01 2.74e+01 angle pdb=" N ASP A 691 " pdb=" CA ASP A 691 " pdb=" C ASP A 691 " ideal model delta sigma weight residual 113.41 109.26 4.15 1.22e+00 6.72e-01 1.16e+01 angle pdb=" N SER B 692 " pdb=" CA SER B 692 " pdb=" C SER B 692 " ideal model delta sigma weight residual 113.19 109.62 3.57 1.19e+00 7.06e-01 8.98e+00 ... (remaining 19455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 7931 17.94 - 35.87: 628 35.87 - 53.81: 114 53.81 - 71.74: 29 71.74 - 89.68: 10 Dihedral angle restraints: 8712 sinusoidal: 3640 harmonic: 5072 Sorted by residual: dihedral pdb=" CB CYS B 126 " pdb=" SG CYS B 126 " pdb=" SG CYS B 155 " pdb=" CB CYS B 155 " ideal model delta sinusoidal sigma weight residual -86.00 -148.27 62.27 1 1.00e+01 1.00e-02 5.13e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 155 " pdb=" CB CYS A 155 " ideal model delta sinusoidal sigma weight residual -86.00 -147.43 61.43 1 1.00e+01 1.00e-02 5.01e+01 dihedral pdb=" CB CYS A 266 " pdb=" SG CYS A 266 " pdb=" SG CYS A 274 " pdb=" CB CYS A 274 " ideal model delta sinusoidal sigma weight residual 93.00 147.12 -54.12 1 1.00e+01 1.00e-02 3.97e+01 ... (remaining 8709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1357 0.034 - 0.068: 490 0.068 - 0.101: 164 0.101 - 0.135: 95 0.135 - 0.169: 4 Chirality restraints: 2110 Sorted by residual: chirality pdb=" CB THR B 690 " pdb=" CA THR B 690 " pdb=" OG1 THR B 690 " pdb=" CG2 THR B 690 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.14e-01 chirality pdb=" CB THR A 690 " pdb=" CA THR A 690 " pdb=" OG1 THR A 690 " pdb=" CG2 THR A 690 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 6.81e-01 chirality pdb=" CB ILE B 174 " pdb=" CA ILE B 174 " pdb=" CG1 ILE B 174 " pdb=" CG2 ILE B 174 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.07e-01 ... (remaining 2107 not shown) Planarity restraints: 2516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 580 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.90e+00 pdb=" C THR B 580 " -0.042 2.00e-02 2.50e+03 pdb=" O THR B 580 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR B 581 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 580 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.00e+00 pdb=" C THR A 580 " -0.039 2.00e-02 2.50e+03 pdb=" O THR A 580 " 0.015 2.00e-02 2.50e+03 pdb=" N TYR A 581 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 836 " 0.020 5.00e-02 4.00e+02 3.09e-02 1.53e+00 pdb=" N PRO A 837 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 837 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 837 " 0.017 5.00e-02 4.00e+02 ... (remaining 2513 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2332 2.77 - 3.30: 13128 3.30 - 3.84: 22468 3.84 - 4.37: 26556 4.37 - 4.90: 45564 Nonbonded interactions: 110048 Sorted by model distance: nonbonded pdb=" OG1 THR A 41 " pdb=" O TYR A 67 " model vdw 2.238 3.040 nonbonded pdb=" NH2 ARG A 14 " pdb=" O VAL B 715 " model vdw 2.241 3.120 nonbonded pdb=" OG1 THR B 41 " pdb=" O TYR B 67 " model vdw 2.244 3.040 nonbonded pdb=" O VAL A 715 " pdb=" NH2 ARG B 14 " model vdw 2.245 3.120 nonbonded pdb=" NE2 GLN A 790 " pdb=" O ASP A 794 " model vdw 2.246 3.120 ... (remaining 110043 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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 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: 3.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 34.650 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.070 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:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 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 : 0.002 0.039 14358 Z= 0.160 Angle : 0.537 10.991 19460 Z= 0.287 Chirality : 0.043 0.169 2110 Planarity : 0.003 0.031 2516 Dihedral : 13.247 89.680 5316 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.35 % Favored : 93.41 % Rotamer: Outliers : 0.32 % Allowed : 0.32 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.71 (0.21), residues: 1700 helix: -0.32 (0.36), residues: 222 sheet: 0.84 (0.30), residues: 334 loop : -0.95 (0.19), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 412 HIS 0.003 0.000 HIS A 440 PHE 0.013 0.001 PHE B 778 TYR 0.014 0.001 TYR B 581 ARG 0.003 0.000 ARG B 578 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 1.682 Fit side-chains revert: symmetry clash REVERT: B 687 CYS cc_start: 0.2703 (OUTLIER) cc_final: 0.2494 (m) REVERT: F 17 GLU cc_start: 0.7541 (mp0) cc_final: 0.7209 (mp0) outliers start: 5 outliers final: 2 residues processed: 72 average time/residue: 0.2566 time to fit residues: 29.5138 Evaluate side-chains 55 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain B residue 689 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 134 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 81 optimal weight: 0.0770 chunk 100 optimal weight: 30.0000 chunk 156 optimal weight: 0.4980 overall best weight: 0.8542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN B 34 GLN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.0813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14358 Z= 0.182 Angle : 0.528 6.638 19460 Z= 0.279 Chirality : 0.044 0.192 2110 Planarity : 0.003 0.029 2516 Dihedral : 4.840 55.746 1905 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.06 % Favored : 93.76 % Rotamer: Outliers : 0.25 % Allowed : 4.11 % Favored : 95.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.56 (0.21), residues: 1700 helix: 0.37 (0.37), residues: 212 sheet: 0.89 (0.30), residues: 322 loop : -0.93 (0.19), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 412 HIS 0.004 0.001 HIS A 440 PHE 0.011 0.001 PHE A 707 TYR 0.014 0.001 TYR E 14 ARG 0.006 0.000 ARG A 782 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 17 GLU cc_start: 0.7324 (mp0) cc_final: 0.7087 (mp0) REVERT: F 14 TYR cc_start: 0.7534 (t80) cc_final: 0.6867 (t80) REVERT: F 17 GLU cc_start: 0.7714 (mp0) cc_final: 0.7491 (mp0) outliers start: 4 outliers final: 2 residues processed: 64 average time/residue: 0.2424 time to fit residues: 25.3520 Evaluate side-chains 52 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 156 optimal weight: 0.0060 chunk 169 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 155 optimal weight: 0.0270 chunk 53 optimal weight: 7.9990 chunk 125 optimal weight: 6.9990 overall best weight: 2.4060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 HIS A 712 HIS ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14358 Z= 0.329 Angle : 0.561 6.994 19460 Z= 0.294 Chirality : 0.045 0.186 2110 Planarity : 0.004 0.033 2516 Dihedral : 4.739 33.233 1900 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.29 % Favored : 93.59 % Rotamer: Outliers : 0.32 % Allowed : 7.77 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.67 (0.21), residues: 1700 helix: 0.47 (0.37), residues: 214 sheet: 0.47 (0.30), residues: 346 loop : -0.96 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 412 HIS 0.007 0.001 HIS B 712 PHE 0.014 0.002 PHE A 89 TYR 0.027 0.001 TYR B 581 ARG 0.004 0.000 ARG A 782 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 1.681 Fit side-chains revert: symmetry clash REVERT: A 98 MET cc_start: 0.8637 (tpt) cc_final: 0.8391 (tpt) REVERT: A 442 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8265 (ttp) REVERT: A 833 MET cc_start: 0.5056 (mmt) cc_final: 0.4527 (tpt) REVERT: E 14 TYR cc_start: 0.7470 (t80) cc_final: 0.7208 (t80) REVERT: E 17 GLU cc_start: 0.7615 (mp0) cc_final: 0.7333 (mp0) outliers start: 5 outliers final: 2 residues processed: 60 average time/residue: 0.2433 time to fit residues: 24.2569 Evaluate side-chains 51 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 157 optimal weight: 8.9990 chunk 166 optimal weight: 7.9990 chunk 82 optimal weight: 9.9990 chunk 148 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 822 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 14358 Z= 0.401 Angle : 0.600 6.105 19460 Z= 0.316 Chirality : 0.047 0.184 2110 Planarity : 0.004 0.036 2516 Dihedral : 5.098 34.120 1900 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.29 % Favored : 92.65 % Rotamer: Outliers : 0.76 % Allowed : 9.86 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.95 (0.21), residues: 1700 helix: 0.28 (0.37), residues: 220 sheet: -0.02 (0.29), residues: 360 loop : -1.07 (0.19), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 412 HIS 0.007 0.001 HIS A 712 PHE 0.015 0.002 PHE B 381 TYR 0.033 0.002 TYR B 581 ARG 0.003 0.000 ARG A 636 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 1.711 Fit side-chains revert: symmetry clash REVERT: A 344 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8838 (mp) REVERT: A 442 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8341 (ttp) REVERT: B 344 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8788 (mp) REVERT: E 14 TYR cc_start: 0.7607 (t80) cc_final: 0.7139 (t80) REVERT: E 17 GLU cc_start: 0.7507 (mp0) cc_final: 0.7132 (mp0) outliers start: 12 outliers final: 3 residues processed: 67 average time/residue: 0.2346 time to fit residues: 26.2596 Evaluate side-chains 57 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 114 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 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 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14358 Z= 0.254 Angle : 0.544 6.545 19460 Z= 0.287 Chirality : 0.044 0.184 2110 Planarity : 0.003 0.035 2516 Dihedral : 4.939 32.079 1900 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.57 % Allowed : 11.25 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.94 (0.21), residues: 1700 helix: 0.37 (0.37), residues: 220 sheet: 0.00 (0.28), residues: 364 loop : -1.08 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 412 HIS 0.004 0.001 HIS A 440 PHE 0.012 0.001 PHE A 707 TYR 0.024 0.001 TYR B 581 ARG 0.002 0.000 ARG A 782 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 1.545 Fit side-chains revert: symmetry clash REVERT: C 21 GLU cc_start: 0.6319 (pm20) cc_final: 0.6083 (pp20) REVERT: E 14 TYR cc_start: 0.7603 (t80) cc_final: 0.7108 (t80) REVERT: E 17 GLU cc_start: 0.7504 (mp0) cc_final: 0.7129 (mp0) outliers start: 9 outliers final: 6 residues processed: 65 average time/residue: 0.2321 time to fit residues: 24.6503 Evaluate side-chains 56 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 166 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 160 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 14358 Z= 0.416 Angle : 0.619 9.676 19460 Z= 0.323 Chirality : 0.047 0.228 2110 Planarity : 0.004 0.038 2516 Dihedral : 5.130 34.855 1900 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 0.82 % Allowed : 12.01 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1700 helix: 0.16 (0.36), residues: 220 sheet: -0.16 (0.28), residues: 374 loop : -1.16 (0.19), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 183 HIS 0.007 0.001 HIS A 712 PHE 0.016 0.002 PHE B 381 TYR 0.024 0.002 TYR B 581 ARG 0.003 0.000 ARG A 556 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 1.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8831 (mp) REVERT: B 344 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8758 (mp) REVERT: B 578 ARG cc_start: 0.7346 (ptt90) cc_final: 0.6940 (ppt170) outliers start: 13 outliers final: 6 residues processed: 72 average time/residue: 0.2507 time to fit residues: 29.2821 Evaluate side-chains 59 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 2.9990 chunk 94 optimal weight: 0.0040 chunk 121 optimal weight: 0.6980 chunk 140 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 165 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 102 optimal weight: 0.0370 chunk 66 optimal weight: 0.9980 overall best weight: 0.5470 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14358 Z= 0.166 Angle : 0.532 7.840 19460 Z= 0.278 Chirality : 0.044 0.189 2110 Planarity : 0.003 0.030 2516 Dihedral : 4.797 33.339 1900 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.76 % Allowed : 12.39 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.91 (0.21), residues: 1700 helix: 0.44 (0.38), residues: 210 sheet: -0.01 (0.28), residues: 374 loop : -1.05 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 412 HIS 0.003 0.000 HIS A 440 PHE 0.017 0.001 PHE A 778 TYR 0.022 0.001 TYR B 512 ARG 0.004 0.000 ARG B 118 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 344 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8658 (mp) outliers start: 12 outliers final: 9 residues processed: 64 average time/residue: 0.2787 time to fit residues: 28.1588 Evaluate side-chains 55 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 112 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 130 optimal weight: 0.7980 chunk 150 optimal weight: 0.3980 chunk 158 optimal weight: 4.9990 chunk 144 optimal weight: 0.0050 overall best weight: 2.0398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 HIS ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14358 Z= 0.286 Angle : 0.563 8.396 19460 Z= 0.292 Chirality : 0.045 0.198 2110 Planarity : 0.003 0.031 2516 Dihedral : 4.836 32.633 1900 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 1.26 % Allowed : 12.26 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.21), residues: 1700 helix: 0.26 (0.37), residues: 220 sheet: -0.07 (0.28), residues: 376 loop : -1.07 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 412 HIS 0.004 0.001 HIS A 712 PHE 0.019 0.002 PHE A 778 TYR 0.021 0.001 TYR B 512 ARG 0.002 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 50 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 581 TYR cc_start: 0.7133 (OUTLIER) cc_final: 0.5981 (t80) REVERT: B 98 MET cc_start: 0.8916 (mmm) cc_final: 0.8389 (tpt) REVERT: B 344 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8716 (mp) REVERT: B 442 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8299 (ttp) outliers start: 20 outliers final: 11 residues processed: 65 average time/residue: 0.2633 time to fit residues: 27.8976 Evaluate side-chains 60 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 0.0370 chunk 158 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 67 optimal weight: 9.9990 chunk 121 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 146 optimal weight: 0.9980 chunk 153 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 163 optimal weight: 10.0000 overall best weight: 0.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 514 ASN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14358 Z= 0.177 Angle : 0.523 9.770 19460 Z= 0.272 Chirality : 0.043 0.177 2110 Planarity : 0.003 0.033 2516 Dihedral : 4.652 33.801 1900 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.88 % Allowed : 12.83 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.21), residues: 1700 helix: 0.12 (0.37), residues: 222 sheet: 0.21 (0.29), residues: 364 loop : -1.05 (0.19), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 412 HIS 0.003 0.001 HIS A 440 PHE 0.020 0.001 PHE A 778 TYR 0.020 0.001 TYR B 512 ARG 0.003 0.000 ARG B 556 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8922 (mmm) cc_final: 0.8488 (tpt) REVERT: B 344 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8630 (mp) REVERT: B 442 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8266 (ttp) outliers start: 14 outliers final: 11 residues processed: 63 average time/residue: 0.2565 time to fit residues: 26.2238 Evaluate side-chains 58 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 171 optimal weight: 0.9990 chunk 157 optimal weight: 9.9990 chunk 136 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 chunk 105 optimal weight: 0.4980 chunk 83 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 145 optimal weight: 9.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14358 Z= 0.302 Angle : 0.551 8.117 19460 Z= 0.287 Chirality : 0.045 0.186 2110 Planarity : 0.003 0.036 2516 Dihedral : 4.759 33.013 1900 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 0.88 % Allowed : 12.64 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.94 (0.21), residues: 1700 helix: 0.24 (0.37), residues: 220 sheet: 0.03 (0.29), residues: 368 loop : -1.07 (0.19), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 834 HIS 0.004 0.001 HIS B 440 PHE 0.023 0.002 PHE A 778 TYR 0.020 0.001 TYR B 512 ARG 0.003 0.000 ARG B 345 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 344 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8727 (mp) REVERT: B 442 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8329 (ttp) outliers start: 14 outliers final: 12 residues processed: 58 average time/residue: 0.2379 time to fit residues: 22.9130 Evaluate side-chains 59 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 20 optimal weight: 0.1980 chunk 37 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 140 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 7 optimal weight: 0.4980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.101719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.068534 restraints weight = 40164.911| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 3.31 r_work: 0.3102 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14358 Z= 0.195 Angle : 0.526 8.241 19460 Z= 0.273 Chirality : 0.044 0.178 2110 Planarity : 0.003 0.036 2516 Dihedral : 4.673 33.272 1900 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 1.14 % Allowed : 12.45 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.92 (0.21), residues: 1700 helix: 0.12 (0.37), residues: 222 sheet: 0.10 (0.29), residues: 368 loop : -1.05 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 834 HIS 0.003 0.001 HIS B 440 PHE 0.022 0.001 PHE A 778 TYR 0.020 0.001 TYR B 512 ARG 0.002 0.000 ARG B 875 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2520.91 seconds wall clock time: 47 minutes 16.62 seconds (2836.62 seconds total)